PaperBLAST
PaperBLAST Hits for tr|Q9I1I5|Q9I1I5_PSEAE Glucose dehydrogenase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=gcd PE=3 SV=1 (803 a.a., MSEGNRSRSR...)
Show query sequence
>tr|Q9I1I5|Q9I1I5_PSEAE Glucose dehydrogenase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=gcd PE=3 SV=1
MSEGNRSRSRLLPSLLGLLILLSGLALLAGGIKLASLGGSLYYLLAGIGLALSGLLLLLG
KRAALGLYALVLFASTVWALWEVGLDWWQLVPRLALWFVFGLLLWLPWFRRPLLADGPAP
LGTAALGVAVVLAGAAAVGSQFTNPGQIVGRIDRDSGMTSTAPAMPDGDWQAYGRTEFGD
RYSPLKQITPANVGQLEEAWRIRTGDLPTADDPLELTNENTPLKVNGMLYACTAHSKVLA
LDPDTGAEIWRFDPQIQSPVGFKGFAHMTCRGVSYYDEEQYARSDVGAPPAALSEAGKAV
AASCPRRLFLPTADARLIAINADNGKVCEDFGVKGAVDLTAGIGPFTPGGYYSTSPAAVT
RNLVIIGGHVTDNESTNEPSGVIRAFDVHDGKLVWNWDSGNPDETEPLAPGKFYTRNSPN
MWSLASVDEKLGQVYLPLGNQMPDQWGGNRTPGAEKFSAGLVALDLNTGKLRWNYQFTHH
DLWDMDVGSQPTLLDLKTADGVKPALIAPTKQGSLYVLDRRDGTPIVPIREVPAPQGAVE
GDHTAPTQARSDLNLLRPPLTERDMWGSSPFDQMLCRIQFRSLRYEGQYTPPSEQGSLIY
PGNVGVFNWGGVSVDPVRQILFTSPNYMAFVSQMVPRDKVPSGSKREGETSGVQPNTGAP
YAVIMHPFMSPIGLPCQAPSWGDVAGIDLTTAKVVWQHKNGTSRDNTPVPIGLTVGVPSM
GGSITTAGGVAFLSGTLDQYLRAYDVKDGKQLWQARLPAGGQATPMSYTGKDGRQYVLIV
AGGHGSFGTRMGDYIIAYALPRQ
Running BLASTp...
Found 272 similar proteins in the literature:
NP_250980 glucose dehydrogenase from Pseudomonas aeruginosa PAO1
PA2290 glucose dehydrogenase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
Hu, Frontiers in microbiology 2024 - “...oxidase subunit II PA1317 NP_250008 996 cyoA cyoA Cytochrome o ubiquinol oxidase subunit II PA2290 NP_250980 2,412 gcd gcd Glucose dehydrogenase PA4771 NP_253459 1,146 lldD lldD L-lactate dehydrogenase PA4640 NP_253330 1,524 mqoB mqo Malate:quinone oxidoreductase PA3452 NP_252142 1,572 mqoA Malate:quinone oxidoreductase PA0139 NP_248829 564 ahpC Alkyl...”
- Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
Hu, Frontiers in microbiology 2024 - “...and the expression of CIO. An intriguing discovery is the presence of glucose dehydrogenase (gcd, PA2290, Supplementary Data 2 ) across all four growth conditions, despite the absence of glucose in mAUM media. This suggests an activated gluconeogenesis pathway that potentially generates glucose as an energy...”
- “...C oxidase subunit II PA1317 NP_250008 996 cyoA cyoA Cytochrome o ubiquinol oxidase subunit II PA2290 NP_250980 2,412 gcd gcd Glucose dehydrogenase PA4771 NP_253459 1,146 lldD lldD L-lactate dehydrogenase PA4640 NP_253330 1,524 mqoB mqo Malate:quinone oxidoreductase PA3452 NP_252142 1,572 mqoA Malate:quinone oxidoreductase PA0139 NP_248829 564 ahpC...”
- The evolutionary trajectories of P. aeruginosa in biofilm and planktonic growth modes exposed to ciprofloxacin: beyond selection of antibiotic resistance
Ahmed, NPJ biofilms and microbiomes 2020 - “...that encodes succinate dehydrogenase was mutated at frequencies higher than 80%. In addition, poxB and PA2290 genes that encodes pyruvate and glucose dehydrogenases were also found to be mutated. In the katA -hypermutable CIP-resistant colonies, the genes related to iron storage and transport were mutated such...”
- Transcriptome Analysis of Pseudomonas aeruginosa Cultured in Human Burn Wound Exudates
Gonzalez, Frontiers in cellular and infection microbiology 2018 - “...2016 ). Interestingly, despite stable expression of glucose porin oprB (PA3186), both glucose dehydrogenase gcd (PA2290) and gluconate permase gnuT (PA2322) showed induction in BWE compared to LB control conditions (Supplementary Table 3 ). These data suggest that P. aeruginosa stimulates the pathway involved in gluconate...”
- The development of a new parameter for tracking post-transcriptional regulation allows the detailed map of the Pseudomonas aeruginosa Crc regulon
Corona, Scientific reports 2018 - “...sodium/alanine/glycine symporter 3,32 0,89 5,85 Catabolism ansA PA2253 L-asparaginase I 2,19 0,31 3,07 CCM/catabolism gcd PA2290 Glucose dehydrogenase 0,8 0,7 1,2 Transport oprB2 PA2291 Probable glucose-sensitive porin 1,37 2,56 5,91 Iron pvdA PA2386 L-ornithine N5-oxygenase 1,39 3,11 7,46 Iron pvdF PA2396 Pyoverdine synthetase F 0,58 2,01...”
- Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism
Vital-Lopez, PLoS computational biology 2015 - “...whose up-regulation increased Psl synthesis had a positive correlation. Notably, with the exception of gcd (PA2290), the opposite was observed in planktonic cultures: the gene expression of the reactions whose down-regulation increased Psl synthesis had a positive correlation with the gene expression of the Psl pathway,...”
- Identification of five structurally unrelated quorum-sensing inhibitors of Pseudomonas aeruginosa from a natural-derivative database
Tan, Antimicrobial agents and chemotherapy 2013 - “...PA0572 PA0792 PA0400 PA5213 PA2951 PA0586 PA2399 PA3924 PA2290 PA2424 PA3148 PA2302 piv, prpL hutU PA2402 PA0852 PA3083 NA PA0588 PA2445 PA0399 PA5172 chiC...”
- Bis-(3'-5')-cyclic dimeric GMP regulates antimicrobial peptide resistance in Pseudomonas aeruginosa
Chua, Antimicrobial agents and chemotherapy 2013 - “...PA0426 PA1288 PA4749 PA5213 PA3478 PA2086 PA4336 PA4595 PA4476 PA2290 PA5237 PA2302 PA4307 PA3707 PA4588 PA4226 lon pchA truA pepA wbpA hslU pchF mexB ompP1...”
- Analysis of Pseudomonas aeruginosa cell envelope proteome by capture of surface-exposed proteins on activated magnetic nanoparticles
Vecchietti, PloS one 2012 - “...PA5117 Regulatory protein TypA 2 IM,3 - P,1 pssA PA4693 Phosphatidylserine synthase 2 IM,3 gcd PA2290 Glucose dehydrogenase 2 IM,3 PA2652 Putative chemotaxis transducer 3 IM,3 oxaA PA5568 Putative protein OxaA OXA1/oxaA 4 IM,3 PA5528 Putative uncharacterized protein 4 IM,3 PA3729 Putative uncharacterized protein 4 IM,3...”
- More
PA14_34970 glucose dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
100% identity, 100% coverage
PputUW4_00989 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas sp. UW4
83% identity, 96% coverage
PFL_4916 quinoprotein glucose dehydrogenase, putative from Pseudomonas fluorescens Pf-5
84% identity, 95% coverage
PchlO6_4960 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas chlororaphis O6
82% identity, 95% coverage
jpw_20390 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas asiatica
79% identity, 100% coverage
- Genomic Analysis of Pseudomonas asiatica JP233: An Efficient Phosphate-Solubilizing Bacterium
Wang, Genes 2022 - “...organic acid responsible for phosphate solubilization in JP233 [ 15 ]. Genes encoding glucose dehydrogenase (jpw_20390 and jpw_21040), the pqqFABCDEG operon (jpw_01865jpw_01895) and the gluconate dehydrogenase operon (jpw_13670jpw_13680) were detected in the JP233 genome ( Figure 5 ). The enzymes pyrophosphatase (PPA) and exopolyphosphatase (PPX) have...”
- “...Genes related to plant growth promotion of JP233. JP233 Gene ID Gene Product Phosphate solubilization jpw_20390 jpw_21040 gcd quinoprotein glucose dehydrogenase jpw_01865 pqqG S9 family peptidase jpw_01870 pqqE pyrroloquinoline quinone biosynthesis protein PqqE jpw_01875 pqqD pyrroloquinoline quinone biosynthesis protein PqqD jpw_01880 pqqC pyrroloquinoline-quinone synthase PqqC jpw_01885...”
PVLB_05240 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas sp. VLB120
79% identity, 100% coverage
JNO42_16315 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas putida
79% identity, 100% coverage
PPUBIRD1_4115 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas putida BIRD-1
79% identity, 100% coverage
- Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria
Lidbury, Environmental microbiology 2016 - “...S4). The abundance of a cytoplasmic glucose6phosphate dehydrogenase (Zwf), as well as two distinct membranebound (PPUBIRD1_4115, PPYBiRD1_2225) glucose dehydrogenases (Gcd, GcdII respectively), all of which are known to play a role in Pi solubilization through gluconic acid production (Miller et al ., 2010 ; Roca et...”
- “...transport, periplasmic binding domain tauA ADR57963 PPUBIRD1_0259 3.10 1.14 Quinoprotein glucose dehydrogenase A gcd ADR61697 PPUBIRD1_4115 2.03 0.86 Methylaccepting chemotaxis sensory transducer ADR61928 PPUBIRD1_4354 1.99 0.38 Phosphate transport regulator phoU ADR62664 PPUBIRD1_5117 2.07 0.32 Proteins whose expression was not affected by PhoBR Cyclopropanefattyacylphospholipid synthase cfa1 ADR57745...”
T1E_2822 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas putida DOT-T1E
79% identity, 100% coverage
- Synthesis of aromatic amino acids from 2G lignocellulosic substrates
Godoy, Microbial biotechnology 2021 - “...C5 sugar into intermediates of the pentose phosphate cycle. In addition, the open reading frame T1E_2822, encoding glucose dehydrogenase, was knockedout to avoid the production of the deadend product xylonate. We generated a set of DOTT1Ederived strains that metabolized glucose and xylose simultaneously in culture medium...”
- “...in the periplasm in a reaction catalysed by glucose dehydrogenase, encoded by the gcd gene (T1E_2822). A DOTT1Ederivative strain devoid of this gene was constructed as described in the Experimental Procedures section (Table 1 ). This mutant did not transform xylose into xylonate (data not shown),...”
PP1444 glucose dehydrogenase (pyrroloquinoline-quinone) from Pseudomonas putida KT2440
PP_1444 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas putida KT2440
79% identity, 100% coverage
- UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023 - Biotransformation of d-xylose to d-xylonate coupled to medium-chain-length polyhydroxyalkanoate production in cellobiose-grown Pseudomonas putida EM42
Dvořák, Microbial biotechnology 2020 - “...). In P. putida KT2440, and correspondingly also in strain EM42, membranebound glucose dehydrogenase Gcd (PP1444) oxidizes xylose to xylonolactone with pyrroloquinoline quinone (PQQ) as a cofactor. Lactone can then open spontaneously in the presence of water or might be converted to xylonate with the help...”
- Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition
van, BMC biotechnology 2013 - “...model, the FVA-calculation for the previously defined mutant with blocked enzymatic activity for glucose dehydrogenase (PP1444) was executed for the old and new conditions without any constraints. Compared to the old values, the new values lead to an decrease in the maximum AcCoA production flux and...”
- “...Consequently, the validation does not cover metabolic pathways outside the central metabolism. The single mutant (PP1444) showed the highest increased synthesis of PHA when characterized by Poblete-Castro et al . [ 26 ]. Based on the FVA-analysis the y x/s max was 0.32 g DCW g...”
- Establishment of oxidative D-xylose metabolism in Pseudomonas putida S12
Meijnen, Applied and environmental microbiology 2009 - “...intermediate -ketoglutarate (18, 20). In addition to Gcd (PP1444), some of the enzymes required for oxidative D-xylose metabolism are expected to be endogenous...”
- Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
Puchałka, PLoS computational biology 2008 - “...isomerase PP4715 d -Fructose 7.7 29.74 0.83 3.5 6-Phosphoglucono lactonase PP1023 2 Glucose dehydrogenase (membrane) PP1444 d -Glucose 7.05 28.51 0.83 4.17 6-Phosphoglucono lactonase PP1023 3 Isocitrate dehydrogenase PP4011 or PP4012 l -Serine 22.41 23.01 6.66 10.67 Formate dehydrogenase PP0490 or PP0491 PP2183 or PP2184 or...”
- Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis
del, Journal of bacteriology 2007 - “...ORFs encoding glucose dehydrogenase (gcd; PP1444), glucokinase (glk; PP1011), gluconokinase (gnuK; PP3416), and 2-ketogluconate-6-phosphate reductase (kguD;...”
- “...genes with an RT-PCR approach. The gcd gene corresponded to ORF PP1444, and it was found to be in a cluster of five genes that are transcribed in the same...”
- Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Dvořák, Nature communications 2024 - “...from E. coli and the deletion of the gcd gene encoding periplasmic membrane-bound glucose dehydrogenase (PP_1444) to fully utilize xylose 18 . This is consistent with the findings of Meijnen et al. 20 , 26 . in P. putida S12 and Elmore and co-workers 19 in...”
- “...The PD310 strain was also deprived of the gcd gene, which encodes periplasmic glucose dehydrogenase (PP_1444) to prevent the transformation of xylose to the dead-end product xylonate (XLN). The exogenous pathway converts xylose to xylulose 5-phosphate (X5P), which enters the EDEMP cycle formed by the reactions...”
- Modification of Glucose Metabolic Pathway to Enhance Polyhydroxyalkanoate Synthesis in Pseudomonas putida
Dong, Current issues in molecular biology 2024 - “...periplasmic space is converted into the para-metabolite gluconate by glucose dehydrogenase (encoded by gcd , PP_1444) in P. putida [ 47 ]. According to previous reports for P. putida , gluconate was detected as a major by-product [ 48 ] and accumulated in large amounts in...”
- Anaerobic glucose uptake in Pseudomonas putida KT2440 in a bioelectrochemical system
Pause, Microbial biotechnology 2024 - “...KTG P. putida KT2440 gcd Inframe gene deletion mutant of glucose dehydrogenase ( gcd , PP_1444 ); streamlined for crossmembrane transportation pathway via glucose SnchezPascuala et al.( 2019 ) KTGL P. putida KT2440 glk gtsABCD gad Inframe gene deletion mutant of glucose ABC transporter ( gtsABCD...”
- Biological Valorization of Lignin-Derived Aromatics in Hydrolysate to Protocatechuic Acid by Engineered Pseudomonas putida KT2440
Jin, Molecules (Basel, Switzerland) 2024 - “...vanillate O-demethylase oxygenase This study KT3 KT02 with scarless deletion of glucose dehydrogenase encoding gcd (PP_1444) and glucose ABC transporter gtsABCD (PP_1015-1018) This study Plasmids pBBR1MCS2 Broad-host-range cloning vector; Km R Lab stock pK18 mobsacB The suicide vector containing the sacB gene; Km R Lab stock...”
- Engineering of Pseudomonas putida for accelerated co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate explained by an upgraded metabolic model
Bujdoš, Metabolic engineering 2023 (PubMed)- “...in a mutant lacking periplasmic glucose dehydrogenase Gcd (PP_1444). However, the cause of the co-utilization phenotype remained to be understood and the...”
- Core and auxiliary functions of one-carbon metabolism in Pseudomonas putida exposed by a systems-level analysis of transcriptional and physiological responses
Turlin, mSystems 2023 - “...(FC) > 4. The PQQ biosynthetic pathway is required by multiple PQQ-dependent oxidases, e.g., Gcd (PP_1444), involved in the initial steps of glucose processing ( 85 ). Moreover, we analyzed different putative or characterized alcohol dehydrogenase genes, the products which could potentially act on methanol. PP_3839...”
- Engineering of Pseudomonas putida for accelerated co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate explained by an upgraded metabolic model
Bujdoš, 2022 - Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production
Czajka, Metabolic engineering communications 2022 - “...S2 ) or the growth rates. The lowered secretion indicated that the targeted knockdown of PP_1444 was successful in reducing periplasmic oxidation rates ( Fig. 1 ) and likely contributed to the increased indigoidine production during fed-batch mode reported in the original PSP strain ( Banerjee...”
- “...and secretion. Similarly, the extracellular data indicated that knockdown of the gluconate forming glucose dehydrogenase (PP_1444) was insufficient to fully prevent secretion of gluconate or 2KG. PP_1444 was therefore selected for deletion to further shift production towards the growth phase. Finally, the phaAZC- II D operon...”
- More
RGM3321_17085 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas sp. RGM 3321
70% identity, 100% coverage
ELZ14_24970 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas brassicacearum
71% identity, 100% coverage
PflSS101_1096 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas lactis
69% identity, 96% coverage
PFLU1086 quinoprotein glucose dehydrogenase from Pseudomonas fluorescens SBW25
70% identity, 96% coverage
PSPTO_4196 glucose dehydrogenase from Pseudomonas syringae pv. tomato str. DC3000
70% identity, 91% coverage
AZOLI_p50302 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Azospirillum lipoferum 4B
54% identity, 92% coverage
AZL_e01560 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Azospirillum sp. B510
55% identity, 95% coverage
A9CG47 Glucose dehydrogenase from Agrobacterium fabrum (strain C58 / ATCC 33970)
Atu4135 glucose dehydrogenase from Agrobacterium tumefaciens str. C58 (Cereon)
51% identity, 98% coverage
MPHASIOC01_004482 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Mangrovibacter phragmitis
50% identity, 99% coverage
JHW33_RS25310 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Rahnella aceris
49% identity, 100% coverage
I4W82_04525 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Klebsiella michiganensis
49% identity, 100% coverage
KP13_32152 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Klebsiella pneumoniae subsp. pneumoniae Kp13
49% identity, 100% coverage
EAI6_31050 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Enterobacter asburiae
48% identity, 100% coverage
Amal_02000 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Acetobacter malorum
50% identity, 98% coverage
Asbog_00903 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Asaia bogorensis NBRC 16594
49% identity, 99% coverage
LKW31_17685 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pantoea agglomerans
48% identity, 100% coverage
AN479_RS18465 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Serratia marcescens
49% identity, 96% coverage
- Complete genome analysis of Serratia marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants
Khan, PloS one 2017 - “...dehydrogenase (EC 1.1.1.37) AN479_RS06600 Oxidation of 3-Isopropylmalate to 4-methyl-2-oxopentanoate, 2-isopropyl-3-oxosuccinate, or4-methyl-2-oxopentanoate 3-Isopropylmalate dehydrogenase (EC 1.1.1.85) AN479_RS18465 Oxidation of beta-D-glucose to D-glucono-1,5-lactone Glucose 1-dehydrogenase (EC 1.1.1.47) AN479_RS03395 Oxidation of (R)-lactate to pyruvate d -Lactate dehydrogenase (EC 1.1.1.28) AN479_RS14060 Oxidation of (S)-lactate to pyruvate using 2 ferricytochrome l...”
- “...Glucose dehydrogenase and the pqq ABCDEF operon were identified in the RSC-14 genome as locus-tags AN479_RS18465 and AN479_21790, AN479_RS21865, AN479_RS21870, AN479_RS21875, AN479_RS20540, AN479_RS21885, respectively. (TIF) Click here for additional data file. S1 Table Annotated important genes from the Serratia marcescens RSC-14 complete genome. (XLSX) Click here...”
AL01_09305 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Bombella intestini
48% identity, 97% coverage
- Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius
Li, PloS one 2016 - “...dihydrolipoyllysine succinyltransferase (AL01_07740); 25, dihydrolipoamide dehydrogenase (AL01_00930); 26, fumarate hydratase (AL01_05840); 27, PQQ-dependent glucose dehydrogenase (AL01_09305); 28, gluconolactonase (AL01_06230); 29, lactate dehydrogenase (AL01_06935); 30, phosphogluconate dehydrogenase (AL01_06120); 31, transketolase (AL01_06110); 32, transaldolase (AL01_06115); 33, gluconate 2-dehydrogenase (AL01_07015); 34, 6-phosphogluconate dehydrogenase (AL01_06120); 35, ribose-5-phosphate isomerase (AL01_06135); 36,...”
- “...and B) respiratory chain of Bombella intestini LMG 28161 T . a, membrane-bound glucose dehydrogenase (AL01_09305); b, gluconate 2-dehydrogenase (AL01_07015); c, membrane-bound lactate dehydrogenase (AL01_06935); d, electron transfer flavoprotein-ubiquinone oxidoreductase (AL01_08300); e, type II NADH dehydrogenase (AL01_05990); f, cytochrome bo3 ubiquinol oxidase (AL01_00470, AL01_00475, AL01_00480 and...”
D0CDE5 Quinoprotein glucose dehydrogenase from Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)
47% identity, 99% coverage
P05465 soluble quinoprotein glucose dehydrogenase (EC 1.1.99.35) from Acinetobacter calcoaceticus (see 3 papers)
47% identity, 99% coverage
A0A0J6JEN3 glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) from Pseudomonas taetrolens (see paper)
49% identity, 98% coverage
bglu_2g12650 Pyrrolo-quinoline quinone from Burkholderia glumae BGR1
47% identity, 94% coverage
DV027_RS05880, WP_130730967 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Komagataeibacter xylinus
49% identity, 95% coverage
- How carbon sources drive cellulose synthesis in two Komagataeibacter xylinus strains
Lasagni, Scientific reports 2024 - “...sequence was retrieved from K2G30s genome project (BioProject accession number PRJNA482510) using scaffold annotations. Locus DV027_RS05880 on scaffold NZ_QQBI01000006.1 was selected because the putative encoded protein (Genebank accession number WP_130730967) shared 91% aminoacidic identity with the gene product of a functionally validated gdh gene (ATU72565) in...”
- “...Locus DV027_RS05880 on scaffold NZ_QQBI01000006.1 was selected because the putative encoded protein (Genebank accession number WP_130730967) shared 91% aminoacidic identity with the gene product of a functionally validated gdh gene (ATU72565) in K. xylinus strain CGMCC 2955 29 . Two primers, gdh-F1 and gdh-R1 (Table S6),...”
Q3J307 Quinoprotein glucose dehydrogenase from Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)
49% identity, 96% coverage
- The potential correlations between cell-free extracts from Rhodobacter sphaeroides grown under low-oxygen conditions and volatile organic compounds in Chinese-style sausage.
Nie, Food chemistry: X 2024 - “...pathway, with 13 proteins (Q3IYF0, A0A7Z6QWH9, A0A7Z6QYK9, A0A239DEP3, Q3IYF1, Q53176, B9KPE0, P29271, Q3IYB9, B9KQK9, A0A3G6WJG0, Q3J307, and Q3IXS0) identified. Microbial metabolism in diverse environments had the largest number of enriched proteins, with 45 differential proteins. The significant enrichment of the CAMP resistance suggests that cultivation under...”
ECs0128 glucose dehydrogenase from Escherichia coli O157:H7 str. Sakai
47% identity, 100% coverage
Gcd / b0124 quinoprotein glucose dehydrogenase (EC 1.1.5.2) from Escherichia coli K-12 substr. MG1655 (see 21 papers)
gcd / P15877 quinoprotein glucose dehydrogenase (EC 1.1.5.2) from Escherichia coli (strain K12) (see 22 papers)
DHG_ECOLI / P15877 Quinoprotein glucose dehydrogenase; Glucose dehydrogenase [pyrroloquinoline-quinone]; EC 1.1.5.2 from Escherichia coli (strain K12) (see 3 papers)
gcd / GB|BAB96699.1 quinoprotein glucose dehydrogenase; EC 1.1.5.2 from Escherichia coli K12 (see 9 papers)
gcd / ECOCYC|GLUCDEHYDROG-MONOMER glucose dehydrogenase from Escherichia coli K12 (see paper)
b0124 glucose dehydrogenase from Escherichia coli str. K-12 substr. MG1655
NP_414666 quinoprotein glucose dehydrogenase from Escherichia coli str. K-12 substr. MG1655
47% identity, 100% coverage
- function: GDH is probably involved in energy conservation rather than in sugar metabolism.
catalytic activity: a ubiquinone + D-glucose = D-glucono-1,5-lactone + a ubiquinol (RHEA:22152)
cofactor: pyrroloquinoline quinone
subunit: Monomer - Ferric Citrate Uptake Is a Virulence Factor in Uropathogenic Escherichia coli
Frick-Cheng, mBio 2022 - “...decarboxylase B 5.2 b1493 gadC l -Glutamate:4-aminobutyrate antiporter 5.4 b1492 gcd Quinoprotein glucose dehydrogenase 4.2 b0124 hchA d -Lactate dehydratase 4.5 b1967 mntH Manganese transport protein 5.6 b2392 nrdE Ribonucleoside-diphosphate reductase 2 subunit alpha 6.1 b2675 nrdF Ribonucleoside-diphosphate reductase 2 subunit beta 6.8 b2676 nrdH Glutaredoxin-like...”
- Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
King, Applied and environmental microbiology 2010 - “...ECs0503 ECs0880 ECs0927 ECs2042 b0802 b0847 b1438 b2530 b0124 b2466 b0449 ECs0512 ECs5566 ECs2316 ECs0252 b0459 b4458 b1610 b0255 ECs2817 b2015 Amino acid...”
- Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli
Brown, Proceedings of the National Academy of Sciences of the United States of America 2004 - “...b1777 (b1777); gapA (b1779) ydeA (b1528) hpt (b0125); ged (b0124) yefQ (b1111); ycfR (b1112) proP (b4111) ygiG (b3073); aer (b3072) -- -- 3.33 9.14 -- -- --...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...Transcriptional regulator for ara operon 0.36* 0.49* 0.83* b0124 gcd 1 Glucose dehydrogenase 3.11* 3.36* 1.14 b0162 yaeG 2 ORF, hypothetical protein 0.42* 0.72...”
- Topological analysis of quinoprotein glucose dehydrogenase in Escherichia coli and its ubiquinone-binding site.
Yamada, The Journal of biological chemistry 1993 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- Biodistribution of 89Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
Li, Poultry science 2023 - “...chaperones Cell inner membrane 350 P0A8Q0 FRDC Energy production and conversion Cell inner membrane 351 P15877 DHG Function unknown Cell inner membrane 352 P69786 PTGCB Carbohydrate transport and metabolism Cell inner membrane 353 P0AAD6 SDAC Amino acid transport and metabolism Cell inner membrane 354 P25714 YIDC...”
- Computational Proteome-Wide Study for the Prediction of Escherichia coli Protein Targeting in Host Cell Organelles and Their Implication in Development of Colon Cancer
Khan, ACS omega 2020 - “...ER membranes with more than 80% expected accuracy ( Table 2 ). Quinoprotein glucose dehydrogenase (P15877), ADP- l -glycero- d -manno-heptose-6-epimerase (P67910), and chain length determinant protein (P76372) targeted the interior of the Golgi apparatus membrane ( Table 3 ). These proteins may alter normal protein...”
- Mutations that disrupt either the pqq or the gdh gene of Rahnella aquatilis abolish the production of an antibacterial substance and result in reduced biological control of grapevine crown gall
Guo, Applied and environmental microbiology 2009 - “...and QGDH_E.col (70.3%) from Escherichia coli (accession number P15877). Regions of transmembrane helices determined for GDH (55) and predicted for QGDH-HX2 are...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...P37192 Tagatose-1,6-bisphosphate aldolase 5.87/30,811.93 Gcd P15877 Quinoprotein glucose dehydrogenase 5.4/86,747.35 GcvT P27248 5.36/40,015.52 GdhA P00370...”
- Hierarchy of carbon source selection in Paracoccus pantotrophus: strict correlation between reduction state of the carbon substrate and aerobic expression of the nap operon
Ellington, Journal of bacteriology 2002 - “...and Biological Sciences Research Council (grants C0866 and P15877 to S.J.F. and D.J.R.) and by a BBSRC PMS committee studentship to M.J.K.E. K.K.B. was...”
CFR77_05025 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Komagataeibacter sucrofermentans
49% identity, 95% coverage
- Enhanced bacterial cellulose production in Komagataeibacter sucrofermentans: impact of different PQQ-dependent dehydrogenase knockouts and ethanol supplementation
Montenegro-Silva, Biotechnology for biofuels and bioproducts 2024 - “...(pUC19-based) catgtgagcaaaaggccagcaa This work pUC_RV KTK_354 plasmid backbone (pUC19-based) tatggtgcactctcagtacaatctgct This work KS003-UF KS001 gDNA CFR77_05025 tgagagtgcaccataATGAATAGCCTCATACGCTCG This work KS003-UR KS001 gDNA CFR77_05025 tacgtgcccgatcaaTGTCCAGGCCACCTTCAG This work KS003-DF KS001 gDNA CFR77_05025 gcgttttttattggtGCAATCTCGGCATGTTCGAA This work KS003-DR KS001 gDNA CFR77_05025 ccttttgctcacatgTCAGTTCCCGTCAGGCAGG This work KS002-UF KS001 gDNA CFR77_01730 tgagagtgcaccataATGCGAGAAACCACCAAGAGG This...”
- “...production. The strains KS002, KS003, KS004, and KS005 were obtained by disrupting the loci CFR77_01730, CFR77_05025, CFR77_00430, and CFR77_09325, respectively. According to the protein annotation, the strains KS002, KS003, and KS005 lack PQQ-mDHs belonging to the glucose/quinate/shikimate family, while KS004 lacks a PQQ-mDH from the methanol/ethanol...”
B0W47_02520 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Komagataeibacter nataicola
49% identity, 95% coverage
- Complete genome sequence of the cellulose-producing strain Komagataeibacter nataicola RZS01
Zhang, Scientific reports 2017 - “...3 Primary membrane-bound dehydrogenases in K. nataicola RZS01. Family Cofactor Genes Glucose dehydrogenase PQQ B0W47_01230, B0W47_02520, B0W47_10950 Glycerol dehydrogenase PQQ B0W47_01005, B0W47_01010 Alcohol dehydrogenase PQQ B0W47_13410 Aldehyde dehydrogenase PQQ B0W47_16410 2-Keto- d -gluconate dehydrogenase FAD B0W47_11030, B0W47_11035, B0W47_11040 Gluconate 2-dehydrogenase FAD B0W47_05395, B0W47_05400, B0W47_05405, B0W47_13405 Adaptation...”
ACIAD2983 glucose dehydrogenase [pyrroloquinoline-quinone] precursor (Quinoprotein glucose DH) from Acinetobacter sp. ADP1
ACIAD_RS13470 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Acinetobacter baylyi ADP1
47% identity, 98% coverage
- Removal of aromatic inhibitors produced from lignocellulosic hydrolysates by Acinetobacter baylyi ADP1 with formation of ethanol by Kluyveromyces marxianus
Singh, Biotechnology for biofuels 2019 - “...glucose, two plasmids were made with a defined deletion of gcd (locus designation ACIAD_RS13470, or ACIAD2983, at position 2,911,9672,914,372, in the ADP1 genome, NC_005966 in NCBI). One of these plasmids, pBAC1565, carries ADP1 DNA surrounding gcd from genomic positions 2,909,747 (downstream of gcd ) to 2,916,396...”
- iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources
Jiang, Frontiers in microbiology 2019 - “...4.66 3.34 Succinate dehydrogenase flavoprotein subunit sdhA ACIAD2880 3.28 1.82 1.85 2.96 Glucose dehydrogenase gcd ACIAD2983 1.43 1.2 1.41 1.22 Pyridine nucleotide transhydrogenase (proton pump), alpha subunit (part1) pntA ACIAD3079 1.31 1.34 6.03 1.84 Ketol-acid reductoisomerase ilvC ACIAD3102 4.21 2.38 2.07 2.78 Malate dehydrogenase mdh ACIAD3155...”
- Metabolic pairing of aerobic and anaerobic production in a one-pot batch cultivation
Salmela, Biotechnology for biofuels 2018 - “...Methods Strains and cultivation medium Acinetobacter baylyi ADP1 (DSM 24193) devoid of glucose dehydrogenase gene ACIAD2983, (referred here as ADP1-g) and Clostridium butyricum , isolated from a hydrogen-producing bioreactor [ 34 ], were used in the study. Unless otherwise indicated, ADP1-g cells cultivated in low-salt Lysogeny...”
- Metabolic engineering of Acinetobacter baylyi ADP1 for removal of Clostridium butyricum growth inhibitors produced from lignocellulosic hydrolysates
Kannisto, Biotechnology for biofuels 2015 - “...flanking regions of the cassette were replaced with the flanking regions for knocking out gcd (ACIAD2983, NCBI Gene ID: 2878488) by cloning them from the genome of wild-type A. baylyi ADP1 with primers having identical annealing regions to those used by de Berardinis et al. [...”
- Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data
Durot, BMC systems biology 2008 - “...ACIAD1711 (pcaH) E step 3 ACIAD2088 (aspQ) E step 3 ACIAD1712 (pcaG) E step 3 ACIAD2983 (gcd) E step 3 ACIAD1744 (aspA) E step 3 presence of an alternate enzyme 6 No precise interpretation 30 ACIAD1231 (argD) D step 2 ACIAD0072 (ugd) E step 2 ACIAD1642...”
- Removal of aromatic inhibitors produced from lignocellulosic hydrolysates by Acinetobacter baylyi ADP1 with formation of ethanol by Kluyveromyces marxianus
Singh, Biotechnology for biofuels 2019 - “...to degrade glucose, two plasmids were made with a defined deletion of gcd (locus designation ACIAD_RS13470, or ACIAD2983, at position 2,911,9672,914,372, in the ADP1 genome, NC_005966 in NCBI). One of these plasmids, pBAC1565, carries ADP1 DNA surrounding gcd from genomic positions 2,909,747 (downstream of gcd )...”
D4P700 glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) from Pantoea ananatis (see paper)
PAJ_3473 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pantoea ananatis AJ13355
47% identity, 100% coverage
GOX0265 Membrane-bound glucose dehydrogenase (PQQ) from Gluconobacter oxydans 621H
P27175 Quinoprotein glucose dehydrogenase from Gluconobacter oxydans (strain 621H)
46% identity, 99% coverage
- 2,5-Diketo-D-Gluconate Hyperproducing Gluconobacter sphaericus SJF2-1 with Reporting Multiple Genes Encoding the Membrane-Associated Flavoprotein-Cytochrome c Complexed Dehydrogenases
Son, Microorganisms 2022 - “...either spontaneously or by a membrane-bound lactonase [ 36 ]. In G. oxydans 621H, the GOX0265 gene (808 aa residues) encodes a PQQ-dependent glucose dehydrogenase [ 37 ]. As a result of searching for the homologous genes in the genome of SJF2-1, the IGS75_01835 gene (808...”
- “...as a quinoprotein, with the same membrane topology and 37.4% amino acid sequence identity as GOX0265. These two enzymes belong to the dehydrogenases of the glucose/quinate/shikimate family. Other genes encoding quinoprotein dehydrogenases include two methanol/ethanol family dehydrogenases, IGS75_06000 (757 aa) and IGS75_08895 (693 aa), and glycerol/sorbitol...”
- The l-rhamnose-dependent regulator RhaS and its target promoters from Escherichia coli expand the genetic toolkit for regulatable gene expression in the acetic acid bacterium Gluconobacter oxydans
Fricke, Frontiers in microbiology 2022 - “...Kovach et al. (1995) pBBR1MCS-5-T gdhM -MCS-T GOX0028 Derivative of pBBR1MCS-5 with terminator sequences of GOX0265 (T gdhM ) and GOX0028 (T GOX0028 ) flanking the multiple cloning site Fricke et al. (2021b) pBBR1MCS-5- rhaSR -P rhaSR -P rhaBAD - mNG Derivative of pBBR1MCS-5-T gdhM -MCS-T...”
- “...for the TetR-P tet system ( Fricke et al., 2021b ). The terminator sequences of GOX0265 (T gdhM ) and GOX0028 (T GOX0028 ) flank the multiple cloning site (MCS) to reduce potential interferences caused by genetic elements on the plasmid backbone. Unless stated otherwise, pBBR1MCS-5-T...”
- Highly tunable TetR-dependent target gene expression in the acetic acid bacterium Gluconobacter oxydans
Fricke, Applied microbiology and biotechnology 2021 - “...Deppenmeier, University of Bonn pBBR1MCS-5-T gdhM -MCS-T 0028 Derivative of pBBR1MCS-5 with terminator sequences of GOX0265 (T gdhM ) and GOX0028 (T 0028 ) flanking the multiple cloning site This work pBBR1MCS-5-T gdhM - tetR -P tet -mNG -T BBa_B1002 -T 0028 Derivative of pBBR1MCS-5-T gdhM...”
- “...vector pBBR1MCS-5-T gdhM -MCS-T 0028 was generated from pBBR1MCS-5. It carries the terminator sequences of GOX0265 (T gdhM ) and GOX0028 (T 0028 ) flanking the multiple cloning site (MCS) to minimize interfering effects between the plasmid backbone and expression of the inserted genes. Plasmid pBBR1MCS-5-T...”
- On the way toward regulatable expression systems in acetic acid bacteria: target gene expression and use cases
Fricke, Applied microbiology and biotechnology 2021 - “...of terminal oxidases on growth and yield of G. oxydans 621H Richhardt et al. 2013 GOX0265 of G. oxydans 621H membrane-bound PQQ-dependent glucose DH (mGHD) with C-terminal Strep-tag P GOX0452 gluconate production; influence of mGDH on O 2 consumption rate; membrane protein purification by Strep-tactin affinity...”
- A tunable L-arabinose-inducible expression plasmid for the acetic acid bacterium Gluconobacter oxydans
Fricke, Applied microbiology and biotechnology 2020 - “...Expression from moderate P GOX0452 has been used to successfully produce membrane-bound PQQ-dependent glucose dehydrogenase (GOX0265) for purification and characterization (Meyer et al. 2013 ). Expression from weak P GOX0384 has been used to successfully produce the succinate dehydrogenase from Acetobacter pasteurianus in G. oxydans as...”
- “...-P BAD -mNG , lacking the regulator gene araC and carrying the terminator of gdhM (GOX0265) upstream of P BAD This work pBBR1MCS-5- araE-araC -P BAD -mNG Derivative of pBBR1MCS-5- araC -P BAD -mNG carrying gene araE encoding l -arabinose transporter AraE This work pBBR1MCS-5- araC...”
- Engineering of glycerol utilization in Gluconobacter oxydans 621H for biocatalyst preparation in a low-cost way
Yan, Microbial cell factories 2018 - “...the strain might be used in other chemicals production. For instance, the membrane-bound glucose dehydrogenase (GOX0265) has the ability to oxidize glucose, xylose, galactose, mannose, allose, and arabinose [ 38 40 ]. To identify the applicability of the whole cells of G. oxydans GOX1068GOX0854 prepared from...”
- “...uncharacterized PQQ-depending dehydrogenase; 6, inositol dehydrogenase (GOX1857); 7, d -lactate dehydrogenase (GOX1253); 8, glucose dehydrogenase (GOX0265); 9, gluconate dehydrogenase (GOX1230, GOX1231 and GOX1232); 10, sorbitol dehydrogenase (GOX2094, GOX2095, GOX2096 and GOX2097). DHA dihydroxyacetone, G3P glycerol-3-phosphate, DHAP dihydroxyacetone phosphate, GAP glyceraldehyde-3-phosphate, GlpF glycerol uptake facilitator protein, GlpK...”
- Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
Kranz, BMC genomics 2018 - “...lines indicate operon genes and genomic orientation. locus tag / operon annotation half-life (min) FPKM GOX0265 membrane-bound glucose dehydrogenase (PQQ) 4.4 146 GOX0516 PQQ-dependent dehydrogenase 4 8.3 22 | GOX0585 cytochrome c subunit of aldehyde dehydrogenase 3.7 32 | GOX0586 membrane-bound aldehyde dehydrogenase, small subunit 3.7...”
- “..., fumarate hydratase (GOX1643); gap , glyceraldehyde 3-phosphate dehydrogenase (GOX0508); gdhM , membrane-bound glucose dehydrogenase (GOX0265); gdhS , soluble glucose dehydrogenase (GOX2015); glk , glucokinase (GOX2419); ( glk ), putative glucokinase (GOX1182); gltA , citrate synthase (GOX1999); gnd , 6-phosphogluconate dehydrogenase (GOX1705); gnk , gluconokinase (GOX1709);...”
- Combinatorial metabolic engineering of industrial Gluconobacter oxydans DSM2343 for boosting 5-keto-D-gluconic acid accumulation
Yuan, BMC biotechnology 2016 (no snippet) - More
- Quantitative Control of Early Flowering in White Lupin (Lupinus albus L.).
Rychel-Bielska, International journal of molecular sciences 2021 - “...found only in several accessions originating from mountainous regions of Ethiopia, particularly in lines P27174, P27175, and P27178 [ 22 ]. Marker-based studies revealed that Ethiopian white lupins are relatively closely related to each other and very distinct from the improved germplasm originating from Europe [...”
- Development of PCR-based markers and whole-genome selection model for anthracnose resistance in white lupin (Lupinus albus L.).
Rychel-Bielska, Journal of applied genetics 2020 - “...and reproducible level of resistance was found only in several Ethiopian landrace accessions, P27172, P27174, P27175, P27178, P28512, P28523, and P28538 (Adhikari et al. 2009 ). The three most resistant lines (P27172, P27174, P27178) were collected in one district, Debre Markos, at altitudes around 2000 m....”
- A high-density consensus linkage map of white lupin highlights synteny with narrow-leafed lupin and provides markers tagging key agronomic traits.
Książkiewicz, Scientific reports 2017 - “...located in mountainous regions of Ethiopia, has been identified. Three most resistant accessions, namely P27174, P27175, and P27178, were collected in one district and are probably related 10 . Phomopsis stem blight is caused by the pathogenic fungus Diaporthe toxica Williamson, whose anamorph was previously classified...”
Bpet4644 gcd from Bordetella petrii DSM 12804
49% identity, 96% coverage
IGS75_01835 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Gluconobacter sphaericus
46% identity, 99% coverage
AD938_10885 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Gluconobacter japonicus
46% identity, 99% coverage
- Determination of Dehydrogenase Activities Involved in D-Glucose Oxidation in Gluconobacter and Acetobacter Strains
Sainz, Frontiers in microbiology 2016 - “...Gene Product Primer name Primer sequence (fwd) Primer sequence (rev) Gluconobacter japonicus NBRC 3271 LHZK00000000 AD938_10885 gcd Membrane-bound glucose dehydrogenase mgdh TGGTTTTCCCGGGTGATCTG GTAGTAGTCCATCGTGCCCG LHZK00000000 AD938_08480 gnd L Gluconate 2-dehydrogenase, large subunit gadh1 TCCTGAGTGCGTTCCAGTTC CGCTTTGGCAATGGGTTCAA LHZK00000000 AD938_03325 Gluconate 2-dehydrogenase, large subunit gadh2 GGCCTATCCCTCGTCAATCG TGCATAACCGCTGCAAAACC LHZK00000000 AD938_10275 sld...”
NBRC3257_0371 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Gluconobacter thailandicus NBRC 3257
46% identity, 99% coverage
- Draft genome sequence of Gluconobacter thailandicus NBRC 3257
Matsutani, Standards in genomic sciences 2014 - “...dependent proteins were investigated. Homologous proteins of membrane-bound PQQ-dependent dehydrogenase (NBRC3257_0292), membrane-bound glucose dehydrogenase (PQQ) (NBRC3257_0371), PQQ-dependent dehydrogenase 4 (NBRC3257_0662), and PQQ-dependent dehydrogenase 3 (NBRC3257_1743), were identified. In addition, two paralogous copies of the PQQ-glycerol dehydrogenase sld AB operon (NBRC3257_0924 to NBRC3257_0925 and NBRC3257_1134 to NBRC3257_1135)...”
VZ55_RS10065 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Gluconobacter oxydans
47% identity, 99% coverage
LKW31_10030 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Pantoea agglomerans
45% identity, 98% coverage
XAC3212 glucose dehydrogenase from Xanthomonas axonopodis pv. citri str. 306
43% identity, 95% coverage
B0W47_10950 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Komagataeibacter nataicola
43% identity, 97% coverage
- Complete genome sequence of the cellulose-producing strain Komagataeibacter nataicola RZS01
Zhang, Scientific reports 2017 - “...Primary membrane-bound dehydrogenases in K. nataicola RZS01. Family Cofactor Genes Glucose dehydrogenase PQQ B0W47_01230, B0W47_02520, B0W47_10950 Glycerol dehydrogenase PQQ B0W47_01005, B0W47_01010 Alcohol dehydrogenase PQQ B0W47_13410 Aldehyde dehydrogenase PQQ B0W47_16410 2-Keto- d -gluconate dehydrogenase FAD B0W47_11030, B0W47_11035, B0W47_11040 Gluconate 2-dehydrogenase FAD B0W47_05395, B0W47_05400, B0W47_05405, B0W47_13405 Adaptation to...”
APA386B_325 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Acetobacter pasteurianus 386B
42% identity, 97% coverage
- Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem
Illeghems, BMC genomics 2013 - “...- APA386B_2134); (4) uncharacterized PQQ-containing oxidoreductases [APA386B_1016 (transmembrane regions: 2042, 4764, 6986, 101120, 127149) and APA386B_325 (transmembrane regions: 729, 3355, 6486, 90107, 120142)]; (5) FAD-dependent sorbitol dehydrogenase (APA386B_1096 - APA386B_1098). (B) Membrane-bound oxidoreductases and terminal oxidases : (6) uncharacterized oxidoreductases [APA386B_1815 (transmembrane region: 133153), APA386B_1888 (transmembrane...”
CFR77_01730 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Komagataeibacter sucrofermentans
43% identity, 97% coverage
- Enhanced bacterial cellulose production in Komagataeibacter sucrofermentans: impact of different PQQ-dependent dehydrogenase knockouts and ethanol supplementation
Montenegro-Silva, Biotechnology for biofuels and bioproducts 2024 - “...gDNA CFR77_05025 gcgttttttattggtGCAATCTCGGCATGTTCGAA This work KS003-DR KS001 gDNA CFR77_05025 ccttttgctcacatgTCAGTTCCCGTCAGGCAGG This work KS002-UF KS001 gDNA CFR77_01730 tgagagtgcaccataATGCGAGAAACCACCAAGAGG This work KS002-UR KS001 gDNA CFR77_01730 tacgtgcccgatcaaGACTTCAAGGTTGAACTCATGACCC This work KS002-DF KS001 gDNA CFR77_01730 gcgttttttattggtTCATGCTGGCCAATGCGAG This work KS002-DR KS001 gDNA CFR77_01730 ccttttgctcacatgTTATTGGGCTGCATTGCCTGCC This work KS004-UF KS001 gDNA CFR77_00430 tgagagtgcaccataATGATTTCTGCCGTTTTCGGAAAAAGACG This...”
- “...BC production. The strains KS002, KS003, KS004, and KS005 were obtained by disrupting the loci CFR77_01730, CFR77_05025, CFR77_00430, and CFR77_09325, respectively. According to the protein annotation, the strains KS002, KS003, and KS005 lack PQQ-mDHs belonging to the glucose/quinate/shikimate family, while KS004 lacks a PQQ-mDH from the...”
GOX0516 Uncharacterized PQQ-dependent dehydrogenase 4 from Gluconobacter oxydans 621H
43% identity, 92% coverage
- Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
Kranz, BMC genomics 2018 - “...FPKM and half-live. The transcripts of the PQQ-dependent mDHs 1 (GOX1857), 3 (GOX1441), and 4 (GOX0516), sorbitol dehydrogenase (GOX209497), and aldehyde dehydrogenase mAcDH (GOX05857) exhibited very low expression values and half-lives from 4min to 9min. Table 3 mRNA half-lives and expression values (FPKM) of genes encoding...”
- “...locus tag / operon annotation half-life (min) FPKM GOX0265 membrane-bound glucose dehydrogenase (PQQ) 4.4 146 GOX0516 PQQ-dependent dehydrogenase 4 8.3 22 | GOX0585 cytochrome c subunit of aldehyde dehydrogenase 3.7 32 | GOX0586 membrane-bound aldehyde dehydrogenase, small subunit 3.7 38 GOX0587 membrane-bound aldehyde dehydrogenase, large subunit...”
NBRC3257_0662 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Gluconobacter thailandicus NBRC 3257
42% identity, 93% coverage
- Draft genome sequence of Gluconobacter thailandicus NBRC 3257
Matsutani, Standards in genomic sciences 2014 - “...Homologous proteins of membrane-bound PQQ-dependent dehydrogenase (NBRC3257_0292), membrane-bound glucose dehydrogenase (PQQ) (NBRC3257_0371), PQQ-dependent dehydrogenase 4 (NBRC3257_0662), and PQQ-dependent dehydrogenase 3 (NBRC3257_1743), were identified. In addition, two paralogous copies of the PQQ-glycerol dehydrogenase sld AB operon (NBRC3257_0924 to NBRC3257_0925 and NBRC3257_1134 to NBRC3257_1135) were identified. It has...”
LKW31_05305 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pantoea agglomerans
40% identity, 97% coverage
- Whole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop (Humulus lupulus L.)
Patakova, Frontiers in microbiology 2024 - “...glucose dehydrogenase (1) LKW31_10030 Membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family LKW31_17685 Glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase LKW31_05305 Glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase PQQ biosynthesis (1a) LKW31_10225 Pyrroloquinoline quinone biosynthesis protein PqqF pqqF LKW31_10230 Pyrroloquinoline quinone biosynthesis protein PqqE pqqE LKW31_10235 Pyrroloquinoline quinone biosynthesis peptide PqqD pqqD LKW31_10240...”
VZ55_RS08395 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Gluconobacter oxydans
41% identity, 93% coverage
IGS75_03370 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Gluconobacter sphaericus
41% identity, 92% coverage
GOX1441 Uncharacterized PQQ-dependent dehydrogenase 3 from Gluconobacter oxydans 621H
38% identity, 98% coverage
- Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
Kranz, BMC genomics 2018 - “...inverse relationship between FPKM and half-live. The transcripts of the PQQ-dependent mDHs 1 (GOX1857), 3 (GOX1441), and 4 (GOX0516), sorbitol dehydrogenase (GOX209497), and aldehyde dehydrogenase mAcDH (GOX05857) exhibited very low expression values and half-lives from 4min to 9min. Table 3 mRNA half-lives and expression values (FPKM)...”
- “...8.5 791 | GOX1232 gluconate 2-dehydrogenase gamma chain 7.8 684 GOX1253 D-lactate dehydrogenase 5.0 159 GOX1441 PQQ-dependent dehydrogenase 3 4.7 31 GOX1857 PQQ-containing dehydrogenase 1 7.1 122 | GOX1968 hypothetical protein 3.6 496 | GOX1969 alcohol dehydrogenase large subunit 3.5 540 GOX1970 GTP-binding protein EngA 4.3...”
KVC_0743, KVU_0226 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Ketogulonicigenium vulgare
39% identity, 96% coverage
- Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome
Wang, Scientific reports 2018 - “...K . vulgare Hbe602 K . vulgare WSH-001 K . vulgare Y25 Glk EMP 1.1.5.2 KVC_0743 KvSKV_08250 KVH_08280 KVU_0226 EIO_1719 Pfk EMP 2.7.1.11 Null Null Null Null Null Fda EMP 4.1.2.13 KVC_1210 KvSKV_05540 KVH_05570 KVU_0671 EIO_1171 TpiA EMP 5.3.1.1 KVC_1436 KvSKV_06720 KVH_06750 KVU_0894 EIO_1404 Gap EMP...”
- “...Hbe602 K . vulgare WSH-001 K . vulgare Y25 Glk EMP 1.1.5.2 KVC_0743 KvSKV_08250 KVH_08280 KVU_0226 EIO_1719 Pfk EMP 2.7.1.11 Null Null Null Null Null Fda EMP 4.1.2.13 KVC_1210 KvSKV_05540 KVH_05570 KVU_0671 EIO_1171 TpiA EMP 5.3.1.1 KVC_1436 KvSKV_06720 KVH_06750 KVU_0894 EIO_1404 Gap EMP 1.2.1.12 KVC_2250 KvSKV_10850...”
GOX1857 Uncharacterized PQQ-containing dehydrogenase 1 from Gluconobacter oxydans 621H
40% identity, 99% coverage
- On the way toward regulatable expression systems in acetic acid bacteria: target gene expression and use cases
Fricke, Applied microbiology and biotechnology 2021 - “..., pqq4 , sldAB from G. oxydans 621H membrane-bound DHs (mDHs) P GOX1067-68 , P GOX1857 , test of promoter strength and enzymatic characterization of mDHs in G. oxydans multi-deletion strain BP.9 Mientus et al. 2017 genes of putative membrane-bound DHs from mother of vinegar DNA...”
- “...lac gluconate and 5-keto- d -gluconic acid accumulation by G. oxydans Merfort et al. 2006b GOX1857 from G. oxydans 621H membrane-bound PQQ-dependent inositol DH P GOX1857 substrate and co-factor analysis of GOX1857 in G. oxydans 621H Hlscher et al. 2007 uidA from E. coli DH5 -...”
- Engineering of glycerol utilization in Gluconobacter oxydans 621H for biocatalyst preparation in a low-cost way
Yan, Microbial cell factories 2018 - “...and GOX0587); 3, polyol dehydrogenase (GOX0854 and GOX0855); 4/5, uncharacterized PQQ-depending dehydrogenase; 6, inositol dehydrogenase (GOX1857); 7, d -lactate dehydrogenase (GOX1253); 8, glucose dehydrogenase (GOX0265); 9, gluconate dehydrogenase (GOX1230, GOX1231 and GOX1232); 10, sorbitol dehydrogenase (GOX2094, GOX2095, GOX2096 and GOX2097). DHA dihydroxyacetone, G3P glycerol-3-phosphate, DHAP dihydroxyacetone...”
- Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
Kranz, BMC genomics 2018 - “...of the inverse relationship between FPKM and half-live. The transcripts of the PQQ-dependent mDHs 1 (GOX1857), 3 (GOX1441), and 4 (GOX0516), sorbitol dehydrogenase (GOX209497), and aldehyde dehydrogenase mAcDH (GOX05857) exhibited very low expression values and half-lives from 4min to 9min. Table 3 mRNA half-lives and expression...”
- “...gamma chain 7.8 684 GOX1253 D-lactate dehydrogenase 5.0 159 GOX1441 PQQ-dependent dehydrogenase 3 4.7 31 GOX1857 PQQ-containing dehydrogenase 1 7.1 122 | GOX1968 hypothetical protein 3.6 496 | GOX1969 alcohol dehydrogenase large subunit 3.5 540 GOX1970 GTP-binding protein EngA 4.3 408 GOX2094 sorbitol dehydrogenase cytochrome c...”
- Combined fluxomics and transcriptomics analysis of glucose catabolism via a partially cyclic pentose phosphate pathway in Gluconobacter oxydans 621H
Hanke, Applied and environmental microbiology 2013 - “...as those for a PQQ-containing myo-inositol dehydrogenase (GOX1857, mRNA ratio of 12.0) (34), for the membrane-bound gluconate 2-dehydrogenase (GOX1230 and...”
- “...Annotation or protein Respiration and energy metabolism GOX1857 GOX0310 GOX0311 GOX0312 GOX0313 GOX0314 GOX2087 GOX2088 GOX2089 GOX2090 GOX2167 GOX2168 GOX2169...”
- Identification of membrane-bound quinoprotein inositol dehydrogenase in Gluconobacter oxydans ATCC 621H
Hölscher, Microbiology (Reading, England) 2007 (PubMed)- “...Universitat Berlin, D-13353 Berlin, Germany The GOX1857 gene, which encodes a putative membrane-bound pyrroloquinoline quinone (PQQ)-dependent dehydrogenase in...”
- “...myo-inositol dehydrogenase activity in vitro, indicating that GOX1857 encodes an inositol dehydrogenase. The association of inositol dehydrogenase with the...”
XC_2659 glucose dehydrogenase from Xanthomonas campestris pv. campestris str. 8004
42% identity, 94% coverage
- Flp, a Fis-like protein, contributes to the regulation of type III secretion and virulence processes in the phytopathogen Xanthomonas campestris pv. campestris
Leng, Molecular plant pathology 2019 - “...ompW Outer membrane protein 2.59 XC_2827 hpaR MarR family transcriptional regulator 2.25 XC_0158 Xylosidase/arabinosidase 2.51 XC_2659 gcd Quinoprotein glucose dehydrogenase 7.31 XC_1273 trkA Voltagegated potassium channel 2.36 XC_1314 lptC Lipopolysaccharide export system protein LptC 2.51 XC_3652 fabB ketoacyl[ACP] synthase 2.05 XC_0783 celS Cellulase S 2.51 16SrRNA...”
- “...by Flp and not HrpX. To confirm this we examined the expression of XC_1273 , XC_2659 , XC_2827 , XC_3129 , XC_3694 and XC_4002 by RTPCR by extracting RNA from wildtype, flp, Cflp and flp/p3X cultured in XVM2, respectively. The RTPCR results confirmed that expression of...”
NP_636946 glucose dehydrogenase from Xanthomonas campestris pv. campestris str. ATCC 33913
42% identity, 94% coverage
VZ55_RS08235 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Gluconobacter oxydans
39% identity, 95% coverage
PPUBIRD1_2225 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase from Pseudomonas putida BIRD-1
40% identity, 98% coverage
NBRC3257_1743 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Gluconobacter thailandicus NBRC 3257
40% identity, 95% coverage
- Draft genome sequence of Gluconobacter thailandicus NBRC 3257
Matsutani, Standards in genomic sciences 2014 - “...dehydrogenase (NBRC3257_0292), membrane-bound glucose dehydrogenase (PQQ) (NBRC3257_0371), PQQ-dependent dehydrogenase 4 (NBRC3257_0662), and PQQ-dependent dehydrogenase 3 (NBRC3257_1743), were identified. In addition, two paralogous copies of the PQQ-glycerol dehydrogenase sld AB operon (NBRC3257_0924 to NBRC3257_0925 and NBRC3257_1134 to NBRC3257_1135) were identified. It has been thought that the respiratory...”
A0A2Z5U248 quinate/shikimate dehydrogenase (quinone) (EC 1.1.5.8) from Gluconobacter oxydans (see paper)
37% identity, 95% coverage
A0A2Z5U421 quinate/shikimate dehydrogenase (quinone) (EC 1.1.5.8) from Gluconobacter oxydans (see paper)
37% identity, 95% coverage
quiA / Q59086 quinate/shikimate dehydrogenase (quinone) (EC 1.1.5.8) from Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1) (see 2 papers)
38% identity, 97% coverage
PP3569 quinate dehydrogenase (pyrroloquinoline-quinone), putative from Pseudomonas putida KT2440
40% identity, 98% coverage
jpw_21040 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Pseudomonas asiatica
39% identity, 94% coverage
- Genomic Analysis of Pseudomonas asiatica JP233: An Efficient Phosphate-Solubilizing Bacterium
Wang, Genes 2022 - “...responsible for phosphate solubilization in JP233 [ 15 ]. Genes encoding glucose dehydrogenase (jpw_20390 and jpw_21040), the pqqFABCDEG operon (jpw_01865jpw_01895) and the gluconate dehydrogenase operon (jpw_13670jpw_13680) were detected in the JP233 genome ( Figure 5 ). The enzymes pyrophosphatase (PPA) and exopolyphosphatase (PPX) have also proposed...”
- “...the genes associated with the synthesis of 2-keto gluconic acid in P. asiatica JP233 genome. jpw_21040 and 20390: glucose dehydrogenase genes ( gcd ); 1367013680: gluconate dehydrogenase operon; 0186501895: PQQ biosynthesis gene cluster. The genes are represented according to their size. Double vertical lines represent intervening...”
Asbog_00451 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Asaia bogorensis NBRC 16594
40% identity, 94% coverage
A1S_1880 pyrroloquinoline-quinone QuiA from Acinetobacter baumannii ATCC 17978
38% identity, 96% coverage
NBRC3257_0292 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Gluconobacter thailandicus NBRC 3257
38% identity, 98% coverage
- Draft genome sequence of Gluconobacter thailandicus NBRC 3257
Matsutani, Standards in genomic sciences 2014 - “...repertories of other membrane-bound PQQ dependent proteins were investigated. Homologous proteins of membrane-bound PQQ-dependent dehydrogenase (NBRC3257_0292), membrane-bound glucose dehydrogenase (PQQ) (NBRC3257_0371), PQQ-dependent dehydrogenase 4 (NBRC3257_0662), and PQQ-dependent dehydrogenase 3 (NBRC3257_1743), were identified. In addition, two paralogous copies of the PQQ-glycerol dehydrogenase sld AB operon (NBRC3257_0924 to...”
XAC1633 glucose dehydrogenase from Xanthomonas axonopodis pv. citri str. 306
45% identity, 80% coverage
B9TTF1 quinate/shikimate dehydrogenase (quinone) (EC 1.1.5.8) from Gluconobacter oxydans (see paper)
37% identity, 95% coverage
PchlO6_1551 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family from Pseudomonas chlororaphis O6
38% identity, 99% coverage
Asbog_02637 pyrroloquinoline quinone-dependent dehydrogenase from Asaia bogorensis NBRC 16594
39% identity, 79% coverage
NBRC3255_0026, NBRC3257_0925 pyrroloquinoline quinone-dependent dehydrogenase from Gluconobacter thailandicus NBRC 3257
40% identity, 79% coverage
- Draft genome sequence of Gluconobacter thailandicus NBRC 3257
Matsutani, Standards in genomic sciences 2014 - “...identified. In addition, two paralogous copies of the PQQ-glycerol dehydrogenase sld AB operon (NBRC3257_0924 to NBRC3257_0925 and NBRC3257_1134 to NBRC3257_1135) were identified. It has been thought that the respiratory chains of Gluconobacter species play key roles in respiratory energy metabolism [ 48 - 51 ]. Therefore,...”
- Draft Genome Sequence of Dihydroxyacetone-Producing Gluconobacter thailandicus Strain NBRC 3255
Matsutani, Genome announcements 2013 - “...3255 lacks the PQQ-dependent dehydrogenase 1, while two paralogous sets of sldAB operons (NBRC3255_0025 to NBRC3255_0026 and NBRC3255_0235 to NBRC3255_0236) were identified. One of the two paralogs, the NBRC3255_0235 operon, is responsible for dihydroxyacetone production from glycerol as a glycerol dehydrogenase ( 9 ), and NBRC...”
AD938_11075 pyrroloquinoline quinone-dependent dehydrogenase from Gluconobacter japonicus
40% identity, 79% coverage
- Determination of Dehydrogenase Activities Involved in D-Glucose Oxidation in Gluconobacter and Acetobacter Strains
Sainz, Frontiers in microbiology 2016 - “...GGCCTATCCCTCGTCAATCG TGCATAACCGCTGCAAAACC LHZK00000000 AD938_10275 sld A Glycerol dehydrogenase large subunit SldA gldh1 CGGGTGAAGAGAAGTGGGTC GAGCTGGTCATACATCGGGG LHZK00000000 AD938_11075 sld A Glycerol dehydrogenase large subunit SldA gldh2 GGTAAGGAGATCTGGCGTCG TGAAACTGCATTTTCCGCCG Gluconobacter oxydans 621H CP000009 GOX0265 gcd Membrane-bound glucose dehydrogenase mgdh CTCGTGTACATCCCGATGGG ACCACCCCACTCGAACATTC CP000009 GOX1231 Gluconate 2-dehydrogenase, large subunit gadh TATTGCAGCGGCTATGACTG...”
IGS75_05190 pyrroloquinoline quinone-dependent dehydrogenase from Gluconobacter sphaericus
39% identity, 85% coverage
CFR77_09325 pyrroloquinoline quinone-dependent dehydrogenase from Komagataeibacter sucrofermentans
38% identity, 79% coverage
- Enhanced bacterial cellulose production in Komagataeibacter sucrofermentans: impact of different PQQ-dependent dehydrogenase knockouts and ethanol supplementation
Montenegro-Silva, Biotechnology for biofuels and bioproducts 2024 - “...gDNA CFR77_00430 gcgttttttattggtGTCTGGCCAACGGCGAAT This work KS004-DR KS001 gDNA CFR77_00430 ccttttgctcacatgTTATGGCTGCTGCTCGGGAATACCG This work KS005-UF KS001 gDNA CFR77_09325 tgagagtgcaccataATGCTGCGCACTCTGCTG This work KS005-UR KS001 gDNA CFR77_09325 tacgtgcccgatcaaGGAAGTGTAATACACCACCGCCTTACAC This work KS005-DF KS001 gDNA CFR77_09325 gcgttttttattggtCGTATGACGAAAAGACCGGTATCCTGA This work KS005-DR KS001 gDNA CFR77_09325 ccttttgctcacatgTCAGTTCACGTCGTCCAGCGC This work Overhangs for assembly with InFusion Cloning...”
- “...KS002, KS003, KS004, and KS005 were obtained by disrupting the loci CFR77_01730, CFR77_05025, CFR77_00430, and CFR77_09325, respectively. According to the protein annotation, the strains KS002, KS003, and KS005 lack PQQ-mDHs belonging to the glucose/quinate/shikimate family, while KS004 lacks a PQQ-mDH from the methanol/ethanol family. The five...”
B0W47_01010 pyrroloquinoline quinone-dependent dehydrogenase from Komagataeibacter nataicola
38% identity, 79% coverage
- Complete genome sequence of the cellulose-producing strain Komagataeibacter nataicola RZS01
Zhang, Scientific reports 2017 - “...nataicola RZS01. Family Cofactor Genes Glucose dehydrogenase PQQ B0W47_01230, B0W47_02520, B0W47_10950 Glycerol dehydrogenase PQQ B0W47_01005, B0W47_01010 Alcohol dehydrogenase PQQ B0W47_13410 Aldehyde dehydrogenase PQQ B0W47_16410 2-Keto- d -gluconate dehydrogenase FAD B0W47_11030, B0W47_11035, B0W47_11040 Gluconate 2-dehydrogenase FAD B0W47_05395, B0W47_05400, B0W47_05405, B0W47_13405 Adaptation to extreme conditions K. nataicola RZS01...”
WP_116701675 pyrroloquinoline quinone-dependent dehydrogenase from Komagataeibacter melaceti
38% identity, 79% coverage
M9MJR9 glycerol dehydrogenase (acceptor) (EC 1.1.99.22) from Gluconobacter thailandicus (see paper)
NBRC3255_0235, NBRC3257_1134 pyrroloquinoline quinone-dependent dehydrogenase from Gluconobacter thailandicus NBRC 3257
40% identity, 79% coverage
- Draft genome sequence of Gluconobacter thailandicus NBRC 3257
Matsutani, Standards in genomic sciences 2014 - “...addition, two paralogous copies of the PQQ-glycerol dehydrogenase sld AB operon (NBRC3257_0924 to NBRC3257_0925 and NBRC3257_1134 to NBRC3257_1135) were identified. It has been thought that the respiratory chains of Gluconobacter species play key roles in respiratory energy metabolism [ 48 - 51 ]. Therefore, the gene...”
- Draft Genome Sequence of Dihydroxyacetone-Producing Gluconobacter thailandicus Strain NBRC 3255
Matsutani, Genome announcements 2013 - “...the PQQ-dependent dehydrogenase 1, while two paralogous sets of sldAB operons (NBRC3255_0025 to NBRC3255_0026 and NBRC3255_0235 to NBRC3255_0236) were identified. One of the two paralogs, the NBRC3255_0235 operon, is responsible for dihydroxyacetone production from glycerol as a glycerol dehydrogenase ( 9 ), and NBRC 3255 was...”
Q70JN9 gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) from Gluconobacter oxydans (see 2 papers)
GOX0854 D-Sorbitol dehydrogenase subunit SldA from Gluconobacter oxydans 621H
39% identity, 85% coverage
- Membrane-bound sorbitol dehydrogenase is responsible for the unique oxidation of D-galactitol to L-xylo-3-hexulose and D-tagatose in Gluconobacter oxydans
Xu, Biochimica et biophysica acta. General subjects 2023 (PubMed)- “...and D-tagatose. The large subunit SldA encoded by GOX0854 was also characterized, and it was discovered that its 24 amino acids signal peptide is...”
- Engineering of glycerol utilization in Gluconobacter oxydans 621H for biocatalyst preparation in a low-cost way
Yan, Microbial cell factories 2018 - “...source. Based on the glycerol utilization mechanism elucidated in this study, the major polyol dehydrogenase (GOX0854) and the membrane-bound alcohol dehydrogenase (GOX1068) can competitively utilize glycerol but play no obvious roles in the biocatalyst preparation. Thus, the genes related to these two enzymes were deleted. Whole...”
- “...assayed. (Black square) G. oxydans 621H, (red circle) G. oxydans GOX1068, (blue triangle) G. oxydans GOX0854, (pink inverted triangle) G. oxydans GOX2088 and (green diamond) G. oxydans GOX1068GOX0854. The error bars represent the standard deviations of three independent experiments As shown in Table 1 , three...”
- Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
Kranz, BMC genomics 2018 - “...membrane-bound aldehyde dehydrogenase, small subunit 3.7 38 GOX0587 membrane-bound aldehyde dehydrogenase, large subunit 9.0 31 GOX0854 polyol dehydrogenase subunit SldA 4.2 2147 | GOX0855 polyol dehydrogenase subunit SldB 4.6 5992 GOX1067 alcohol dehydrogenase cytochrome c subunit precursor 4.0 1807 | GOX1068 alcohol dehydrogenase large subunit 3.4...”
- “...ribulosephosphate 3-epimerase (GOX1352); rpi , ribose 5-phosphate isomerase (GOX1708); sldA , polyol dehydrogenase subunit SldA (GOX0854); sldB , polyol dehydrogenase subunit SldB (GOX0855); tal / pgi , bifunctional transaldolase (GOX1704); tkt , transketolase (GOX1703); tpi , triosephosphate isomerase (GOX2217); zwf , glucose-6-phosphate 1-dehydrogenase (GOX0145). Metabolites: 1,3-BPG,...”
- Combinatorial metabolic engineering of industrial Gluconobacter oxydans DSM2343 for boosting 5-keto-D-gluconic acid accumulation
Yuan, BMC biotechnology 2016 (no snippet) - Determination of Dehydrogenase Activities Involved in D-Glucose Oxidation in Gluconobacter and Acetobacter Strains
Sainz, Frontiers in microbiology 2016 - “...glucose dehydrogenase mgdh CTCGTGTACATCCCGATGGG ACCACCCCACTCGAACATTC CP000009 GOX1231 Gluconate 2-dehydrogenase, large subunit gadh TATTGCAGCGGCTATGACTG CATGGTCGAAATTCATGCTG CP000009 GOX0854 sld A Glycerol dehydrogenase large subunit SldA gldh GCGACGGGTAAGGAGATCTG TTTCTTCAGGGCTACGCAGG Gluconobacter oxydans NBRC 3293 AB985494 kgd L Large subunit of 2-keto- D -gluconate dehydrogenase 2kgdh GGAAAACTGGCGCAACATGTCG CCCGAACGGGATCATGTC Acetobacter malorum strain...”
- Combined fluxomics and transcriptomics analysis of glucose catabolism via a partially cyclic pentose phosphate pathway in Gluconobacter oxydans 621H
Hanke, Applied and environmental microbiology 2013 - “...the periplasm by the membrane-bound major polyol dehydrogenase (GOX0854 and GOX0855) is unlikely, as this enzyme has its optimum activity for this reaction at...”
- Mutational analysis of the pentose phosphate and Entner-Doudoroff pathways in Gluconobacter oxydans reveals improved growth of a Δedd Δeda mutant on mannitol
Richhardt, Applied and environmental microbiology 2012 - “...to fructose by the major polyol dehydrogenase SldAB (GOX0854 and GOX0855). In the second growth phase, which starts when mannitol is almost completely converted...”
AD938_10275 pyrroloquinoline quinone-dependent dehydrogenase from Gluconobacter japonicus
40% identity, 79% coverage
- Determination of Dehydrogenase Activities Involved in D-Glucose Oxidation in Gluconobacter and Acetobacter Strains
Sainz, Frontiers in microbiology 2016 - “...large subunit gadh1 TCCTGAGTGCGTTCCAGTTC CGCTTTGGCAATGGGTTCAA LHZK00000000 AD938_03325 Gluconate 2-dehydrogenase, large subunit gadh2 GGCCTATCCCTCGTCAATCG TGCATAACCGCTGCAAAACC LHZK00000000 AD938_10275 sld A Glycerol dehydrogenase large subunit SldA gldh1 CGGGTGAAGAGAAGTGGGTC GAGCTGGTCATACATCGGGG LHZK00000000 AD938_11075 sld A Glycerol dehydrogenase large subunit SldA gldh2 GGTAAGGAGATCTGGCGTCG TGAAACTGCATTTTCCGCCG Gluconobacter oxydans 621H CP000009 GOX0265 gcd Membrane-bound glucose...”
sldA / Q8KIL1 D-sorbitol dehydrogenase large subunit (EC 1.1.99.21) from Gluconobacter thailandicus (see 4 papers)
39% identity, 79% coverage
sldA / BAC02909.1 D-Sorbitol dehydrogenase from Gluconobacter oxydans (see paper)
38% identity, 79% coverage
ATSB10_10580 pyrroloquinoline quinone-dependent dehydrogenase from Dyella thiooxydans
39% identity, 79% coverage
Msil_2867 Pyrrolo-quinoline quinone from Methylocella silvestris BL2
28% identity, 79% coverage
- The effect of lanthanum on growth and gene expression in a facultative methanotroph
Crombie, Environmental microbiology 2022 - “...MxaF, XoxF5, XoxF5(2), XoxF1 and XoxF3, respectively. The genome also contains two predicted PQQADH sequences, Msil_2867 and Msil_3733, clustering with group 9 PQQADH (Keltjens et al ., 2014 ), both of which also contain the Lncoordinating Asp residue, but whose function is unknown. Despite the fact...”
MexAM1_META1p4973 pyrroloquinoline quinone-dependent dehydrogenase from Methylorubrum extorquens AM1
MexAM1_META1p4973 putative Quinoprotein alcohol dehydrogenase from Methylobacterium extorquens AM1
27% identity, 79% coverage
Msil_3733 Pyrrolo-quinoline quinone from Methylocella silvestris BL2
26% identity, 78% coverage
Saro_2870 Pyrrolo-quinoline quinone from Novosphingobium aromaticivorans DSM 12444
27% identity, 79% coverage
- Catabolism of β-5 linked aromatics by Novosphingobium aromaticivorans
Metz, mBio 2024 - “...protein concentration with either DC-A or DC-L with and without NAD + (or PQQ for Saro_2870). We used differences in absorption spectra (Fig. S7) to monitor conversion from DC-A to DC-L and DC-L to DC-C. Control experiments show that none of the cell extracts containing recombinant...”
- “...the absorbance of PQQ at 370 nm, the activity assay for the putative PQQ-dependent ALDH Saro_2870 was performed as described above except 15 L samples were collected from the reaction at each indicated time point and diluted 1:1 with 40% acetonitrile, 40% methanol, and 100 mM...”
1kb0A / Q46444 Crystal structure of quinohemoprotein alcohol dehydrogenase from comamonas testosteroni (see paper)
28% identity, 80% coverage
- Ligands: calcium ion; heme c; tetrahydrofuran-2-carboxylic acid; pyrroloquinoline quinone (1kb0A)
qheDH / Q46444 alcohol dehydrogenase (azurin) (EC 1.1.9.1) from Comamonas testosteroni (see 3 papers)
QHED_COMTE / Q46444 Quinohemoprotein alcohol dehydrogenase; QH-ADH; Alcohol dehydrogenase (azurin); PQQ-containing alcohol dehydrogenase; PQQ-dependent ADH; Quinohaemoprotein ethanol dehydrogenase type I; QH-EDHI; EC 1.1.9.1 from Comamonas testosteroni (Pseudomonas testosteroni) (see 2 papers)
Q46444 alcohol dehydrogenase (azurin) (EC 1.1.9.1) from Comamonas testosteroni (see paper)
28% identity, 79% coverage
- function: Catalyzes the dye-linked oxidation of primary alcohols to the corresponding aldehydes and the (subsequent) oxidation of the aldehydes to carboxylic acids. Methanol is not a substrate.
catalytic activity: 2 oxidized [azurin] + a primary alcohol = 2 reduced [azurin] + an aldehyde + 2 H(+) (RHEA:51148)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit (PubMed:11714714, PubMed:3521592). PQQ is inserted between disulfide Cys-147-Cys-148 and the plane of Trp- 276 (PubMed:11714714).)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
cofactor: heme c (Binds 1 heme c group per subunit.)
subunit: Monomer. - Catalytic and molecular properties of the quinohemoprotein tetrahydrofurfuryl alcohol dehydrogenase from Ralstonia eutropha strain Bo
Zarnt, Journal of bacteriology 2001 - “...various quinoprotein ADHs: QH-EDH from C. testosteroni (Q46444); GS-ADH, quinoprotein ADH from Gluconobacter suboxydans (O05542); AA-ADH, quinoprotein ADH from...”
SSPN_RS0118165 PQQ-dependent dehydrogenase, methanol/ethanol family from Saccharopolyspora spinosa NRRL 18395
25% identity, 83% coverage
Maq22A_1p30675 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylobacterium aquaticum
26% identity, 75% coverage
- Lanthanide-Dependent Methanol and Formaldehyde Oxidation in Methylobacterium aquaticum Strain 22A
Yanpirat, Microorganisms 2020 - “...study [ 38 ]. Gene deletion mutants for xoxF2 (Maq22A_c27990), adh4 (Maq22A_1p32165), exaF (Maq22A_c07235), adh6 (Maq22A_1p30675), and mxbD (Maq22A_c05310) were generated using the allele-replacement vector pK18mobSacB as previously reported [ 38 , 39 ]. In brief, each 1 kb upstream and downstream region of the target...”
- “...type 2b) and can be categorized as PQQ-ADH type 6b; and Adh4 (Maq22A_1p32165) and Adh6 (Maq22A_1p30675) can be categorized as PQQ-ADH type 6a. To understand which genes are involved in methylotrophy in strain 22A, we generated single-gene remaining mutants to determine their growth on methanol. 3.2....”
MHY1_02202 lanthanide-dependent methanol dehydrogenase XoxF5 from Methylovirgula sp. HY1
28% identity, 82% coverage
- Sulfur and methane oxidation by a single microorganism
Gwak, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...monooxygenase, sMMO (MHY1_029022908). The produced methanol is oxidized to formaldehyde via the lanthanide-dependent MDH, XoxF (MHY1_02202 was the most abundant MDH). Formaldehyde oxidation to formate then proceeds via the tetrahydromethanopterin (H 4 MPT) pathway, and C1 incorporation into the serine cycle is mediated by the tetrahydrofolate...”
- “...why methane oxidation was observed only in methane-grown cells ( Table 2 ). MDH XoxF5 (MHY1_02202; 3.9 to 7.0% of proteins) and cytochrome c 553i , XoxG5 (MHY1_00490; 0.12 to 0.27% of proteins) were constitutively expressed on all growth substrates. Proteins involved in H 4 MPT-mediated...”
C7W88_RS07670 PQQ-dependent dehydrogenase, methanol/ethanol family from Novosphingobium sp. THN1
26% identity, 80% coverage
QHED_PSEPU / Q8GR64 Quinohemoprotein alcohol dehydrogenase ADH IIB; ADH IIB; Alcohol dehydrogenase (azurin); EC 1.1.9.1 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see 8 papers)
Q8GR64 alcohol dehydrogenase (azurin) (EC 1.1.9.1); aldehyde dehydrogenase (quinone) (EC 1.2.5.2) from Pseudomonas putida (see 2 papers)
26% identity, 77% coverage
- function: Catalyzes the dye-linked oxidation of primary alcohols to the corresponding aldehydes and the (subsequent) oxidation of the aldehydes to carboxylic acids. Exhibits activity with longer mono-alcohols (C-4 to C-7) but not with methanol or glycerol. Reacts with 1,2-propanediol and 1,3-propanediol but not with sugar alcohols such as D-sorbitol.
catalytic activity: 2 oxidized [azurin] + a primary alcohol = 2 reduced [azurin] + an aldehyde + 2 H(+) (RHEA:51148)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit. PQQ is inserted between disulfide Cys-127-Cys-128 and the plane of Trp-254.)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
cofactor: heme c (Binds 1 heme c group per subunit.)
subunit: Monomer.
1kv9A / Q8GR64 Structure at 1.9 a resolution of a quinohemoprotein alcohol dehydrogenase from pseudomonas putida hk5 (see paper)
26% identity, 77% coverage
- Ligands: calcium ion; pyrroloquinoline quinone; heme c; acetone (1kv9A)
SLG_05620 / G2ILH4 dehydrodiconiferyl alcohol dehydrogenase from Sphingobium sp. (strain NBRC 103272 / SYK-6) (see 2 papers)
SLG_05620 PQQ-dependent dehydrogenase, methanol/ethanol family from Sphingobium sp. SYK-6
26% identity, 80% coverage
6damA / A0A3F2YLY8 Crystal structure of lanthanide-dependent methanol dehydrogenase xoxf from methylomicrobium buryatense 5g (see paper)
26% identity, 79% coverage
- Ligand: pyrroloquinoline quinone (6damA)
bll6220 bll6220 from Bradyrhizobium japonicum USDA 110
26% identity, 79% coverage
- Proteomic Characterization of Bradyrhizobium diazoefficiens Bacteroids Reveals a Post-Symbiotic, Hemibiotrophic-Like Lifestyle of the Bacteria within Senescing Soybean Nodules
Strodtman, International journal of molecular sciences 2018 - “...propanoate metabolism, leading to a source of acetyl-CoA, and propanoyl-CoA, a putative alcohol dehydrogenase precursor (bll6220) and carbonic anhydrase (bll2065). Superoxide dismutase (bll7774) and alkyl hydroperoxide reductase (bll1777), proteins involved in reactive oxygen metabolism, were found. Several soybean proteins, histone H4, histone H3, and glu/leu/phe/val dehydrogenase...”
- “...NP_772236 Cytoplasm RecA protein bll5755 NP_772395 Periplasm Hypothetical protein bll6069 NP_772709 Periplasm PQQ-dependent alcohol dehydrogenase bll6220 NP_772860 Cytoplasm Peptidyl-dipeptidase bll7756 NP_774396 Periplasm Superoxide dismutase bll7774 NP_774414 Cytoplasm ABC transporter substrate-binding protein (Putative oligopeptide binding protein) bll7921 NP_774561 Both Hypothetical protein bll8229 NP_774869 Periplasm Heat shock protein...”
- Soybean seed extracts preferentially express genomic loci of Bradyrhizobium japonicum in the initial interaction with soybean, Glycine max (L.) Merr
Wei, DNA research : an international journal for rapid publication of reports on genes and genomes 2008 - “...(bll6184blr6185 in LOS 18, bll7306bll7307 in LOS 21) and alcohol dehydrogenase (blr6207, blr6213, blr6215, and bll6220 in LOS 18) were repressed. 3.4. Expression loci shared between SSE- and genistein-treated cells In addition to genomic loci covering nod genes, six loci outside symbiosis island were induced with...”
- Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress
Cytryn, Journal of bacteriology 2007 - “...blr6736 blr6738 blr6739 bll0332 bll0333 bll6220 Pyrroloquinoline synthesis protein (pqqA) Pyrroloquinoline synthesis protein (pqqB) Pyrroloquinoline synthesis...”
- “...three pqq-associated alcohol dehydrogenases (bll0332, bll0333, and bll6220). Since many of the same proteins were produced under conditions of desiccation...”
Q9KH03 aldehyde dehydrogenase (quinone) (EC 1.2.5.2) from Cupriavidus necator (see paper)
26% identity, 83% coverage
XOXF_METBY / A0A3F2YLY8 Lanthanide-dependent methanol dehydrogenase XoxF; Lanthanide-dependent MDH; Ln(3+)-dependent MDH; EC 1.1.2.10 from Methylotuvimicrobium buryatense (Methylomicrobium buryatense) (see 2 papers)
A0A3F2YLY8 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Methylotuvimicrobium buryatense (see 2 papers)
26% identity, 76% coverage
- function: Catalyzes the oxidation of methanol to formaldehyde in the presence of lanthanides (Ln) (PubMed:30132076). Contributes to methane/methanol metabolism when La(3+) is present in the natural environment of the bacterium, allowing bacterial growth with methane as carbon and energy source. Thereby is an essential enzyme for Ln- dependent methylotrophy (PubMed:26858104). Uses a specific cytochrome cL, encoded by the adjacent gene in the locus, as electron acceptor (Probable).
catalytic activity: 2 Fe(III)-[cytochrome cL] + methanol = 2 Fe(II)-[cytochrome cL] + formaldehyde + 2 H(+) (RHEA:51008)
cofactor: La(3+) (Binds one lanthanum ion per subunit.)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit.)
subunit: Monomer (PubMed:30132076). Interacts with its cognate particulate methane monooxygenase (pMMO); this interaction underscores the potential importance of lanthanide-dependent MDHs in biological methane oxidation (PubMed:30132076).
disruption phenotype: Cells lacking this gene display a wild-type growth rate in the absence of lanthanum (when the MxaFI enzyme is maximally expressed) but show a marked growth defect (about a 70% decrease in growth rate) in the presence of lanthanum (a condition under which mxa expression is significantly reduced).
J7Q447 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylocystis sp. (strain SC2)
27% identity, 77% coverage
Maq22A_1p32165 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylobacterium aquaticum
25% identity, 77% coverage
- Lanthanide-Dependent Methanol and Formaldehyde Oxidation in Methylobacterium aquaticum Strain 22A
Yanpirat, Microorganisms 2020 - “...generated in our previous study [ 38 ]. Gene deletion mutants for xoxF2 (Maq22A_c27990), adh4 (Maq22A_1p32165), exaF (Maq22A_c07235), adh6 (Maq22A_1p30675), and mxbD (Maq22A_c05310) were generated using the allele-replacement vector pK18mobSacB as previously reported [ 38 , 39 ]. In brief, each 1 kb upstream and downstream...”
- “...(strain AM1, PQQ-ADH type 2b) and can be categorized as PQQ-ADH type 6b; and Adh4 (Maq22A_1p32165) and Adh6 (Maq22A_1p30675) can be categorized as PQQ-ADH type 6a. To understand which genes are involved in methylotrophy in strain 22A, we generated single-gene remaining mutants to determine their growth...”
blr6213 methanol dehydrogenase large subunit-like protein from Bradyrhizobium japonicum USDA 110
26% identity, 77% coverage
- Lanthanide-dependent methanol dehydrogenase from the legume symbiotic nitrogen-fixing bacterium Bradyrhizobium diazoefficiens strain USDA110
Wang, Enzyme and microbial technology 2019 (PubMed)- “...medium; the protein was identified as XoxF5-type MDH (blr6213). The purified XoxF contained 0.58 cerium atoms per enzyme subunit. Moreover, the in-solution...”
- “...methanol/Ce3+ medium. Table 2 Encoding gene xoxF (blr6213) Molecular wight of subunit 64 kDa. Cofactor content 0.58 Ce3+ atom/subunit Optimum temperature...”
- Influence of elevated atmospheric carbon dioxide on transcriptional responses of Bradyrhizobium japonicum in the soybean rhizoplane
Sugawara, Microbes and environments 2013 - “...Ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit blr2587 cbbX 2.4 2.0 CbbX protein C1 and alcohol metabolism blr6213 mxaF 2.7 Methanol dehydrogenase large subunit-like blr6215 flhA 2.2 2.1 Glutathione-dependent formaldehyde dehydrogenase blr6216 gfa 3.4 Glutathione-dependent formaldehyde-activating enzyme bll3135 fdhD 1.6 1.8 Formate dehydrogenase bll3136 fdhF 2.0 2.0 Formate...”
- Aerobic vanillate degradation and C1 compound metabolism in Bradyrhizobium japonicum
Sudtachat, Applied and environmental microbiology 2009 - “...data that included locus 10 (see the text). mxaF (blr6213) encodes a putative methanol dehydrogenase at locus 10 (12). The numbers in parentheses in the loci...”
- Soybean seed extracts preferentially express genomic loci of Bradyrhizobium japonicum in the initial interaction with soybean, Glycine max (L.) Merr
Wei, DNA research : an international journal for rapid publication of reports on genes and genomes 2008 - “...two component sensor/regulator (bll6184blr6185 in LOS 18, bll7306bll7307 in LOS 21) and alcohol dehydrogenase (blr6207, blr6213, blr6215, and bll6220 in LOS 18) were repressed. 3.4. Expression loci shared between SSE- and genistein-treated cells In addition to genomic loci covering nod genes, six loci outside symbiosis island...”
sS8_0935 methanol/ethanol family PQQ-dependent dehydrogenase from Methylocaldum marinum
23% identity, 78% coverage
D2SZY4 alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) from Acetobacter pasteurianus (see paper)
25% identity, 80% coverage
APA386B_1575 PQQ-dependent dehydrogenase, methanol/ethanol family from Acetobacter pasteurianus 386B
C7JAW8 Alcohol dehydrogenase large subunit from Acetobacter pasteurianus (strain NBRC 105184 / IFO 3283-01)
25% identity, 80% coverage
- Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem
Illeghems, BMC genomics 2013 - “...adhS ; APA386B_2212) was separated from the other two genes ( adhAB ; APA386B_1574 - APA386B_1575). This gene organization in A. pasteurianus has been suggested before [ 52 ]. Further, the genome of A. pasteurianus 386B contained two uncharacterized, membrane-bound, PQQ-dependent oxidoreductases with five transmembrane helices...”
- “...Acetobacter pasteurianus 386B. (A) Membrane-bound PQQ- and FAD-dependent dehydrogenases: (1) PQQ-dependent alcohol dehydrogenase (APA386B_1574 - APA386B_1575); (2) membrane-bound acetaldehyde dehydrogenase (APA386B_2542 - APA386B_2544); (3) PQQ-dependent glucose dehydrogenase (APA386B_2133 - APA386B_2134); (4) uncharacterized PQQ-containing oxidoreductases [APA386B_1016 (transmembrane regions: 2042, 4764, 6986, 101120, 127149) and APA386B_325 (transmembrane regions:...”
- Improving Acetic Acid Production by Over-Expressing PQQ-ADH in Acetobacter pasteurianus
Wu, Frontiers in microbiology 2017 - “...C7JBD3 Alkyl hydroperoxide reductase AhpD 5.73 175 18.4 5.87 576 response to oxidative stress 8 C7JAW8 Alcohol dehydrogenase large subunit 5.05 742 81.6 6.77 305 oxidoreductase activity 9 C7JG48 Aconitate hydratase 2.34 897 97.7 6.21 1098 aconitate hydratase activity 10 C7JFQ0 50S ribosomal protein L1 4.17...”
C9K501 alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) from Acetobacter pasteurianus (see paper)
25% identity, 80% coverage
ATSB10_32210 methanol/ethanol family PQQ-dependent dehydrogenase from Dyella thiooxydans
23% identity, 78% coverage
QGDA_PSEPU / Q4W6G0 Quinohemoprotein alcohol dehydrogenase ADH-IIG; ADH IIG; Alcohol dehydrogenase (azurin); EC 1.1.9.1 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see 4 papers)
Q4W6G0 aldehyde dehydrogenase (quinone) (EC 1.2.5.2) from Pseudomonas putida (see paper)
25% identity, 84% coverage
- function: Catalyzes the dye-linked oxidation of primary alcohols to the corresponding aldehydes and the (subsequent) oxidation of the aldehydes to carboxylic acids. Active with primary alcohols, glycerol, 1,2- propanediol, 1,3-propanediol but not with methanol or sugar alcohols such as D-sorbitol.
catalytic activity: 2 oxidized [azurin] + a primary alcohol = 2 reduced [azurin] + an aldehyde + 2 H(+) (RHEA:51148)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit. PQQ is inserted between disulfide Cys-138-Cys-139 and the plane of Trp-266.)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
cofactor: heme c (Binds 1 heme c group per subunit.)
subunit: Monomer.
A0A7G1H3Z0 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Bradyrhizobium sp. MAFF 211645 (see paper)
26% identity, 77% coverage
P38539 methanol dehydrogenase (cytochrome c) (subunit 2/2) (EC 1.1.2.7) from Methylophilus methylotrophus (see 5 papers)
25% identity, 75% coverage
4aahA / P38539 Methanol dehydrogenase from methylophilus w3a1 (see paper)
25% identity, 75% coverage
- Ligands: calcium ion; pyrroloquinoline quinone (4aahA)
C7G3B7 alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) from Acetobacter pasteurianus (see paper)
25% identity, 80% coverage
1yiqA / Q4W6G0 Molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase adhiig from pseudomonas putida hk5. Compariison to the other quinohemoprotein alcohol dehydrogenase adhiib found in the same microorganism. (see paper)
25% identity, 78% coverage
- Ligands: calcium ion; pyrroloquinoline quinone; heme c (1yiqA)
Msil_3387 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylocella silvestris BL2
24% identity, 76% coverage
- The effect of lanthanum on growth and gene expression in a facultative methanotroph
Crombie, Environmental microbiology 2022 - “...The M. silvestris genome contains five predicted PQQdependent MDH genes, Msil_0471, Msil_1587, Msil_2260, Msil_3149 and Msil_3387. Based on amino acid sequence and the presence of the Lncoordinating aspartate residue in XoxMDH, these can be identified as encoding Mxa and XoxMDHs from clades 5 (two copies), clade...”
- “...were expressed at appreciable levels. XoxF5(2) (Msil_2260) was not detected in any sample, and XoxF3 (Msil_3387) was expressed at very low levels ranging from 0.00003% to 0.00017% of total protein, Supporting Information Table S1 . In comparison, MxaF and XoxF5 were among the most abundant proteins...”
MPNT_10387 methanol/ethanol family PQQ-dependent dehydrogenase from Candidatus Methylacidithermus pantelleriae
25% identity, 77% coverage
B0W47_13410 PQQ-dependent dehydrogenase, methanol/ethanol family from Komagataeibacter nataicola
24% identity, 83% coverage
- Complete genome sequence of the cellulose-producing strain Komagataeibacter nataicola RZS01
Zhang, Scientific reports 2017 - “...Genes Glucose dehydrogenase PQQ B0W47_01230, B0W47_02520, B0W47_10950 Glycerol dehydrogenase PQQ B0W47_01005, B0W47_01010 Alcohol dehydrogenase PQQ B0W47_13410 Aldehyde dehydrogenase PQQ B0W47_16410 2-Keto- d -gluconate dehydrogenase FAD B0W47_11030, B0W47_11035, B0W47_11040 Gluconate 2-dehydrogenase FAD B0W47_05395, B0W47_05400, B0W47_05405, B0W47_13405 Adaptation to extreme conditions K. nataicola RZS01 possesses the ability to...”
Mfla_2044 Pyrrolo-quinoline quinone from Methylobacillus flagellatus KT
24% identity, 75% coverage
- Lanpepsy is a novel lanthanide-binding protein involved in the lanthanide response of the obligate methylotroph Methylobacillus flagellatus
Hemmann, The Journal of biological chemistry 2023 - “...(Mfla_20342035, Mfla_20372043), which are part of the Ca 2+ -dependent MDH system. The MDH MxaF (Mfla_2044) also showed an eightfold decrease, although with a q value (0.0504) just slightly above the applied threshold (<0.05). Furthermore, we identified two regulatory proteins, the histidine kinase Mfla_0817 and the...”
- Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners
Haft, BMC genomics 2011 - “...enzyme Mfla_1717 84 104 285 -61.969 PQQ-dependent enzyme Mfla_1451 84 108 282 -59.198 PQQ-dependent enzyme Mfla_2044 77 94 210 -57.525 PQQ-dependent enzyme Mfla_0344 79 100 268 -56.680 PQQ-dependent enzyme Mfla_1681 53 53 83 -51.646 PQQ biosynthesis protein PqqD Mfla_2043 42 43 69 -39.341 extracellular solute-binding protein...”
- Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy
Hendrickson, Journal of bacteriology 2010 - “...(GroEL) Mfla_2453 Mfla_0265 Mfla_0535 Mfla_0751 (Hsp70) Mfla_2044 (MxaF) Mfla_1578 Mfla_0250 (Hps) Mfla_0016 Mfla_2249 (Tkt) Mfla_0548 (MauB) Mfla_2744...”
- “...(20). Accordingly, the large subunit of MDH (MxaF, Mfla_2044) was one of the most frequently detected proteins in both methanol- and methylamine-grown cultures...”
AYM39_15615 methanol/ethanol family PQQ-dependent dehydrogenase from Methylomonas sp. DH-1
26% identity, 76% coverage
- Improvement of succinate production from methane by combining rational engineering and laboratory evolution in Methylomonas sp. DH-1
Jo, Microbial cell factories 2024 - “...vector for the citrate synthase ( gltA , AYM39_19030) gene, the strong promoter, P mxaF (AYM39_15615), was used. The sequences of the P mxaF and gltA genes were assembled as one fragment by overlap extension PCR. The assembled DNA fragment was cloned at the SbfI site...”
- “...monooxygenase subunit A 26,255 5597 0.21 7 AYM39_11910 Protein Hypothetical protein 17,722 48 0.00 8 AYM39_15615 Protein Methanol dehydrogenase 13,706 4962 0.36 9 AYM39_15600 Protein Methanol dehydrogenase 11,638 6170 0.53 10 AYM39_02740 Protein 3-hexulose-6-phosphate synthase 8076 2515 0.31 11 AYM39_13140 Protein hypothetical protein 6170 3378 0.55...”
X5Q003 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Mesorhizobium sp. LSJC280B00 (see paper)
25% identity, 75% coverage
P18278 alcohol dehydrogenase (quinone) (EC 1.1.5.5) from Acetobacter aceti (see 3 papers)
25% identity, 80% coverage
A2SLA7 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Methylibium petroleiphilum (see paper)
24% identity, 84% coverage
F8JBP2 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Hyphomicrobium sp. (see paper)
25% identity, 75% coverage
A3FJ48 methanol dehydrogenase (cytochrome c) (subunit 3/3) (EC 1.1.2.7) from Methylophaga aminisulfidivorans (see 2 papers)
25% identity, 76% coverage
5xm3A / A3FJ48 Crystal structure of methanol dehydrogenase from methylophaga aminisulfidivorans (see paper)
25% identity, 76% coverage
- Ligands: pyrroloquinoline quinone; magnesium ion (5xm3A)
7o6zA / A0A7R8L7W4 Structure of a neodymium-containing, xoxf1-type methanol dehydrogenase (see paper)
24% identity, 77% coverage
- Ligands: neodymium ion; methanol (7o6zA)
NBRC3257_3117 PQQ-dependent dehydrogenase, methanol/ethanol family from Gluconobacter thailandicus NBRC 3257
25% identity, 79% coverage
- Draft genome sequence of Gluconobacter thailandicus NBRC 3257
Matsutani, Standards in genomic sciences 2014 - “...adh subunit III (NBRC3257_1024). A unique orphan gene of adh subunit I was also identified (NBRC3257_3117). The gene repertories of other membrane-bound PQQ dependent proteins were investigated. Homologous proteins of membrane-bound PQQ-dependent dehydrogenase (NBRC3257_0292), membrane-bound glucose dehydrogenase (PQQ) (NBRC3257_0371), PQQ-dependent dehydrogenase 4 (NBRC3257_0662), and PQQ-dependent dehydrogenase...”
MSMEG_3726 alcohol dehydrogenase from Mycobacterium smegmatis str. MC2 155
25% identity, 79% coverage
- Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners
Haft, BMC genomics 2011 - “...the PQQ-dependent dehydrogenase, methanol/ethanol family. By contrast, Mycobacterium smegmatis carries only one PQQ-dependent alcohol dehydrogenase, MSMEG_3726, readily identified by PPP. This lone member, the top scoring protein not involved in PQQ biosynthesis, lies in the same cassette as the biosynthesis enzymes. These results show a familiar...”
ATSB10_32660 methanol/ethanol family PQQ-dependent dehydrogenase from Dyella thiooxydans
25% identity, 77% coverage
Mfla_1717 Pyrrolo-quinoline quinone from Methylobacillus flagellatus KT
25% identity, 80% coverage
- Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners
Haft, BMC genomics 2011 - “...97 97 135 -94.521 PQQ biosynthesis protein PqqE Mfla_2314 73 80 157 -61.969 PQQ-dependent enzyme Mfla_1717 84 104 285 -61.969 PQQ-dependent enzyme Mfla_1451 84 108 282 -59.198 PQQ-dependent enzyme Mfla_2044 77 94 210 -57.525 PQQ-dependent enzyme Mfla_0344 79 100 268 -56.680 PQQ-dependent enzyme Mfla_1681 53 53...”
- Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy
Hendrickson, Journal of bacteriology 2010 - “...MDH, MxaF, are encoded in the genome (Mfla_344, Mfla_1451, Mfla_1717, and Mfla_2314). Of these, three were detected at low spectral counts and one was not...”
EXAF_METEA / C5AXV8 Lanthanide-dependent ethanol dehydrogenase; Lanthanide-dependent EtDH; Ln-dependent EtDH; Lanthanide-dependent formaldehyde dehydrogenase; PQQ-dependent ethanol dehydrogenase; EC 1.1.2.-; EC 1.2.2.- from Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (Methylobacterium extorquens) (see 2 papers)
C5AXV8 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Methylorubrum extorquens (see paper)
Mext_1339 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylobacterium extorquens PA1
MexAM1_META1p1139 Quinoprotein ethanol dehydrogenase precursor (QEDH) from Methylobacterium extorquens AM1
MexAM1_META1p1139 PQQ-dependent methanol/ethanol family dehydrogenase from Methylorubrum extorquens AM1
23% identity, 85% coverage
- function: Catalyzes the oxidation of ethanol to acetaldehyde or acetate, but only in the presence of lanthanides (Ln). Contributes to ethanol metabolism when La(3+) is present in the natural environment of the bacterium, allowing bacterial growth with ethanol as carbon and energy source (PubMed:27573017). Exhibits relatively low methanol dehydrogenase activity (PubMed:27573017, PubMed:30862918). Is also capable of in vivo formaldehyde oxidation to formate during methanol growth. Thereby, can function as an auxiliary Ln-dependent formaldehyde oxidation system in a condition where formaldehyde accumulates, to prevent inhibitory or lethal accumulation of this toxic intermediate (PubMed:30862918). Uses a specific cytochrome c, encoded by an adjacent gene in the locus, as electron acceptor (Probable).
catalytic activity: ethanol + 2 Fe(III)-[cytochrome c] = acetaldehyde + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:62200)
catalytic activity: acetaldehyde + 2 Fe(III)-[cytochrome c] + H2O = 2 Fe(II)- [cytochrome c] + acetate + 3 H(+) (RHEA:79343)
catalytic activity: 2 Fe(III)-[cytochrome c] + formaldehyde + H2O = 2 Fe(II)- [cytochrome c] + formate + 3 H(+) (RHEA:79539)
cofactor: La(3+) (Binds one lanthanide ion per subunit.)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit.)
subunit: Homodimer.
disruption phenotype: Cells lacking this gene are not affected for growth with ethanol, with or without exogenous La(3+), indicating that either XoxF-type MDH (in the presence of La(3+) or MxaFI-type MDH (in the absence of La(3+))) can support growth with ethanol as well (PubMed:27573017). The triple mutant lacking mxaF, xoxF1 and xoxF2 can grow with ethanol only when exogenous La(3+) is added to the growth medium, and additional loss of exaF eliminates this growth (PubMed:27573017). Deletion of exaF alone does not impact growth with methanol, with or without lanthanide, demonstrating that ExaF is not a primary methanol oxidation system (PubMed:30862918). But a quadruple mutant lacking mxaF, xoxF1, xoxF2 and exaF can no longer grow on methanol in minimal medium with added lanthanum (La(3+)), while the triple mutant (mxaF, xoxF1, xoxF2) is able to grow poorly with methanol in the same conditions (PubMed:27573017). - Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1
Ochsner, Molecular microbiology 2019 - “...2016 ), the remaining growth is due to the REEdependent ethanol dehydrogenase ExaF (encoded by Mext_1339) (Fig. S1 ). Notably, xoxF was essential for growth on the standard REEfree methanol medium (thus, in the presence of Ca 2+ and an intact mxaF gene). These findings are...”
- Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization
Müller, Molecular & cellular proteomics : MCP 2016 - “...a Molecular & Cellular Proteomics 15.10 Mext_1339 Mext_2630 Mext_1209 Mext_3309 Mext_4207 Mext_2560 Mext_4729 Mext_2213 Mext_0067 Mext_2148 Mext_3817 Mext_4152...”
- “...methanol dehydrogenase-like proteins, Mext_1809 (XoxF) and Mext_1339, to be up-regulated during plant colonization (supplemental Table S2, supplemental Fig....”
- Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1
Roszczenko-Jasińska, Scientific reports 2020 - “...MexAM1_META1p1740 and xoxF2 : MexAM1_META1p2757 ), and an ExaF-type ethanol dehydrogenase (encoded by exaF : MexAM1_META1p1139 ) 17 , 18 . The XoxF enzymes from M. extorquens AM1 share 90% amino acid similarity, and are named as XoxF1 and XoxF2 to distinguish them from one another...”
CFR77_00430 PQQ-dependent dehydrogenase, methanol/ethanol family from Komagataeibacter sucrofermentans
24% identity, 83% coverage
- Enhanced bacterial cellulose production in Komagataeibacter sucrofermentans: impact of different PQQ-dependent dehydrogenase knockouts and ethanol supplementation
Montenegro-Silva, Biotechnology for biofuels and bioproducts 2024 - “...gDNA CFR77_01730 gcgttttttattggtTCATGCTGGCCAATGCGAG This work KS002-DR KS001 gDNA CFR77_01730 ccttttgctcacatgTTATTGGGCTGCATTGCCTGCC This work KS004-UF KS001 gDNA CFR77_00430 tgagagtgcaccataATGATTTCTGCCGTTTTCGGAAAAAGACG This work KS004-UR KS001 gDNA CFR77_00430 tacgtgcccgatcaaGCCATCAACCGTGTAGGAACGC This work KS004-DF KS001 gDNA CFR77_00430 gcgttttttattggtGTCTGGCCAACGGCGAAT This work KS004-DR KS001 gDNA CFR77_00430 ccttttgctcacatgTTATGGCTGCTGCTCGGGAATACCG This work KS005-UF KS001 gDNA CFR77_09325 tgagagtgcaccataATGCTGCGCACTCTGCTG This...”
- “...The strains KS002, KS003, KS004, and KS005 were obtained by disrupting the loci CFR77_01730, CFR77_05025, CFR77_00430, and CFR77_09325, respectively. According to the protein annotation, the strains KS002, KS003, and KS005 lack PQQ-mDHs belonging to the glucose/quinate/shikimate family, while KS004 lacks a PQQ-mDH from the methanol/ethanol family....”
JCM7686_0090 methanol/ethanol family PQQ-dependent dehydrogenase from Paracoccus aminophilus JCM 7686
25% identity, 75% coverage
- Genome-guided insight into the methylotrophy of Paracoccus aminophilus JCM 7686
Dziewit, Frontiers in microbiology 2015 - “...in this strain. Nevertheless, a gene encoding another type of MeOH dehydrogenase ( xoxF ; JCM7686_0090) was identified within the JCM 7686 chromosome. XoxF represents a group of homodimeric methanol dehydrogenases, related to the large subunit of MxaFI, which bind rare-earth elements instead of calcium (Keltjens...”
MCA0299 methanol dehydrogenase protein, large subunit, putative from Methylococcus capsulatus str. Bath
25% identity, 78% coverage
IGS75_06000 PQQ-dependent dehydrogenase, methanol/ethanol family from Gluconobacter sphaericus
27% identity, 47% coverage
Msil_1587 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylocella silvestris BL2
26% identity, 77% coverage
- The effect of lanthanum on growth and gene expression in a facultative methanotroph
Crombie, Environmental microbiology 2022 - “...discussion MDH gene transcription The M. silvestris genome contains five predicted PQQdependent MDH genes, Msil_0471, Msil_1587, Msil_2260, Msil_3149 and Msil_3387. Based on amino acid sequence and the presence of the Lncoordinating aspartate residue in XoxMDH, these can be identified as encoding Mxa and XoxMDHs from clades...”
- “...Msil_1585 XoxJ5 (SBP) 2.5 5.6E07 3.4 1.5E06 Msil_1586 XoxG5 (Cyt c) 3.1 5.0E11 4.2 3.1E10 Msil_1587 XoxF5 (large s/u) 5.8 2.3E15 9.8 7.0E15 XoxF1MDH Msil_3147 XoxG1 (Cyt c) 2.7 4.3E09 2.5 3.0E03 Msil_3148 XoxJ1 (SBP) 6.0 2.3E15 4.5 4.8E11 Msil_3149 XoxF1 (large s/u) 2.9 5.1E10 3.3...”
- Genome Scale Metabolic Model of the versatile methanotroph Methylocella silvestris
Bordel, Microbial cell factories 2020 - “...methanol dehydrogenase (Msil_0471) and a PQQ-containing ADH with 73% identity to xoxF from Methylobacterium extorquens (Msil_1587). For modelling purposes, it is essential to elucidate if the oxidation of 1-propanol and 2-propanol, to propanal and acetone respectively, is coupled to NAD(P)H generation, or coupled to transfer of...”
A0A0C6F7V8 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Methylobacterium aquaticum (see 2 papers)
25% identity, 75% coverage
N0B5Z3 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Hyphomicrobium denitrificans (see paper)
27% identity, 75% coverage
adhA / O05542 alcohol dehydrogenase acceptor subunit (EC 1.1.5.5) from Gluconobacter oxydans (strain 621H) (see 2 papers)
ADHA_GLUOX / O05542 Alcohol dehydrogenase (quinone), dehydrogenase subunit; ADH; Alcohol dehydrogenase (quinone), acceptor subunit; Alcohol dehydrogenase (quinone), subunit I; Ethanol:Q2 reductase; G3-ADH subunit I; Quinohemoprotein alcohol dehydrogenase; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 from Gluconobacter oxydans (strain 621H) (Gluconobacter suboxydans) (see 5 papers)
GOX1068 Alcohol dehydrogenase large subunit from Gluconobacter oxydans 621H
27% identity, 47% coverage
- function: Dehydrogenase component of the alcohol dehydrogenase multicomponent enzyme system which is involved in the production of acetic acid and in the ethanol oxidase respiratory chain. Quinohemoprotein alcohol dehydrogenase (ADH) catalyzes the oxidation of ethanol to acetaldehyde by transferring electrons to the ubiquinone embedded in the membrane phospholipids (PubMed:1646200, PubMed:18838797, PubMed:7592433, PubMed:8617755, PubMed:9878716). The electrons transfer from ethanol to membranous ubiquinone occurs from pyrroloquinoline quinone (PQQ) to one heme c in subunit I (AdhA), and finally to two heme c in subunit II (AdhB) (PubMed:18838797, PubMed:8617755, PubMed:9878716). Besides ubiquinone reduction, ADH also has a ubiquinol (QH2) oxidation reaction which mediates electron transfer from ubiquinol to the non-energy generating bypass oxidase system (PubMed:9878716). The electrons transfer occurs from ubiquinol (QH2) to the additional heme c within subunit II (AdhB) (PubMed:8617755, PubMed:9878716). Also able to use quinone analogs such as 2,3-dimethoxy-5-methyl-6-n-decyl-1,4-benzoquinone (DB) and 2,3- dimethoxy-5-methyl-6-n-pentyl-1,4-benzoquinone (PB) (PubMed:9878716).
catalytic activity: ethanol + a ubiquinone = a ubiquinol + acetaldehyde (RHEA:26442)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit.)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
cofactor: heme c (Binds 1 heme c group covalently per subunit.)
subunit: The alcohol dehydrogenase multicomponent enzyme system is composed of a dehydrogenase subunit I (AdhA), a cytochrome c subunit II (AdhB) and a subunit III (AdhS). - Engineering of glycerol utilization in Gluconobacter oxydans 621H for biocatalyst preparation in a low-cost way
Yan, Microbial cell factories 2018 - “...mechanism elucidated in this study, the major polyol dehydrogenase (GOX0854) and the membrane-bound alcohol dehydrogenase (GOX1068) can competitively utilize glycerol but play no obvious roles in the biocatalyst preparation. Thus, the genes related to these two enzymes were deleted. Whole cells of G. oxydans GOX1068GOX0854 can...”
- “..., and glycerate d were assayed. (Black square) G. oxydans 621H, (red circle) G. oxydans GOX1068, (blue triangle) G. oxydans GOX0854, (pink inverted triangle) G. oxydans GOX2088 and (green diamond) G. oxydans GOX1068GOX0854. The error bars represent the standard deviations of three independent experiments As shown...”
- Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
Kranz, BMC genomics 2018 - “...dehydrogenase subunit SldB 4.6 5992 GOX1067 alcohol dehydrogenase cytochrome c subunit precursor 4.0 1807 | GOX1068 alcohol dehydrogenase large subunit 3.4 1706 GOX1230 gluconate 2-dehydrogenase, cytochrome c subunit 9.0 208 | GOX1231 gluconate 2-dehydrogenase alpha chain 8.5 791 | GOX1232 gluconate 2-dehydrogenase gamma chain 7.8 684...”
- Efficient Production of 2,5-Diketo-d-Gluconate via Heterologous Expression of 2-Ketogluconate Dehydrogenase in Gluconobacter japonicus
Kataoka, Applied and environmental microbiology 2015 - “...carrying a putative promoter region for adhAB (gox1067 and gox1068) of G. oxydans 621H was used for expression of the kgdSLC genes (23). Kataoka et al. 3556...”
- Catalytic and molecular properties of the quinohemoprotein tetrahydrofurfuryl alcohol dehydrogenase from Ralstonia eutropha strain Bo
Zarnt, Journal of bacteriology 2001 - “...(Q46444); GS-ADH, quinoprotein ADH from Gluconobacter suboxydans (O05542); AA-ADH, quinoprotein ADH from A. aceti (P18278); MDH, methanol dehydrogenase from...”
8gy2A / O05542 Cryo-em structure of membrane-bound alcohol dehydrogenase from gluconobacter oxydans
27% identity, 47% coverage
- Ligands: heme c; pyrroloquinoline quinone; calcium ion (8gy2A)
WP_036262132 lanthanide-dependent methanol dehydrogenase XoxF5 from Methylocapsa aurea
25% identity, 80% coverage
WP_012321131 methanol/ethanol family PQQ-dependent dehydrogenase from Methylobacterium radiotolerans
26% identity, 77% coverage
IGS75_08895 PQQ-dependent dehydrogenase, methanol/ethanol family from Gluconobacter sphaericus
27% identity, 46% coverage
YP_002965446 Methanol dehydrogenase subunit 1 precursor (MDH large alpha subunit) (MEDH) from Methylobacterium extorquens AM1
26% identity, 77% coverage
ADHA_GLUPO / P28036 Alcohol dehydrogenase (quinone), dehydrogenase subunit; ADH; Alcohol dehydrogenase (quinone), acceptor subunit; Alcohol dehydrogenase (quinone), subunit I; Ethanol:Q2 reductase; G3-ADH subunit I; Quinohemoprotein alcohol dehydrogenase; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 from Gluconacetobacter polyoxogenes (Acetobacter polyoxogenes) (see paper)
27% identity, 50% coverage
- function: Dehydrogenase component of the alcohol dehydrogenase multicomponent enzyme system which is involved in the production of acetic acid and in the ethanol oxidase respiratory chain (By similarity). Quinohemoprotein alcohol dehydrogenase (ADH) catalyzes the oxidation of ethanol to acetaldehyde by transferring electrons to the ubiquinone embedded in the membrane phospholipids (PubMed:2001402). The electrons transfer from ethanol to membranous ubiquinone occurs from pyrroloquinoline quinone (PQQ) to one heme c in subunit I (AdhA), and finally to two heme c in subunit II (AdhB) (By similarity). Besides ubiquinone reduction, ADH also has a ubiquinol (QH2) oxidation reaction which mediates electron transfer from ubiquinol to the non-energy generating bypass oxidase system (By similarity). The electrons transfer occurs from ubiquinol (QH2) to the additional heme c within subunit II (AdhB) (By similarity).
catalytic activity: ethanol + a ubiquinone = a ubiquinol + acetaldehyde (RHEA:26442)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit.)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
cofactor: heme c (Binds 1 heme c group covalently per subunit.)
subunit: The alcohol dehydrogenase multicomponent enzyme system is composed of a dehydrogenase subunit I (AdhA) and a cytochrome c subunit II (AdhB).
7cdlC / Q60AR6 Holo-methanol dehydrogenase (mdh) with cys131-cys132 reduced from methylococcus capsulatus (bath) (see paper)
24% identity, 77% coverage
- Ligands: calcium ion; pyrroloquinoline quinone (7cdlC)
mxaF / P15279 methanol dehydrogenase large subunit (EC 1.1.2.7) from Methylobacterium organophilum (see 2 papers)
P15279 Methanol dehydrogenase [cytochrome c] subunit 1 from Methylobacterium organophilum
25% identity, 77% coverage
mxaF / P16027 methanol dehydrogenase large subunit (EC 1.1.2.7) from Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (see 2 papers)
DHM1_METEA / P16027 Methanol dehydrogenase [cytochrome c] subunit 1; MDH large subunit alpha; MEDH; EC 1.1.2.7 from Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (Methylobacterium extorquens) (see 2 papers)
P16027 lanthanide-dependent methanol dehydrogenase (subunit 3/3) (EC 1.1.2.10); methanol dehydrogenase (cytochrome c) (subunit 2/2) (EC 1.1.2.7) from Methylorubrum extorquens (see 13 papers)
MexAM1_META1p4538, Mext_4150 methanol/ethanol family PQQ-dependent dehydrogenase from Methylorubrum extorquens AM1
Mext_4150 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylobacterium extorquens PA1
Mchl_4518 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylobacterium chloromethanicum CM4
26% identity, 77% coverage
- function: Catalyzes the oxidation of primary alcohols including methanol
catalytic activity: 2 Fe(III)-[cytochrome cL] + a primary alcohol = 2 Fe(II)- [cytochrome cL] + an aldehyde + 2 H(+) (RHEA:51004)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit.) PQQ is inserted between disulfide Cys-130-Cys-131 and the indole ring of Trp-270
cofactor: Ca(2+) Note=Binds 1 Ca(2+) ion per subunit
subunit: Heterotetramer composed of 2 alpha and 2 beta subunits. - Isolation and Characterization of Homologically Expressed Methanol Dehydrogenase from Methylorubrum extorquens AM1 for the Development of Bioelectrocatalytical Systems
Karaseva, International journal of molecular sciences 2022 - “.... Amplification of DNA fragment from Methylorubrum extorquens AM1 containing mxaF gene (GenBank locus tag: MexAM1_META1p4538, chromosome accession: NC_012808) was carried out using specific primers and the genomic DNA of the strain as a template. The resulting PCR fragment containing full-length mxaF gene ORF with encoded...”
- “...Vector for Expression/Production of the Recombinant Protein Gene mxaF from M. extorquens (GenBank locus tag: MexAM1_META1p4538, chromosome accession: NC_012808) (2248 bp) was amplified using the designed primers: forward, 5-CTAAT GCATGC GCCCGTTGACGACAACGGTG-3, and reverse, 5-TA GAATTC TCAGTGGTGGTGGTGGTGGTGCTTGGCGGCCGACTTCCACTC-3. The reverse primer contains a sequence encoding poly-His-tag (shown by...”
- Structural diversity of the coenzyme methylofuran and identification of enzymes for the biosynthesis of its polyglutamate side chain
Hemmann, The Journal of biological chemistry 2021 - “...sequencing. For unknown reasons, the deletion of orf17 could only be obtained in a mxaF (Mext_4150) background. However, the additional mxaF deletion is not affecting MYFR biosynthesis. Complementation of the orf17M. extorquens mutant To complement the orf17 mutant, the orf17 gene (Mext_1835) was amplified from genomic...”
- Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1
Roszczenko-Jasińska, Scientific reports 2020 - “.... Methylorubrum extorquens AM1 (formerly Methylobacterium extorquens AM1) produces a MxaFI-type MeDH (encoded by mxaF: MexAM1_META1p4538 and mxaI: MexAM1_META1p4535 ), two XoxF (type 5) MeDHs (encoded by xoxF1 : MexAM1_META1p1740 and xoxF2 : MexAM1_META1p2757 ), and an ExaF-type ethanol dehydrogenase (encoded by exaF : MexAM1_META1p1139 )...”
- Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1
Ochsner, Molecular microbiology 2019 - “...selection. Construction of gene deletions, expression plasmids and promoter fusions Markerless gene deletions of mxaF (Mext_4150), xoxF (Mext_1809), Mext_1854, Mext_18068, Mext_1594, Mext_1595, Mext_1853, Mext_18567 and Mext_184851 were generated using pK18_ mob _ sacB (Schfer et al ., 1994 ). Deletion and subsequent replacement of mxbD (Mext_1821)...”
- The 380 kb pCMU01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin B12- and tetrahydrofolate-dependent chloromethane metabolism in Methylobacterium extorquens CM4: a proteomic and bioinformatics study
Roselli, PloS one 2013 - “...n.d. n.d. 278 51 75 n.d. n.d. n.d. MxaF, methanol dehydrogenase (EC 1.1.99.8) large subunit Mchl_4518 mxaF CH 3 Cl/+++ f 68.4 5.9 129 16 19 364 63 54 82 8 20 Sga, serine glyoxylate aminotransferase (EC 2.6.1.45) Mchl_2131 sga f 43.2 6.9 n.d. n.d. n.d....”
1w6sC / P16027 The high resolution structure of methanol dehydrogenase from methylobacterium extorquens (see paper)
25% identity, 77% coverage
- Ligands: pyrroloquinoline quinone; calcium ion (1w6sC)
MCA0779 methanol dehydrogenase protein, large subunit from Methylococcus capsulatus str. Bath
24% identity, 77% coverage
- Transcriptional Regulation of Methanol Dehydrogenases in the Methanotrophic Bacterium Methylococcus capsulatus Bath by Soluble and Insoluble Lanthanides
Xie, Microbes and environments 2023 - “...lanthanide chelator(s) were expected to be down-regulated in the Ce-supplemented culture. The genes for MxaFI-MDH (MCA0779 and 0782), its putative regulatory genes (MCA0776-0778), and its accessory genes (MCA0780-0781 and 783-789) were shown to be down-regulated under Ce-supplemented conditions. Furthermore, genes for formate dehydrogenase (FDH) (MCA2576-2577) and...”
- Computational and experimental analysis of the secretome of Methylococcus capsulatus (Bath)
Indrelid, PloS one 2014 - “...subtilase family 68 Y Y Y 20 15 Y N N N N SP Extracellular MCA0779 Methanol dehydrogenase protein, large subunit 66 Y Y Y 23 25 Y N N N N SP Periplasm MCA2589 Surface-associated protein 58 Y Y Y 15 21 Y N N...”
- “...surface domains and was predicted to be periplasmic proteins by the in silico analysis (MCA0155, MCA0779, MCA1082). Of these MCA1082 was found by CD-blast [57] to contain a periplasmic metal-binding domain. This protein was only detected in culture supernatants during early exponential growth. One possible explanation...”
- Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)
Ward, PLoS biology 2004 - “...and Dalton 1999 ) best matches the N-terminal of the large subunit of methanol dehydrogenase (MCA0779), although the sequences differ slightly. The sequence of modifin, the 8.6-kDa subunit thought to confer substrate specificity to the enzyme ( Stirling and Dalton 1978 ; Tate and Dalton 1999...”
S6D3Q2 1-butanol dehydrogenase (quinone) (EC 1.1.5.11) from Frateuria aurantia (see paper)
27% identity, 47% coverage
SMb20173 putative methanol dehydrogenase protein, large subunit from Sinorhizobium meliloti 1021
25% identity, 75% coverage
- ExoS/ChvI Two-Component Signal-Transduction System Activated in the Absence of Bacterial Phosphatidylcholine
Geiger, Frontiers in plant science 2021 - “...and Supplementary Table 1 ). In CS111, transcripts for the putative quinoprotein methanol dehydrogenase MxaF (SMb20173), cytochromes C (SMb20172, SMb20174), a methanol oxidation protein (SMb20175), and transcripts (SMb20204, SMb20207) required for the formation of the pyrroloquinoline (PQQ) cofactor of bacterial methanol dehydrogenases are increased which would...”
- “...(gfa) glutathione-dependent formaldehyde-activating enzyme 3.58 SMb20204 (pqqA) putative pyrroloquinoline quinone synthesis protein A (PqqA) 3.17 SMb20173 (mxaF) putative methanol dehydrogenase, large subunit 2.20 SMb20171 (fgh) putative S -formylglutathione hydrolase 1.45 SMb20325 (thuE) probable trehalose/maltose-binding protein 1.43 SMc02156 conserved hypothetical protein 1.39 SMb20174 (cytC1) putative cytochrome C...”
Q44002 alcohol dehydrogenase (quinone) (EC 1.1.5.5) from Komagataeibacter europaeus (see paper)
27% identity, 50% coverage
MMSR116_00880, MMSR116_RS00865 methanol/ethanol family PQQ-dependent dehydrogenase from Methylobacterium mesophilicum SR1.6/6
25% identity, 77% coverage
- Transcriptome and Secretome Analyses of Endophyte Methylobacterium mesophilicum and Pathogen Xylella fastidiosa Interacting Show Nutrient Competition
Dourado, Microorganisms 2023 - “...MMSR116_RS20190 MMSR116_20455 branched-chain amino acid ABC transporter substrate-binding protein 43 9 25|26 37 20 MMSR116_RS00865 MMSR116_00880 Methanol/ethanol family PQQ-dependent dehydrogenase 69 3 24|25 38 19 MMSR116_RS20480 MMSR116_20745 Polyribonucleotide nucleotidyltransferase Pnp 80 3 39 23 MMSR116_RS29630 MMSR116_29970 Ketol-acid reductoisomerase IlvC 37 5 40 - MMSR116_RS11180 MMSR116_11330 Adenylosuccinate...”
- “...- MMSR116_RS20190 MMSR116_20455 branched-chain amino acid ABC transporter substrate-binding protein 43 9 25|26 37 20 MMSR116_RS00865 MMSR116_00880 Methanol/ethanol family PQQ-dependent dehydrogenase 69 3 24|25 38 19 MMSR116_RS20480 MMSR116_20745 Polyribonucleotide nucleotidyltransferase Pnp 80 3 39 23 MMSR116_RS29630 MMSR116_29970 Ketol-acid reductoisomerase IlvC 37 5 40 - MMSR116_RS11180 MMSR116_11330...”
MexAM1_META1p2757 XoxF from Methylobacterium extorquens AM1
C5ATJ3 XoxF from Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)
MexAM1_META1p2757 methanol/ethanol family PQQ-dependent dehydrogenase from Methylorubrum extorquens AM1
24% identity, 75% coverage
XOXF1_METEA / C5B120 Lanthanide-dependent methanol dehydrogenase; Lanthanide-dependent MDH; Ln(3+)-dependent MDH; La(3+)- and PQQ-dependent MDH; La(3+)-dependent methanol dehydrogenase; La(3+)-dependent MDH; EC 1.1.2.10 from Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (Methylobacterium extorquens) (see 3 papers)
C5B120 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Methylorubrum extorquens (see 4 papers)
Mext_1809 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylobacterium extorquens PA1
YP_002962861 XoxF, PQQ-linked dehydrogenase of unknown function from Methylobacterium extorquens AM1
MexAM1_META1p1740 lanthanide-dependent methanol dehydrogenase XoxF1 from Methylorubrum extorquens PA1
25% identity, 75% coverage
- function: Catalyzes the oxidation of methanol to formaldehyde, but only in the presence of lanthanides (Ln). Contributes to methanol metabolism when La(3+) is present in the natural environment of the bacterium, allowing bacterial growth with methanol as carbon and energy source. Thereby is an essential enzyme for Ln-dependent methylotrophy (PubMed:23209751, PubMed:30862918, PubMed:32366463). Uses a specific cytochrome cL (XoxG), encoded by the adjacent gene in the locus, as electron acceptor (Probable). Also plays a role in the transcriptional regulation of the mxa and xox1 operons, most likely acting as a lanthanide sensory module (PubMed:32366463). Is also able to oxidize formaldehyde to formate in vitro, but this activity does not occur in vivo (PubMed:30862918).
catalytic activity: 2 Fe(III)-[cytochrome cL] + methanol = 2 Fe(II)-[cytochrome cL] + formaldehyde + 2 H(+) (RHEA:51008)
cofactor: La(3+) Nd(3+) (Exhibits enzymatic activity only in the presence of lanthanide ions (PubMed:30862918, PubMed:32366463). Is inactive when binding Ca(2+) ions in the absence of La(3+) (PubMed:32366463). Binds one lanthanide ion per subunit (PubMed:30862918, PubMed:32366463).)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit.)
subunit: Homodimer. - Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1
Ochsner, Molecular microbiology 2019 - “...Mext_1594 Hypothetical 3.01E06 3.80 x Mext_1806 Substrate binding protein of ABC transporter 5.12E05 3.70 x Mext_1809 XoxF 6.72E06 4.46 x Mext_1810 XoxG 5.51E05 4.05 x Mext_1811 XoxJ 1.47E06 4.76 x Mext_1845 Hypothetical 1.78E05 2.10 x Mext_1854 Lanmodulin (REEbinding protein) 6.83E07 4.67 x John Wiley & Sons,...”
- “...of gene deletions, expression plasmids and promoter fusions Markerless gene deletions of mxaF (Mext_4150), xoxF (Mext_1809), Mext_1854, Mext_18068, Mext_1594, Mext_1595, Mext_1853, Mext_18567 and Mext_184851 were generated using pK18_ mob _ sacB (Schfer et al ., 1994 ). Deletion and subsequent replacement of mxbD (Mext_1821) with the...”
- Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization
Müller, Molecular & cellular proteomics : MCP 2016 - “...Mext_3817 Mext_4152 Mext_0663 Mext_0393 Mext_0882 Mext_1809 Mext_4651 Mext_1767 Mext_1440 Mext_2776 Mext_1324 Mext_0392 Mext_1378 Mext_2496 Mext_2760 Mext_3408...”
- “...we found two other methanol dehydrogenase-like proteins, Mext_1809 (XoxF) and Mext_1339, to be up-regulated during plant colonization (supplemental Table S2,...”
- The methanol dehydrogenase gene, mxaF, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments
Lau, PloS one 2013 - “...Mrad 2831 1932 (NC_010505) Methyloversatilis universalis strain FAM5 (EU548068)Burkholderiales bacterium RZ18-153 (EU548065) Methylobacterium extorquens PA1 Mext_1809 (NC_010172) Methylobacterium chloromethanicum CM4 Mchl2145 (NC_011757) Methylobacterium extorquens AM1 MexAM1 META1p1740 (NC_012808) Methylobacterium sp. 446 M446 5752 (NC_010511) Methylobacterium radiotolerans JCM 2831 Mrad 2831 0508 (NC_010505) Methylobacterium sp. 446 M446...”
- Metagenomic analysis of the bacterial community associated with the taproot of sugar beet
Tsurumaru, Microbes and environments 2015 - “...YP_001601525 and YP_002875095, respectively, and those for xoxF and mxaF in M. extorquens AM1 were YP_002962861 and YP_002965446, respectively. The frequency of detection of potential functional genes was calculated as follows: Frequency = (Number of sequence reads for a target gene/Gene length) (100,000/Total number of sequence...”
- Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1
Roszczenko-Jasińska, Scientific reports 2020 - “...mxaF: MexAM1_META1p4538 and mxaI: MexAM1_META1p4535 ), two XoxF (type 5) MeDHs (encoded by xoxF1 : MexAM1_META1p1740 and xoxF2 : MexAM1_META1p2757 ), and an ExaF-type ethanol dehydrogenase (encoded by exaF : MexAM1_META1p1139 ) 17 , 18 . The XoxF enzymes from M. extorquens AM1 share 90% amino...”
- “...MexAM1_META1p1292 cycL c -type cytochrome biogenesis MexAM1_META1p1293 cycK Heme lyase MexAM1_META1p1294 cycJ Periplasmic heme chaperone MexAM1_META1p1740 xoxF1 Ln-dependent methanol dehydrogenase MexAM1_META1p1741 xoxG Cytochrome c MexAM1_META1p1742 xoxJ Periplasmic binding protein MexAM1_META1p1746 orf6 Unknown MexAM1_META1p1747 orf7 Unknown MexAM1_META1p1748 pqqE PQQ biosynthesis MexAM1_META1p1749 pqqCD PQQ biosynthesis MexAM1_META1p1750 pqqB PQQ...”
- Rare earth element alcohol dehydrogenases widely occur among globally distributed, numerically abundant and environmentally important microbes
Huang, The ISME journal 2019 - “...XoxF5_M.e.1 Methylorubrum extorquens AM1 272630 MexAM1_META1p1740 XoxF5_M.e.2 Methylorubrum extorquens AM1 272630 MexAM1_META1p2757 XoxF5_M.d. Methyloversatilis...”
6oc6A / C5B120 Lanthanide-dependent methanol dehydrogenase xoxf from methylobacterium extorquens, in complex with lanthanum and pyrroloquinoline quinone (see paper)
25% identity, 75% coverage
- Ligand: pyrroloquinoline quinone (6oc6A)
NBRC3257_1378 PQQ-dependent dehydrogenase, methanol/ethanol family from Gluconobacter thailandicus NBRC 3257
27% identity, 49% coverage
- Draft genome sequence of Gluconobacter thailandicus NBRC 3257
Matsutani, Standards in genomic sciences 2014 - “...indicated that NBRC 3257 has membrane-bound PQQ-dependent alcohol dehydrogenase, adh AB operon (locus_tag NBRC3257_1377 and NBRC3257_1378) and adh subunit III (NBRC3257_1024). A unique orphan gene of adh subunit I was also identified (NBRC3257_3117). The gene repertories of other membrane-bound PQQ dependent proteins were investigated. Homologous proteins...”
S101446_02993 PQQ-dependent dehydrogenase, methanol/ethanol family from Komagataeibacter europaeus
27% identity, 50% coverage
bdh / Q9AF95 1-butanol dehydrogenase (cytochrome c) (EC 1.1.2.9) from Thauera butanivorans (strain ATCC 43655 / DSM 2080 / JCM 20651 / NBRC 103042 / IAM 12574 / Bu B1211) (see 3 papers)
BDH_THABB / Q9AF95 1-butanol dehydrogenase (cytochrome c); BDH; NAD-independent 1-butanol dehydrogenase; PQQ-containing alcohol dehydrogenase; Quinohemoprotein; EC 1.1.2.9 from Thauera butanivorans (strain ATCC 43655 / DSM 2080 / JCM 20651 / CCUG 51053 / NBRC 103042 / IAM 12574 / Bu B1211) (Pseudomonas butanovora) (see 3 papers)
Q9AF95 1-butanol dehydrogenase (cytochrome c) (EC 1.1.2.9) from Thauera butanivorans (see paper)
24% identity, 78% coverage
- function: Involved in the metabolism of butane (PubMed:11889098). Could be important in the detoxification of 1-butanol (PubMed:12142403). Catalyzes the oxidation of 1-butanol to butyraldehyde (PubMed:11238982, PubMed:12142403). Also able to use 1-propanol, 2-pentanol, propionaldehyde and butyraldehyde as substrates (PubMed:11238982).
catalytic activity: butan-1-ol + 2 Fe(III)-[cytochrome c] = butanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:43432)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit.)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
cofactor: heme c (Binds 1 heme c group per subunit.)
subunit: Monomer.
disruption phenotype: Cells lacking this gene show a delayed growth on butane and are unable to tolerate high level of 1-butanol (PubMed:11889098, PubMed:12142403). When both bdh and boh genes are inactivated, growth on butane and 1-butanol is eliminated (PubMed:11889098).
MDMS009_1502 methanol/ethanol family PQQ-dependent dehydrogenase from Methylophaga thiooxydans DMS010
24% identity, 76% coverage
RSP_2578 putative pqq dehydrogenase protein from Rhodobacter sphaeroides 2.4.1
25% identity, 75% coverage
- The sRNA SorY confers resistance during photooxidative stress by affecting a metabolite transporter in Rhodobacter sphaeroides
Adnan, RNA biology 2015 - “...argI Arginase 0.82 RSP_2580 xoxJ putative methanol oxidation protein 0.83 RSP_2577 cycI isocytochrome c2 1.04 RSP_2578 xoxF putative pqq dehydrogenase protein(EC:1.1.99.8) 1.11 12.56 3 50 128 165 RSP_2576 adhI Alcohol dehydrogenase class III(EC:1.2.1.1) 1.15 10.01 37 50 16 2 To test whether the mRNAs are direct...”
- A cluster of four homologous small RNAs modulates C1 metabolism and the pyruvate dehydrogenase complex in Rhodobacter sphaeroides under various stress conditions
Billenkamp, Journal of bacteriology 2015 - “...xoxJ (RSP_2580, putative methanol oxidation protein), xoxF (RSP_2578, putative PQQ dehydrogenase protein), cycB (RSP_2579, cytochrome c533i), and coxS and coxL...”
- “...Alcohol dehydrogenase class III Isocytochrome c2 0.43 0.48 RSP_2578 (xoxF), 1 RSP_2579 (cycB), 2 RSP_2580 (xoxJ), 3 RSP_2581, 4 Putative pqq dehydrogenase...”
I3UDT0 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Advenella kashmirensis (see paper)
24% identity, 77% coverage
GL4_0421 methanol/ethanol family PQQ-dependent dehydrogenase from Methyloceanibacter caenitepidi
24% identity, 75% coverage
blr6207 exaA from Bradyrhizobium japonicum USDA 110
24% identity, 77% coverage
- Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation
Nishihata, BMC microbiology 2018 - “...TGCAGCGCACAA 21.88 9.39 2.33 probable sulfite oxidase bll6206 CGCGCCGCACAA 74.19 35.28 2.10 hypothetical protein exaA (blr6207) CGCGCCGCACAA 93.32 23.85 3.91 probable quinoprotein ethanol dehydrogenase precursor blr6443 TGCAATGCAACA 13.79 2.83 4.87 ABC transporter permease protein blr6465 CGCGATGCACAA 39.03 14.29 2.73 putative steroid monooxygenase bll6733 TGCGACGAAGCA 45.09 21.88...”
- “...binding to DNA fragments of the promoter regions of pckA (bll8141) ( a ), exaA (blr6207) ( b ), pdhAB (bll4783-bll4779) operon ( c ), ppc (blr2955) ( d ), bll5961-blr5962 operon ( e ), and phbB (bll0225) ( f ). Experimental conditions and lane assignments...”
- Influence of elevated atmospheric carbon dioxide on transcriptional responses of Bradyrhizobium japonicum in the soybean rhizoplane
Sugawara, Microbes and environments 2013 - “...bll4784 1.5 Aldehyde dehydrogenase bll5504 1.5 Putative polyvinyl-alcohol dehydrogenase bll5655 * 1.6 2.6 Alcohol dehydrogenase blr6207 exaA 2.0 Quinoprotein ethanol dehydrogenase blr0335 1.5 Putative carbon monoxide dehydrogenase small chain bll5664 cooxM 2.3 Putative carbon monoxide dehydrogenase medium subunit Dicarboxylic acid blr1277 mdcL 1.6 Malonate carrier protein...”
- Soybean seed extracts preferentially express genomic loci of Bradyrhizobium japonicum in the initial interaction with soybean, Glycine max (L.) Merr
Wei, DNA research : an international journal for rapid publication of reports on genes and genomes 2008 - “...encoding two component sensor/regulator (bll6184blr6185 in LOS 18, bll7306bll7307 in LOS 21) and alcohol dehydrogenase (blr6207, blr6213, blr6215, and bll6220 in LOS 18) were repressed. 3.4. Expression loci shared between SSE- and genistein-treated cells In addition to genomic loci covering nod genes, six loci outside symbiosis...”
C8S0N8 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Rhodobacter sp. SW2 (see paper)
25% identity, 75% coverage
WP_012317515 lanthanide-dependent methanol dehydrogenase XoxF1 from Methylobacterium radiotolerans
25% identity, 75% coverage
2d0vA / Q4AE26 Crystal structure of methanol dehydrogenase from hyphomicrobium denitrificans (see paper)
24% identity, 76% coverage
- Ligands: calcium ion; pyrroloquinoline quinone (2d0vA)
XC_0679 methanol dehydrogenase heavy chain from Xanthomonas campestris pv. campestris str. 8004
24% identity, 76% coverage
- The lolB gene in Xanthomonas campestris pv. campestris is required for bacterial attachment, stress tolerance, and virulence
Liao, BMC microbiology 2022 - “...strain; they were genes encoding a dipeptidyl anmnopeptidase ( XC_0253 ), a methanol dehydrogenase ( XC_0679 ), an alkaline phosphatase ( XC_1519 ), and two hypothetical proteins ( XC_0677 and XC_3831 ). Table 4 Comparison of expression of putative lipoprotein encoding genes in the wild type...”
- “...Dipeptidyl anmnopeptidase MQRLLLASSLLLA LSAC SDKS 3.10150.1651 0.0361 XC_0677 Hypothetical protein MKYLLSAALCVAA LSGC TDRE 6.95350.4812 0.0312 XC_0679 Methanol dehydrogenase MHQSSCRSARGGVLLMLALSAV LAGC KKDT 5.39560.3450 0.0348 XC_0707 Rare lipoprotein A MNSITGPKWLIPMALMLG LAAC SSAP 3.09530.2584 0.0733 XC_1519 Alkaline phosphatase MPMRYRLPALAALTTLC VAAC ASTA 1.78760.0305 0.0177 XC_1584 Cyanoglobin MMTRWLRYSLLCVLT LSAC ATTQ 3.05300.3839...”
azo3865 putative quinoprotein ethanol dehydrogenase from Azoarcus sp. BH72
27% identity, 45% coverage
- Diverse Bacterial Genes Modulate Plant Root Association by Beneficial Bacteria
do, mBio 2020 - “...such genes in A. olearius DQS4 T is a homolog of the BH72 exaA5 gene (azo3865), predicted to encode a pyrroloquinoline quinone-dependent alcohol dehydrogenase (DQS_RS19730) involved in methanol oxidation. Consistent with these findings, previous reports showed that mutation of ADH genes inhibited competitive colonization of rice...”
CYCPU_RS0111520 PQQ-dependent dehydrogenase, methanol/ethanol family from Cycloclasticus pugetii PS-1
23% identity, 77% coverage
Maq22A_1p33165 methanol/ethanol family PQQ-dependent dehydrogenase from Methylobacterium aquaticum
25% identity, 77% coverage
Msil_0471 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylocella silvestris BL2
23% identity, 77% coverage
- The effect of lanthanum on growth and gene expression in a facultative methanotroph
Crombie, Environmental microbiology 2022 - “...and discussion MDH gene transcription The M. silvestris genome contains five predicted PQQdependent MDH genes, Msil_0471, Msil_1587, Msil_2260, Msil_3149 and Msil_3387. Based on amino acid sequence and the presence of the Lncoordinating aspartate residue in XoxMDH, these can be identified as encoding Mxa and XoxMDHs from...”
- “...hypothetical proteins of unknown function. Fourdigit gene identifications refer to abbreviated locus tags, e.g. 0471, Msil_0471 ( mxaF ). YVTN RP, 40 residue YVTN repeat protein; TonB, TonBdependent receptor. Figure 3 MDH gene transcription in cells grown on methane or propane in the presence or absence...”
- Genome Scale Metabolic Model of the versatile methanotroph Methylocella silvestris
Bordel, Microbial cell factories 2020 - “...to encode NAD(P)-dependent alcohol dehydrogenases (ADHs), as well as a pyrroloquinoline quinone (PQQ)-containing methanol dehydrogenase (Msil_0471) and a PQQ-containing ADH with 73% identity to xoxF from Methylobacterium extorquens (Msil_1587). For modelling purposes, it is essential to elucidate if the oxidation of 1-propanol and 2-propanol, to propanal...”
N0B8G3 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Hyphomicrobium denitrificans (see paper)
24% identity, 77% coverage
azo2975 putative quinoprotein ethanol dehydrogenase from Azoarcus sp. BH72
27% identity, 44% coverage
- Defining the Genetic Basis of Plant⁻Endophytic Bacteria Interactions
Pinski, International journal of molecular sciences 2019 - “...subsp. indica cv. IR36 decrease in root colonisation [ 52 ] Azoarcus sp. BH72 exaA3 (azo2975) quino(hemo)protein alcohol dehydrogenase, PQQ-dependent (EC 1.1.2.8) O. sativa subsp. indica cv. IR36 decrease in root colonisation [ 52 ] Stress protection G. diazotrophicus PAL5 sodB (GDI_2168) superoxide dismutase [Mn/Fe] (EC...”
Mfla_0344 Pyrrolo-quinoline quinone from Methylobacillus flagellatus KT
24% identity, 79% coverage
- Lanpepsy is a novel lanthanide-binding protein involved in the lanthanide response of the obligate methylotroph Methylobacillus flagellatus
Hemmann, The Journal of biological chemistry 2023 - “...proteins included known components of the lanthanome such as the Ln 3+ -dependent MDH XoxF (Mfla_0344, Mfla_2314), the c -type cytochrome XoxG (Mfla_2312), and the TonB-dependent receptor involved in Ln 3+ uptake (Mfla_1253). We also identified two 54 -dependent transcriptional regulators, Mfla_1254 and Mfla_0343. The gene...”
- “...involved in the regulation of its expression. Mfla_0343 is located directly upstream of xoxF ( Mfla_0344 , reverse orientation) and might regulate xoxF expression. Supporting this hypothesis, a putative 54 promoter sequence was predicted upstream of xoxF by iPro54-PseKNC ( 24 ). Figure1 Proteomic response of...”
- Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners
Haft, BMC genomics 2011 - “...enzyme Mfla_1451 84 108 282 -59.198 PQQ-dependent enzyme Mfla_2044 77 94 210 -57.525 PQQ-dependent enzyme Mfla_0344 79 100 268 -56.680 PQQ-dependent enzyme Mfla_1681 53 53 83 -51.646 PQQ biosynthesis protein PqqD Mfla_2043 42 43 69 -39.341 extracellular solute-binding protein Mfla_2313 42 43 59 -39.341 extracellular solute-binding...”
A0A1V0GRH2 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Paracoccus yeei (see paper)
27% identity, 44% coverage
J7QHX8 Methanol dehydrogenase MxaF from Methylocystis sp. (strain SC2)
23% identity, 76% coverage
Bdiaspc4_01330 PQQ-dependent methanol/ethanol family dehydrogenase from Bradyrhizobium diazoefficiens
28% identity, 44% coverage
Msil_3149 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylocella silvestris BL2
25% identity, 77% coverage
- The effect of lanthanum on growth and gene expression in a facultative methanotroph
Crombie, Environmental microbiology 2022 - “...gene transcription The M. silvestris genome contains five predicted PQQdependent MDH genes, Msil_0471, Msil_1587, Msil_2260, Msil_3149 and Msil_3387. Based on amino acid sequence and the presence of the Lncoordinating aspartate residue in XoxMDH, these can be identified as encoding Mxa and XoxMDHs from clades 5 (two...”
- “...operon (Msil_04720485), downregulated between sixfold and 28fold. Interestingly, and as predicted by RTqPCR data, XoxF1 (Msil_3149) was also downregulated (sevenfold) by Ln, together with its associated cytochrome c L , XoxG (Msil_3147) and solutebinding protein XoxJ (Msil_3148) (sevenfold and 62fold, respectively). Of the XoxMDH enzymes, clades...”
bll0333 bll0333 from Bradyrhizobium japonicum USDA 110
28% identity, 44% coverage
- Identification of the Important Genes of Bradyrhizobium diazoefficiens 113-2 Involved in Soybean Nodule Development and Senescence
Yuan, Frontiers in microbiology 2021 - “...group peptidase, beta-lactamase class C family 113-2GL000144 blr0694 Serine protease, subtilase family 113-2GL000369 blr0497 113-2GL000546 bll0333 Glucose dehydrogenase 113-2GL000547 bll0332 Cytochrome c, mono- and diheme variants 113-2GL000923 113-2GL007956 blr1693,bll8244 113-2GL000935 bll8232 L-lysine 2,3-aminomutase (EF-P beta-lysylation pathway) 113-2GL000936 bll8231 Gamma-glutamyltranspeptidase 113-2GL000937 bll8230 113-2GL000966 bll8195 Retron-type reverse transcriptase...”
- Identification of Genes Regulated by the Antitermination Factor NasT during Denitrification in Bradyrhizobium diazoefficiens
Sánchez, Microbes and environments 2019 - “...blr3168 glxR ; oxidoreductase; putative tartronate semialdehyde reductase 5.09 bll0332 Cytochrome- c like protein 2.94 bll0333 Putative alcohol dehydrogenase 3.07 bll7610 Conserved hypothetical protein 2.31 blr2827 Conserved hypothetical protein 2.29 blr3159 Conserved hypothetical protein 2.02 blr6840 Conserved hypothetical protein 2.52 bsr2315 Conserved hypothetical protein 2.31 bll4571...”
- An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens
Fernández, Frontiers in microbiology 2019 - “...conditions in comparison to oxic conditions ( p -value 0.2) Bdiaspc4_01330 PQQ-dependent dehydrogenase, methanol/ethanol family bll0333 0.8 Bdiaspc4_05515 Sugar ABC transporter substrate-binding protein blr1123 3.0 Bdiaspc4_36200 Flagellin fliC/lafA2 bll6865 1.8 Bdiaspc4_39525 GMC Family oxidoreductase blr7491 2.3 Seventy-one genes/proteins showing increased expression in microoxic conditions in comparison...”
- Reactive oxygen species-inducible ECF σ factors of Bradyrhizobium japonicum
Masloboeva, PloS one 2012 - “...of genes. Common to both regulons are only four clustered genes (bll03310333; blr0337) of which bll0333 encodes a precursor of a putative alcohol dehydrogenase and blr0337 a subunit of a predicted carbon monoxide dehydrogenase. Notably, genes blr0335 and blr0336 encoding two additional subunits of the latter...”
- Soybean seed extracts preferentially express genomic loci of Bradyrhizobium japonicum in the initial interaction with soybean, Glycine max (L.) Merr
Wei, DNA research : an international journal for rapid publication of reports on genes and genomes 2008 - “...for one locus (covering genes from bll0330 to blr0336), including a probable alcohol dehydrogenase precursor (bll0333) (Fig. 1 ), suggesting that the expression patterns were mainly obtained by the SSE or genistein in itself. Figure 1 Genome-wide expression profiling of B. japonicum USDA 110 in response...”
- Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress
Cytryn, Journal of bacteriology 2007 - “...(bll1464), putative alcohol dehydrogenases (bll0332 and bll0333), pyrroloquinoline quinone synthase protein A (bsr6735), pilus assembly proteins (bsl1442,...”
- “...bsr6735 blr6736 blr6738 blr6739 bll0332 bll0333 bll6220 Pyrroloquinoline synthesis protein (pqqA) Pyrroloquinoline synthesis protein (pqqB) Pyrroloquinoline...”
1lrwA / P12293 Crystal structure of methanol dehydrogenase from p. Denitrificans (see paper)
23% identity, 76% coverage
- Ligands: calcium ion; pyrroloquinoline quinone (1lrwA)
METTRDRAFT_RS0210410 methanol/ethanol family PQQ-dependent dehydrogenase from Methylosinus trichosporium OB3b
23% identity, 77% coverage
mxaF / P12293 methanol dehydrogenase large subunit (EC 1.1.2.7) from Paracoccus denitrificans (see 2 papers)
DHM1_PARDE / P12293 Methanol dehydrogenase [cytochrome c] subunit 1; MDH large subunit alpha; MEDH; EC 1.1.2.7 from Paracoccus denitrificans (see paper)
GB|AAA88366.1 methanol dehydrogenase, PQQ-dependent; EC 1.1.99.8 from Paracoccus denitrificans (see paper)
23% identity, 83% coverage
- function: Catalyzes the oxidation of primary alcohols including methanol.
catalytic activity: 2 Fe(III)-[cytochrome cL] + a primary alcohol = 2 Fe(II)- [cytochrome cL] + an aldehyde + 2 H(+) (RHEA:51004)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit. PQQ is inserted between disulfide Cys-135-Cys-136 and the indole ring of Trp-275.)
cofactor: Ca(2+) (Binds 1 Ca(2+) ion per subunit.)
subunit: Heterotetramer composed of 2 alpha and 2 beta subunits.
Msip34_0016 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylovorus sp. SIP3-4
23% identity, 78% coverage
- Comparative transcriptomics in three Methylophilaceae species uncover different strategies for environmental adaptation
Vorobev, PeerJ 2013 - “...4A , Tables S5 S7 ). The homolog of mmol_1770 in M. glucosotrophus SIP3-4 ( msip34_0016 ) was significantly (100-fold) over expressed in in situ conditions compared to laboratory conditions, but the expression level was relatively low ( Figs. 4A , Tables S8 S10 ). The...”
- “...or mxaG ) revealed a similar expression pattern, suggesting a role in electron transfer from Msip34_0016. 10.7717/peerj.115/fig-4 Figure 4 Relative abundance of transcripts reflecting expression of central pathways for carbon assimilation and dissimilation. (A) Abundance of transcripts from different homologs of xoxF genes and genes implicated...”
Msil_2260 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylocella silvestris BL2
24% identity, 75% coverage
- The effect of lanthanum on growth and gene expression in a facultative methanotroph
Crombie, Environmental microbiology 2022 - “...MDH gene transcription The M. silvestris genome contains five predicted PQQdependent MDH genes, Msil_0471, Msil_1587, Msil_2260, Msil_3149 and Msil_3387. Based on amino acid sequence and the presence of the Lncoordinating aspartate residue in XoxMDH, these can be identified as encoding Mxa and XoxMDHs from clades 5...”
- “...five predicted PQQdependent MDHs, only MxaF, XoxF5 and XoxF1 were expressed at appreciable levels. XoxF5(2) (Msil_2260) was not detected in any sample, and XoxF3 (Msil_3387) was expressed at very low levels ranging from 0.00003% to 0.00017% of total protein, Supporting Information Table S1 . In comparison,...”
Mmol_2048 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylotenera mobilis JLW8
23% identity, 78% coverage
- Lanthanide-Dependent Methanol Dehydrogenases of XoxF4 and XoxF5 Clades Are Differentially Distributed Among Methylotrophic Bacteria and They Reveal Different Biochemical Properties
Huang, Frontiers in microbiology 2018 - “...these genomes were identified through BLAST analyses using queries representing XoxF4 ( M. mobilis protein Mmol_2048) and XoxF5 ( Methylomonas sp. LW13 protein U373DRAFT_03409) enzymes. Only sequences showing >31% amino acid identity were included in analyses. Phylogenetic Analysis Protein sequences were aligned using the CLUSTAL W...”
- “...this study. Strain Reference Methylotenera mobilis JLW8 Wild-type Kalyuzhnaya et al., 2006 XoxF4-1 mutant ( mmol_2048 ) Mustakhimov et al., 2013 XoxF4-2 mutant ( mmol_1770 ) Mustakhimov et al., 2013 XoxF4-1 XoxF4-2 double mutant ( mmol_1770 mmol_2048 ) Mustakhimov et al., 2013 XoxF4-1 XoxF4-2 double mutant...”
- Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions
Krause, Proceedings of the National Academy of Sciences of the United States of America 2017 - “...we used the MDH mutants xoxF1 (mmol_1170), xoxF2 (mmol_2048), and xoxF12 (mmol_1770, mmol_2048) of M. mobilis JLW8, which were created in an earlier study...”
- Insights into denitrification in Methylotenera mobilis from denitrification pathway and methanol metabolism mutants
Mustakhimov, Journal of bacteriology 2013 - “...Km resistant mutant with lesion in the xoxF2 gene (mmol_2048). Mutants were selected on methylamine in the presence of Km and Gm, and double-crossover mutants...”
- “...mmol_1063) and each of two xoxF genes (mmol_1770 and mmol_2048) that encode homologs of the large subunit of methanol dehydrogenase (11, 14, 19, 20). In...”
- Comparative transcriptomics in three Methylophilaceae species uncover different strategies for environmental adaptation
Vorobev, PeerJ 2013 - “...1138, 1269, 1497-1499, 1896, 1897, 2516 ). The second xoxF homolog in M. mobilis JLW8, mmol_2048 was also slightly over-expressed in in situ conditions. The corresponding genes in M. versatilis 301 and M. glucosotrophus SIP3-4 were also most highly expressed in situ , compared to the...”
- An integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in Methylotenera mobilis
Beck, Journal of bacteriology 2011 - “...NADH:flavin oxidoreductase Mmol_0791 Mmol_1770 Mmol_2045 Mmol_2047 Mmol_2048 Mmol_0733 899.3 3.5 819.0 500.0 306.1 731.5 Nitrogen metabolism Nitrogen regulatory...”
- “...more abundant on methanol (150-fold), while the other (Mmol_2048) was present at similar, relatively high abundances on both methanol and methylamine (Table 1)....”
B1N7J5 alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) from Pseudomonas putida (see paper)
pedH / GI|150014706 quinoprotein decanol dehydrogenase; EC 1.1.-.- from Pseudomonas putida (see paper)
25% identity, 43% coverage
LUH_PSESP / Q934G0 Lupanine 17-hydroxylase [cytochrome c]; Quinohemoprotein lupanine hydroxylase; EC 1.17.2.2 from Pseudomonas sp. (see 2 papers)
Q934G0 lupanine 17-hydroxylase (cytochrome c) (EC 1.17.2.2) from Pseudomonas sp. (see 2 papers)
luh / GI|15485646 lupanine hydroxylase; EC 1.-.-.- from Pseudomonas sp. DH2001 (see paper)
24% identity, 78% coverage
- function: Catalyzes the first reaction in the catabolism of the alkaloid lupanine. It dehydrogenates lupanine, which can then be hydrated to produce 17-hydroxylupanine.
catalytic activity: lupanine + 2 Fe(III)-[cytochrome c] + H2O = 17-hydroxylupanine + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:32643)
cofactor: pyrroloquinoline quinone Note=Binds 1 PQQ group per subunit
cofactor: heme c Note=Binds 1 heme c group covalently per subunit
subunit: Monomer.
Mfla_2314 Pyrrolo-quinoline quinone from Methylobacillus flagellatus KT
23% identity, 76% coverage
- Lanpepsy is a novel lanthanide-binding protein involved in the lanthanide response of the obligate methylotroph Methylobacillus flagellatus
Hemmann, The Journal of biological chemistry 2023 - “...included known components of the lanthanome such as the Ln 3+ -dependent MDH XoxF (Mfla_0344, Mfla_2314), the c -type cytochrome XoxG (Mfla_2312), and the TonB-dependent receptor involved in Ln 3+ uptake (Mfla_1253). We also identified two 54 -dependent transcriptional regulators, Mfla_1254 and Mfla_0343. The gene Mfla_1254...”
- Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners
Haft, BMC genomics 2011 - “...136 -94.521 PQQ biosynthesis protein PqqB Mfla_1680 97 97 135 -94.521 PQQ biosynthesis protein PqqE Mfla_2314 73 80 157 -61.969 PQQ-dependent enzyme Mfla_1717 84 104 285 -61.969 PQQ-dependent enzyme Mfla_1451 84 108 282 -59.198 PQQ-dependent enzyme Mfla_2044 77 94 210 -57.525 PQQ-dependent enzyme Mfla_0344 79 100...”
- Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy
Hendrickson, Journal of bacteriology 2010 - “...are encoded in the genome (Mfla_344, Mfla_1451, Mfla_1717, and Mfla_2314). Of these, three were detected at low spectral counts and one was not detected (see...”
PEDH_PSEPK / Q88JH0 Quinoprotein alcohol dehydrogenase PedH; Lanthanide-dependent pyrroloquinoline quinone-dependent alcohol dehydrogenase; Lanthanide-dependent PQQ-ADH; EC 1.1.2.- from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) (see paper)
PP2679, PP_2679 quinoprotein ethanol dehydrogenase, putative from Pseudomonas putida KT2440
25% identity, 43% coverage
- function: Alcohol dehydrogenase that catalyzes the oxidation of a range of substrates, including linear and aromatic primary and secondary alcohols, as well as aldehydes, but only in the presence of lanthanides, allowing bacterial growth with a variety of volatile organic compounds (VOCs) as carbon and energy sources. Is also involved in the transcriptional regulation of pedE and pedH, most likely acting as a lanthanide sensory module (PubMed:28655819). Uses a specific inducible cytochrome c550, encoded by the adjacent gene in the locus, as electron acceptor (By similarity).
catalytic activity: a primary alcohol + 2 Fe(III)-[cytochrome c] = an aldehyde + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:51020)
catalytic activity: ethanol + 2 Fe(III)-[cytochrome c] = acetaldehyde + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:62200)
catalytic activity: butan-1-ol + 2 Fe(III)-[cytochrome c] = butanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:43432)
catalytic activity: butan-2-ol + 2 Fe(III)-[cytochrome c] = butan-2-one + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:79327)
catalytic activity: 2-phenylethanol + 2 Fe(III)-[cytochrome c] = 2- phenylacetaldehyde + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:79319)
catalytic activity: octan-1-ol + 2 Fe(III)-[cytochrome c] = octanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:79323)
catalytic activity: hexan-1-ol + 2 Fe(III)-[cytochrome c] = hexanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:79331)
catalytic activity: cinnamyl alcohol + 2 Fe(III)-[cytochrome c] = cinnamaldehyde + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:79335)
catalytic activity: farnesol + 2 Fe(III)-[cytochrome c] = farnesal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:79359)
catalytic activity: an aldehyde + 2 Fe(III)-[cytochrome c] + H2O = a carboxylate + 2 Fe(II)-[cytochrome c] + 3 H(+) (RHEA:79339)
catalytic activity: acetaldehyde + 2 Fe(III)-[cytochrome c] + H2O = 2 Fe(II)- [cytochrome c] + acetate + 3 H(+) (RHEA:79343)
catalytic activity: butanal + 2 Fe(III)-[cytochrome c] + H2O = butanoate + 2 Fe(II)-[cytochrome c] + 3 H(+) (RHEA:79347)
catalytic activity: hexanal + 2 Fe(III)-[cytochrome c] + H2O = hexanoate + 2 Fe(II)-[cytochrome c] + 3 H(+) (RHEA:79351)
catalytic activity: octanal + 2 Fe(III)-[cytochrome c] + H2O = octanoate + 2 Fe(II)-[cytochrome c] + 3 H(+) (RHEA:79355)
cofactor: Pr(3+) Nd(3+) La(3+) Ce(3+) Sm(3+) (Exhibits enzymatic activity only in the presence of lanthanide ions; maximal activity is observed with Pr(3+) and Nd(3+), and the activity decreases gradually with lanthanides with atomic masses higher than that of Nd(3+). PedH activity is found with lanthanide concentrations as low as 10 nM and up to 100 uM, with a peak in activity at 1 uM.)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit. {ECO:0000269|Ref.)3}
disruption phenotype: Cells lacking this gene grow efficiently with ethanol, 1-butanol, and 2-phenylethanol in the absence of La(3+), like wild-type strain, and the addition of 20 uM La(3+) to the agar medium restricts the growth of the mutant strain. Cells lacking both pedE and pedH show no growth under both conditions. - Changes in growth, lanthanide binding, and gene expression in <i>Pseudomonas alloputida</i> KT2440 in response to light and heavy lanthanides
Gorniak, mSphere 2024 - “...The Ln element-dependent gene expression ratios of the PQQ ADH-encoding genes pedE (PP_2674) and pedH (PP_2679) were calculated based on RPKM values ( B ). The figure shows a heatmap of gene expression with log2 CPM and fold change downregulation across samples. Features a scatter plot...”
- β-oxidation-polyhydroxyalkanoates synthesis relationship in Pseudomonas putida KT2440 revisited
Liu, Applied microbiology and biotechnology 2023 - “...mutants The genes of interest, including phaJ1 (PP_4552), phaJ4 (PP_4817), maoC (PP_0580), phaG (PP_1408), pedH (PP_2679), pedE (PP_2674) and hibch (PP_1412), in P. putida KT2440, were scarlessly deleted using modified CRISPR/Cas9 systems and methodology (Cook et al. 2018 ; Liu et al. 2022 ). All primers...”
- “...statistically significant fold change 2 were further analysed (Table S4). Two quinoprotein ethanol dehydrogenases, PedH (PP_2679) and PedE (PP_2674), which have been shown to participate in the metabolism of different substrates such as ethylene glycol and n-butanol (Muckschel et al. 2012 ; Simon et al. 2015...”
- Providing octane degradation capability to Pseudomonas putida KT2440 through the horizontal acquisition of oct genes located on an integrative and conjugative element
Duque, Environmental microbiology reports 2022 - “...octanal and of the latter to octanoic as we found that a PQQdependent alcohol dehydrogenase (PP_2679) and an aldehyde dehydrogenase (PP_2680) were induced. This agrees with the notion that octane is being oxidized to octanoic acid. Among the proteins with the higher fold change were enzymes...”
- “...octane, there were a set of membrane proteins (PP_2662, PP_2663 PP_2667, PP_2669, PP_2674, PP_2675, PP_2678, PP_2679 and PP_2680). FIGURE 3 Schematic representation of octane metabolism in the EM24. Octane likely enters the cells via porins and is oxidized to octanoic acid at the membrane level. Upon...”
- Genome analysis of the metabolically versatile Pseudomonas umsongensis GO16: the genetic basis for PET monomer upcycling into polyhydroxyalkanoates
Narancic, Microbial biotechnology 2021 - “...2017 ). In P. putida KT2440 this function is assigned to PedE (PP_2674) and PedH (PP_2679) (Wehrmann etal ., 2017 ). In the next step, catalysed by cytoplasmic aldehyde dehydrogenases PedI (PP_2680) and PP_0545 in KT2440, glycolaldehyde is converted to glycolate, followed by oxidation to glyoxylate...”
- “...gene pedI F6476_19660 Aldehyde dehydrogenase 100 92 PP_2680 pedH F6476_19665 Quinoprotein ethanol dehydrogenase 99 91 PP_2679 pedE F6476_19690 PQQ dependent dehydrogenase 100 94 PP_2674 aldBI F6476_27375 Aldehyde dehydrogenase 100 92 PP_0545 gcl F6476_01220 Carboxylate ligase 100 86 PP_4297 hyi F6476_01215 Hydroxypyruvate isomerase 100 78 PP_4298 glxR...”
- Dehydrogenation Mechanism of Three Stereoisomers of Butane-2,3-Diol in Pseudomonas putida KT2440
Liu, Frontiers in bioengineering and biotechnology 2021 - “...,3 R )-2,3-BDO and meso -2,3-BDO dehydrogenation. Two quinoprotein alcohol dehydrogenases, PedE (PP2674) and PedH (PP2679), were confirmed to be responsible for (2 S ,3 S )-2,3-BDO dehydrogenation. The function redundancy and inverse regulation of PedH and PedE by lanthanide availability provides a mechanism for the...”
- “...Utilization of P. putida KT2440 Two pyrroloquinoline quinone (PQQ)-dependent ethanol dehydrogenases (PQQ-EDHs), PP2674 (PedE) and PP2679 (PedH), were annotated in the genome of P. putida KT2440. PedH and PedE exhibit enzyme activity toward a range of substrates, including 2,3-BDO ( Takeda et al., 2013 ; Wehrmann...”
- Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing
Thompson, Applied and environmental microbiology 2020 (secret) - The Cellular Response to Lanthanum Is Substrate Specific and Reveals a Novel Route for Glycerol Metabolism in Pseudomonas putida KT2440
Wehrmann, mBio 2020 - “...La 3+ during growth on all tested carbon sources. The Ln 3+ -dependent PQQ-ADH PedH (PP_2679) showed increased abundance in response to La 3+ during growth on glucose, glycerol, and 2-phenylethanol, whereas an uncharacterized pentapeptide repeat-containing protein (PP_2673) that is encoded by a gene directly upstream...”
- “...(log 2 ) log 10 ( P value) PP_2426 CalA Coniferyl alcohol dehydrogenase 6.28 4.03 PP_2679 PedH Quinoprotein ethanol dehydrogenase 4.75 3.80 PP_3426 MexF Multidrug efflux RND transporter 3.93 3.24 PP_3425 MexE Efflux transporter RND family 3.74 2.18 PP_4921 Transporter, NCS1 nucleoside transporter family 3.65 2.46...”
- Engineering thermal stability and solvent tolerance of the soluble quinoprotein PedE from Pseudomonas putida KT2440 with a heterologous whole-cell screening approach
Wehrmann, Microbial biotechnology 2018 - “...lanthanide (Ln 3+ )dependent PQQADHs from different organisms, namely PedE (Ca 2+ ) and PedH (PP_2679; Ln 3+ ) of P.putida KT2440 (Takeda etal ., 2013 ; Wehrmann etal ., 2017 ) as well as ExaA (PA1982; Ca 2+ ) of Pseudomonas aeruginosa (Rupp and Grisch,...”
- More
6zcvA / Q88JH0 Crystal structure of lanthanide-dependent alcohol dehydrogenase pedh from pseudomonas putida kt2440
25% identity, 43% coverage
- Ligands: calcium ion; pyrroloquinoline quinone (6zcvA)
Minf_0992 Methanol dehydrogenase large subunit protein from Methylacidiphilum infernorum V4
24% identity, 67% coverage
- Growth on Formic Acid Is Dependent on Intracellular pH Homeostasis for the Thermoacidophilic Methanotroph Methylacidiphilum sp. RTK17.1
Carere, Frontiers in microbiology 2021 - “...growth. Nevertheless, in response to formic acid-dependent growth, genes encoding the lanthanide-dependent methanol dehydrogenase, xoxF (Minf_0992; 1.72 Log 2 FC, p = 0.014) and xoxJ (Minf_0995; 3.69 Log 2 FC, p < 0.001), were down regulated. Transcriptional regulation of these XoxF-type methanol dehydrogenase genes has previously...”
- Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia
Hou, Biology direct 2008 - “...7 ]. A homologue of mxaF (or xoxF ), encoding the methanol dehydrogenase large subunit (Minf_0992), was identified in the M. infernorum genome together with genes for two proteins required for its catalytic function: a methanol-binding periplasmic protein (Minf_0995) and a cytochrome c family protein (Minf_0996)....”
- “...wide specificity spectrum. The genome of M. infernorum encodes only one protein from this family (Minf_0992). Other potential activities of this enzyme, i.e. glucose dehydrogenase or alcohol dehydrogenase, seem unlikely: glucose dehydrogenase is rarely found in autotrophic organisms, and there are better candidates (e.g., Minf_0269, Minf_1850)...”
Mfla_1451 Pyrrolo-quinoline quinone from Methylobacillus flagellatus KT
26% identity, 46% coverage
- Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners
Haft, BMC genomics 2011 - “...PqqE Mfla_2314 73 80 157 -61.969 PQQ-dependent enzyme Mfla_1717 84 104 285 -61.969 PQQ-dependent enzyme Mfla_1451 84 108 282 -59.198 PQQ-dependent enzyme Mfla_2044 77 94 210 -57.525 PQQ-dependent enzyme Mfla_0344 79 100 268 -56.680 PQQ-dependent enzyme Mfla_1681 53 53 83 -51.646 PQQ biosynthesis protein PqqD Mfla_2043...”
- Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy
Hendrickson, Journal of bacteriology 2010 - “...of MDH, MxaF, are encoded in the genome (Mfla_344, Mfla_1451, Mfla_1717, and Mfla_2314). Of these, three were detected at low spectral counts and one was not...”
F6476_19665 PQQ-dependent methanol/ethanol family dehydrogenase from Pseudomonas umsongensis
25% identity, 43% coverage
exaA / Q9Z4J7 alcohol dehydrogenase (cytochrome c550) monomer (EC 1.1.2.8) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 4 papers)
QEDH_PSEAE / Q9Z4J7 Quinoprotein ethanol dehydrogenase; QEDH; Quinoprotein alcohol dehydrogenase (cytochrome c); Quinoprotein alcohol dehydrogenase (cytochrome c550); EC 1.1.2.8 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 6 papers)
Q9Z4J7 alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) from Pseudomonas aeruginosa (see paper)
NP_250672 quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa PAO1
PA1982 quinoprotein alcohol dehydrogenase from Pseudomonas aeruginosa PAO1
25% identity, 44% coverage
- function: Catalyzes the oxidation of ethanol and other primary alcohols to the corresponding aldehydes, except methanol, which is a very poor substrate. Uses a specific inducible cytochrome c550, encoded by the adjacent gene in the locus, as electron acceptor. Is a key enzyme of the carbon and energy metabolism during growth of P.aeruginosa on ethanol as the sole carbon and energy source. Is also able to use secondary alcohols as well as aminoalcohols like ethanolamine and 1- amino-2-propanol, and aldehydes as substrates.
catalytic activity: a primary alcohol + 2 Fe(III)-[cytochrome c] = an aldehyde + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:51020)
catalytic activity: ethanol + 2 Fe(III)-[cytochrome c] = acetaldehyde + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:62200)
catalytic activity: butan-1-ol + 2 Fe(III)-[cytochrome c] = butanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:43432)
catalytic activity: propan-2-ol + 2 Fe(III)-[cytochrome c] = acetone + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:62196)
catalytic activity: 1-propanol + 2 Fe(III)-[cytochrome c] = propanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:62204)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group non-covalently per subunit (PubMed:10736230, PubMed:3144289). PQQ is embedded between the ring structure formed from a disulfide bridge between adjacent cysteines Cys-139 and Cys-140 and the indole ring of Trp-282 (PubMed:10736230).)
cofactor: Ca(2+) (Binds 2 calcium ions per subunit. One is located in the active- site cavity near PQQ and the second calcium binds at the N-terminus and contributes to the stability of the native enzyme.)
subunit: Homodimer. Interacts with cytochrome c550 (PubMed:19224199). - PQQ-dependent alcohol dehydrogenase (QEDH) of Pseudomonas aeruginosa is involved in catabolism of acyclic terpenes.
Chattopadhyay, Journal of basic microbiology 2010 (PubMed)- GeneRIF: Inactivation of PA1982 by insertion mutagenesis resulted in inability of the mutant to utilise ethanol and in reduced growth on geraniol.
- Structure of the pyrroloquinoline quinone radical in quinoprotein ethanol dehydrogenase.
Kay, The Journal of biological chemistry 2006 (PubMed)- GeneRIF: Quinoprotein alcohol dehydrogenases use the pyrroloquinoline quinone cofactor to catalyze the oxidation of alcohols.
- Convergent Within-Host Adaptation of Pseudomonas aeruginosa through the Transcriptional Regulatory Network
Gatt, mSystems 2023 - “...when growing on ethanol ( 37 ). This PQQ-dependent system comprises a quinoprotein ethanol dehydrogenase (PA1982), cytochrome C550 (PA1983), and an NAD-dependent acetaldehyde dehydrogenase (PA1984). The genes encoding all these components have high HS and low mROS values ( Fig.4A ; TableS2 ) (mROS, 0.2 to...”
- Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype
Thöming, NPJ biofilms and microbiomes 2020 - “...PA0466 2.9 PA14_38850 PA1983 exaB 6.8 PA14_04650 PA0355 pfpI 3.2 PA14_06180 PA0472 fiuI 2.5 PA14_38860 PA1982 exaA 5.8 PA14_06650 PA0509 nirN 3.0 PA14_07355 PA0565 3.6 PA14_38880 PA1981 5.7 PA14_06660 PA0510 nirE 3.3 PA14_09980 PA4167 dkgB 2.7 PA14_38900 PA1980 exaE 2.9 PA14_06670 PA0511 nirJ 3.5 PA14_10170 PA4159...”
- Engineering thermal stability and solvent tolerance of the soluble quinoprotein PedE from Pseudomonas putida KT2440 with a heterologous whole-cell screening approach
Wehrmann, Microbial biotechnology 2018 - “...KT2440 (Takeda etal ., 2013 ; Wehrmann etal ., 2017 ) as well as ExaA (PA1982; Ca 2+ ) of Pseudomonas aeruginosa (Rupp and Grisch, 1988 ; Chattopadhyay etal ., 2010 ), were expressed in E.coli BL21(DE3) cells and activities for all enzymes were determined. With...”
- The Pseudomonas aeruginosa Isohexenyl Glutaconyl Coenzyme A Hydratase (AtuE) Is Upregulated in Citronellate-Grown Cells and Belongs to the Crotonase Family
Poudel, Applied and environmental microbiology 2015 - “...dehydrogenase with verified terpene alcohol dehydrogenase activity (PA1982, exaA) were increased in abundance (27). Interestingly, the abundance of a gene...”
- “...12, 2017 by University of California, Berkeley PA1535 PA1982 PA1984 PA2011 PA2012 PA2013 PA2014 PA2015 PA2886 PA2887 PA2888 PA2889 PA2890 PA2891 PA2892 PA4330...”
- Flexible survival strategies of Pseudomonas aeruginosa in biofilms result in increased fitness compared with Candida albicans
Purschke, Molecular & cellular proteomics : MCP 2012 - “...A ToxA (PA1148), quinoprotein ethanol dehydrogenase ExaA (PA1982), heme acquisition protein HasAp (PA3407), and two unknown proteins related to ferric...”
- “...of the periplasma localized quinoprotein ethanol dehydrogenase ExaA (PA1982) is induced at later time points indicating the appearance of alcohols in the medium...”
- The biofilm-specific antibiotic resistance gene ndvB is important for expression of ethanol oxidation genes in Pseudomonas aeruginosa biofilms
Beaudoin, Journal of bacteriology 2012 - “...PA3044 PA2715 PA2700 PA2210 PA1989 PA1987 PA1986 PA1983 PA1982 PA1980 PA1978 PA1976 PA1975 PA1015 PA0931 PA4407 PA4540 PA4857 PA4894 PA5312 PA5397 2.36 2.76...”
- PQQ-dependent alcohol dehydrogenase (QEDH) of Pseudomonas aeruginosa is involved in catabolism of acyclic terpenes
Chattopadhyay, Journal of basic microbiology 2010 (PubMed)- “...isovalerate-grown cells. The spot was identified as PA1982 gene product a pyrroloquinoline quinone (PQQ) dependent ethanol oxidoreductase (QEDH). Inactivation...”
- “...was restored by transferring an intact copy of the PA1982 gene into the mutant. The PA1982 gene product was purified from recombinant Escherichia coli and...”
- Induction by cationic antimicrobial peptides and involvement in intrinsic polymyxin and antimicrobial peptide resistance, biofilm formation, and swarming motility of PsrA in Pseudomonas aeruginosa
Gooderham, Journal of bacteriology 2008 - “...PA1648 PA1649 PA1650 PA1828 PA1881 PA1883 PA1927 PA1976 PA1978 PA1982 PA1983 PA1984 PA1985 PA2124 PA2277 PA2278 PA2339 PA2350 coxA mdcR clpC 3.4 4.8 3.5 3.2 4.8...”
- More
BJA_RS38750 pyrroloquinoline quinone-dependent dehydrogenase from Bradyrhizobium diazoefficiens USDA 110
26% identity, 49% coverage
- Isolation and Characterization of High-Temperature-Tolerant Mutants of Bradyrhizobium diazoefficiens USDA110 by Carbon-Ion Beam Irradiation
Satoh, Microorganisms 2024 - “...kinase Asn192Asp 6,724,936 AT > CG BJA_RS30910 SOS response-associated peptidase Asn128Thr 8,383,126 AT > CG BJA_RS38750 PQQ-binding-like beta-propeller repeat protein Leu71Arg 8,637,494 1 bp BJA_RS39985 Adenylate/guanylate cyclase domain-containing protein frameshift M14 strain Position Mutation Gene Annotation Alteration 2,002,453 AT > GC BJA_RS09250 Hypothetical protein His177Arg 2,201,526...”
PA14_38860 PQQ-linked alcohol dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
25% identity, 44% coverage
1flgA / Q9Z4J7 Crystal structure of the quinoprotein ethanol dehydrogenase from pseudomonas aeruginosa (see paper)
25% identity, 44% coverage
- Ligands: calcium ion; pyrroloquinoline quinone (1flgA)
azo2972 ExaA2 protein from Azoarcus sp. BH72
22% identity, 79% coverage
- Defining the Genetic Basis of Plant⁻Endophytic Bacteria Interactions
Pinski, International journal of molecular sciences 2019 - “...the plant, increased sensitivity to formaldehyde and methanol [ 51 ] Azoarcus sp. BH72 exaA2 (azo2972) quino(hemo)protein alcohol dehydrogenase, pyrroloquinoline quinone (PQQ)-dependent (EC 1.1.2.8) O. sativa subsp. indica cv. IR36 decrease in root colonisation [ 52 ] Azoarcus sp. BH72 exaA3 (azo2975) quino(hemo)protein alcohol dehydrogenase, PQQ-dependent...”
Maq22A_c07235 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylobacterium aquaticum
24% identity, 77% coverage
- Lanthanide-Dependent Methanol and Formaldehyde Oxidation in Methylobacterium aquaticum Strain 22A
Yanpirat, Microorganisms 2020 - “...the mxa cluster was downregulated and that of the xox cluster was upregulated; a gene (Maq22A_c07235) encoding a putative ExaF-type alcohol dehydrogenase (ADH) was also upregulated. Second, the genes for formaldehyde oxidation (H 4 MPT pathway and glutathione-dependent formaldehyde dehydrogenase, GSH pathway) were downregulated. Third, strain...”
- “...our previous study [ 38 ]. Gene deletion mutants for xoxF2 (Maq22A_c27990), adh4 (Maq22A_1p32165), exaF (Maq22A_c07235), adh6 (Maq22A_1p30675), and mxbD (Maq22A_c05310) were generated using the allele-replacement vector pK18mobSacB as previously reported [ 38 , 39 ]. In brief, each 1 kb upstream and downstream region of...”
MDMS009_1767 methanol/ethanol family PQQ-dependent dehydrogenase from Methylophaga thiooxydans DMS010
27% identity, 44% coverage
- Identification of Proteins and Genes Expressed by Methylophaga thiooxydans During Growth on Dimethylsulfide and Their Presence in Other Members of the Genus
Kröber, Frontiers in microbiology 2019 - “...tag MDMS009_1502 encoding the alpha subunit, and MDMS009_1410, beta subunit) and three XoxF-type methanol dehydrogenases (MDMS009_1767, _2058, and _2642) which are homologs of the MDH enzymes shown to require rare earth elements as co-factors ( Keltjens et al., 2014 ). Genes pqqBCDE (encoded by MDMS009_2015, MDMS009_1956,...”
- “...in a four gene cluster in the vicinity of two of the XoxF encoding genes (MDMS009_1767 and MDMS009_2058). Formaldehyde Metabolism Formaldehyde generated through primary metabolism of C 1 substrates such as methanol, DMS and methanethiol can be conjugated to tetrahydromethanopterin (H 4 MPT) by formaldehyde activating...”
XOXF_METFB / I0JWN7 Lanthanide-dependent methanol dehydrogenase; Lanthanide-dependent MDH; Ln(3+)-dependent MDH; Ln-MDH; EC 1.1.2.10 from Methylacidiphilum fumariolicum (strain SolV) (see 2 papers)
27% identity, 45% coverage
- function: Catalyzes the oxidation of methanol to formaldehyde or formate in the presence of lanthanides (Ln). Is a key enzyme in methane/methanol metabolism, allowing M.fumariolicum to grow on methane as the sole carbon and energy source. Can also act on other primary alcohols in vitro, such as ethanol, 1-propanol, 1-butanol, and 1- hexanol, but is not able to oxidize secondary alcohols and acetaldehyde (PubMed:24034209). Uses a specific cytochrome cL, encoded by the adjacent gene in the locus, as electron acceptor (By similarity).
catalytic activity: 2 Fe(III)-[cytochrome cL] + methanol = 2 Fe(II)-[cytochrome cL] + formaldehyde + 2 H(+) (RHEA:51008)
catalytic activity: 4 Fe(III)-[cytochrome cL] + methanol + H2O = 4 Fe(II)- [cytochrome cL] + formate + 5 H(+) (RHEA:56272)
catalytic activity: 2 Fe(III)-[cytochrome cL] + a primary alcohol = 2 Fe(II)- [cytochrome cL] + an aldehyde + 2 H(+) (RHEA:51004)
cofactor: Ce(3+) La(3+) Nd(3+) Pr(3+) Eu(3+) (Appears to be able to bind and use several lanthanides. Binds one lanthanide ion per subunit.)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit.)
subunit: Homodimer.
4maeA / I0JWN7 Methanol dehydrogenase from methylacidiphilum fumariolicum solv (see paper)
27% identity, 45% coverage
- Ligands: cerium (iii) ion; pyrroloquinoline quinone (4maeA)
V5SGT2 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Hyphomicrobium nitrativorans (see paper)
23% identity, 75% coverage
BN844_0564 quinoprotein ethanol dehydrogenase from Pseudomonas sp. SHC52
23% identity, 44% coverage
A0A0A8K0T2 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Methyloceanibacter caenitepidi (see paper)
GL4_1130 PQQ-dependent dehydrogenase, methanol/ethanol family from Methyloceanibacter caenitepidi
24% identity, 78% coverage
- Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8
Takeuchi, PloS one 2019 - “...small subunit mxaI 18826 21130 0.17 0.041 GL4_0437 Methanol dehydrogenase xoxF1 1117 1368 0.29 0.001 GL4_1130 Methanol dehydrogenase xoxF2 80 98 0.29 0.001 GL4_1360 Methanol dehydrogenase xoxF3 1123 547 -1.04 0.000 GL4_1361 Methanol dehydrogenase xoxF4 1918 1115 -0.78 0.000 Serine cycle GL4_1969 Serine hydroxymethyltransferase glyA 523...”
- “...the expression of GL4_1360 and 1361 was significantly downregulated, whereas the expression of GL4_0437 and GL4_1130 was upregulated with log2FC values of 0.29 in co-culture ( S5 Fig , Table 1 ). These results highlighted the divergent response of xoxF genes in M . caenitepidi Gela4...”
MDMS009_2058 methanol/ethanol family PQQ-dependent dehydrogenase from Methylophaga thiooxydans DMS010
26% identity, 44% coverage
PS417_17460 Quinoprotein ethanol dehydrogenase QedA (EC 1.1.2.8) from Pseudomonas simiae WCS417
25% identity, 44% coverage
- mutant phenotype: Important for ethanol utilization. Milder phenotypes on L-Arginine and L-Citrulline are not explained. 90% identical to A8R3S4 , which acts on longer primary alcohols as well
A0A0A8JZD4 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Methyloceanibacter caenitepidi (see paper)
GL4_0437 PQQ-dependent dehydrogenase, methanol/ethanol family from Methyloceanibacter caenitepidi
22% identity, 77% coverage
- Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8
Takeuchi, PloS one 2019 - “...In addition, four genes encoding a methanol dehydrogenase large subunit similar to xoxF were found (GL4_0437, 1130, 1360, and 1361). The amino acid sequences of four XoxF proteins shared 70%94% identity with each other. All genes coding for enzymes involved in tetrahydromethanopterin (H 4 MPT)-mediated (...”
- “...mxaG 7201 6546 -0.14 0.074 GL4_0424 Methanol dehydrogenase, small subunit mxaI 18826 21130 0.17 0.041 GL4_0437 Methanol dehydrogenase xoxF1 1117 1368 0.29 0.001 GL4_1130 Methanol dehydrogenase xoxF2 80 98 0.29 0.001 GL4_1360 Methanol dehydrogenase xoxF3 1123 547 -1.04 0.000 GL4_1361 Methanol dehydrogenase xoxF4 1918 1115 -0.78...”
QEDH_PSEPU / A8R3S4 Quinoprotein ethanol dehydrogenase; QEDH; Quinoprotein alcohol dehydrogenase (cytochrome c); Quinoprotein alcohol dehydrogenase (cytochrome c550); Quinoprotein alcohol dehydrogenase ADH I; ADH I; EC 1.1.2.8 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see 3 papers)
24% identity, 44% coverage
- function: Catalyzes the oxidation of ethanol and other primary alcohols to the corresponding aldehydes, except methanol, which is not a substrate (PubMed:7730276). Uses a specific inducible cytochrome c550, encoded by the adjacent gene in the locus, as electron acceptor (By similarity). Is a key enzyme of the carbon and energy metabolism during growth of P.putida on ethanol as the sole carbon and energy source (PubMed:18218017). Displays lower activity on secondary alcohols, aldehydes and diols. Is not active with sugar alcohols such as glycerol and D-sorbitol (PubMed:7730276). In vitro, reacts well with phenazine methosulfate (PMS) as an electron acceptor but not with NAD(P), potassium ferricyanide, or molecular oxygen (PubMed:7730276).
catalytic activity: a primary alcohol + 2 Fe(III)-[cytochrome c] = an aldehyde + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:51020)
catalytic activity: ethanol + 2 Fe(III)-[cytochrome c] = acetaldehyde + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:62200)
catalytic activity: ethanol + A = acetaldehyde + AH2 (RHEA:33567)
catalytic activity: 1-propanol + 2 Fe(III)-[cytochrome c] = propanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:62204)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group non-covalently per subunit (PubMed:7730276). PQQ is inserted between disulfide Cys-139-Cys-140 and the plane of Trp-282 (By similarity).)
cofactor: Ca(2+) (Binds 2 calcium ions per subunit. One is located in the active- site cavity near PQQ and the second calcium binds at the N-terminus and contributes to the stability of the native enzyme.)
subunit: Homodimer.
disruption phenotype: Cells lacking this gene show a strong reduction in the growth rate on ethanol, however growth on 1-butanol or 1,2- propanediol is not influenced.
F6476_19690 quinoprotein ethanol dehydrogenase from Pseudomonas umsongensis
24% identity, 44% coverage
Dshi_2673 Pyrrolo-quinoline quinone from Dinoroseobacter shibae DFL 12
24% identity, 43% coverage
PEDE_PSEPK / Q88JH5 Quinoprotein alcohol dehydrogenase PedE; Ca(2+)-dependent pyrroloquinoline quinone-dependent alcohol dehydrogenase; Ca(2+)-dependent PQQ-ADH; EC 1.1.2.8 from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) (see paper)
Q88JH5 alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) from Pseudomonas putida (see 2 papers)
PP2674, PP_2674 quinoprotein ethanol dehydrogenase from Pseudomonas putida KT2440
24% identity, 44% coverage
- function: Alcohol dehydrogenase that catalyzes the oxidation of a range of substrates, including linear and aromatic primary and secondary alcohols, as well as aldehydes, allowing bacterial growth with a variety of volatile organic compounds (VOCs) as carbon and energy sources (PubMed:28655819). Uses a specific inducible cytochrome c550, encoded by the adjacent gene in the locus, as electron acceptor (By similarity).
catalytic activity: a primary alcohol + 2 Fe(III)-[cytochrome c] = an aldehyde + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:51020)
catalytic activity: ethanol + 2 Fe(III)-[cytochrome c] = acetaldehyde + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:62200)
catalytic activity: butan-1-ol + 2 Fe(III)-[cytochrome c] = butanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:43432)
catalytic activity: butan-2-ol + 2 Fe(III)-[cytochrome c] = butan-2-one + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:79327)
catalytic activity: 2-phenylethanol + 2 Fe(III)-[cytochrome c] = 2- phenylacetaldehyde + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:79319)
catalytic activity: octan-1-ol + 2 Fe(III)-[cytochrome c] = octanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:79323)
catalytic activity: hexan-1-ol + 2 Fe(III)-[cytochrome c] = hexanal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:79331)
catalytic activity: cinnamyl alcohol + 2 Fe(III)-[cytochrome c] = cinnamaldehyde + 2 Fe(II)-[cytochrome c] + 2 H(+) (RHEA:79335)
catalytic activity: farnesol + 2 Fe(III)-[cytochrome c] = farnesal + 2 Fe(II)- [cytochrome c] + 2 H(+) (RHEA:79359)
catalytic activity: an aldehyde + 2 Fe(III)-[cytochrome c] + H2O = a carboxylate + 2 Fe(II)-[cytochrome c] + 3 H(+) (RHEA:79339)
catalytic activity: acetaldehyde + 2 Fe(III)-[cytochrome c] + H2O = 2 Fe(II)- [cytochrome c] + acetate + 3 H(+) (RHEA:79343)
catalytic activity: butanal + 2 Fe(III)-[cytochrome c] + H2O = butanoate + 2 Fe(II)-[cytochrome c] + 3 H(+) (RHEA:79347)
catalytic activity: hexanal + 2 Fe(III)-[cytochrome c] + H2O = hexanoate + 2 Fe(II)-[cytochrome c] + 3 H(+) (RHEA:79351)
catalytic activity: octanal + 2 Fe(III)-[cytochrome c] + H2O = octanoate + 2 Fe(II)-[cytochrome c] + 3 H(+) (RHEA:79355)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group non-covalently per subunit.)
cofactor: Ca(2+) (Binds 2 calcium ions per subunit. One is located in the active- site cavity near PQQ and the second calcium binds at the N-terminus and contributes to the stability of the native enzyme.)
subunit: Homodimer. Interacts with cytochrome c550.
disruption phenotype: Cells lacking this gene are unable to grow with ethanol, 1-butanol, and 2-phenylethanol in the absence of La(3+), but the addition of 20 uM La(3+) to the agar medium restores the growth of the mutant strain. Cells lacking both pedE and pedH show no growth under both conditions. - Changes in growth, lanthanide binding, and gene expression in <i>Pseudomonas alloputida</i> KT2440 in response to light and heavy lanthanides
Gorniak, mSphere 2024 - “...; Tables S4 to S13) (log 2 FC values between 1.29 and 6.98). Only pedE (PP_2674) was differentially expressed when comparing incubations with Er and without added Ln (log 2 FC 0.96). Depending on the added Ln element, pedE gene expression differed by more than two...”
- “...gene is reduced. The Ln element-dependent gene expression ratios of the PQQ ADH-encoding genes pedE (PP_2674) and pedH (PP_2679) were calculated based on RPKM values ( B ). The figure shows a heatmap of gene expression with log2 CPM and fold change downregulation across samples. Features...”
- Genome-scale metabolic model of the versatile bacterium Paracoccus denitrificans Pd1222
Bordel, mSystems 2024 - “...P. putida KT2440 BLAST matches in the proteome of P. denitrificans E -scores from BLAST PP_2674 peg.20 peg.3083 E = 4 10 89 E = 2 10 86 PP_2680 peg.2425 peg.5153 E = 0 E = 10 80 PP_2049 peg.245 peg.4723 E = 10 63 E...”
- β-oxidation-polyhydroxyalkanoates synthesis relationship in Pseudomonas putida KT2440 revisited
Liu, Applied microbiology and biotechnology 2023 - “...genes of interest, including phaJ1 (PP_4552), phaJ4 (PP_4817), maoC (PP_0580), phaG (PP_1408), pedH (PP_2679), pedE (PP_2674) and hibch (PP_1412), in P. putida KT2440, were scarlessly deleted using modified CRISPR/Cas9 systems and methodology (Cook et al. 2018 ; Liu et al. 2022 ). All primers and DNA...”
- “...change 2 were further analysed (Table S4). Two quinoprotein ethanol dehydrogenases, PedH (PP_2679) and PedE (PP_2674), which have been shown to participate in the metabolism of different substrates such as ethylene glycol and n-butanol (Muckschel et al. 2012 ; Simon et al. 2015 ; Wehrmann et...”
- Providing octane degradation capability to Pseudomonas putida KT2440 through the horizontal acquisition of oct genes located on an integrative and conjugative element
Duque, Environmental microbiology reports 2022 - “...the presence of octane, there were a set of membrane proteins (PP_2662, PP_2663 PP_2667, PP_2669, PP_2674, PP_2675, PP_2678, PP_2679 and PP_2680). FIGURE 3 Schematic representation of octane metabolism in the EM24. Octane likely enters the cells via porins and is oxidized to octanoic acid at the...”
- Genome analysis of the metabolically versatile Pseudomonas umsongensis GO16: the genetic basis for PET monomer upcycling into polyhydroxyalkanoates
Narancic, Microbial biotechnology 2021 - “...Wehrmann etal ., 2017 ). In P. putida KT2440 this function is assigned to PedE (PP_2674) and PedH (PP_2679) (Wehrmann etal ., 2017 ). In the next step, catalysed by cytoplasmic aldehyde dehydrogenases PedI (PP_2680) and PP_0545 in KT2440, glycolaldehyde is converted to glycolate, followed by...”
- “...pedH F6476_19665 Quinoprotein ethanol dehydrogenase 99 91 PP_2679 pedE F6476_19690 PQQ dependent dehydrogenase 100 94 PP_2674 aldBI F6476_27375 Aldehyde dehydrogenase 100 92 PP_0545 gcl F6476_01220 Carboxylate ligase 100 86 PP_4297 hyi F6476_01215 Hydroxypyruvate isomerase 100 78 PP_4298 glxR F6476_01210 Tartronate reductase 100 86 PP_4299 ttuD F6476_01205...”
- Dehydrogenation Mechanism of Three Stereoisomers of Butane-2,3-Diol in Pseudomonas putida KT2440
Liu, Frontiers in bioengineering and biotechnology 2021 - “...in (2 R ,3 R )-2,3-BDO and meso -2,3-BDO dehydrogenation. Two quinoprotein alcohol dehydrogenases, PedE (PP2674) and PedH (PP2679), were confirmed to be responsible for (2 S ,3 S )-2,3-BDO dehydrogenation. The function redundancy and inverse regulation of PedH and PedE by lanthanide availability provides a...”
- “...,3 S )-2,3-BDO Utilization of P. putida KT2440 Two pyrroloquinoline quinone (PQQ)-dependent ethanol dehydrogenases (PQQ-EDHs), PP2674 (PedE) and PP2679 (PedH), were annotated in the genome of P. putida KT2440. PedH and PedE exhibit enzyme activity toward a range of substrates, including 2,3-BDO ( Takeda et al.,...”
- Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing
Thompson, Applied and environmental microbiology 2020 (secret) - Unraveling 1,4-Butanediol Metabolism in Pseudomonas putida KT2440
Li, Frontiers in microbiology 2020 - “...highest expressed proteins during growth on glucose as well as 1,4-butanediol were PedE (ethanol dehydrogenase PP_2674), PedI (aldehyde dehydrogenase PP_2680) and Tu-B (PP_0452), an elongation factor which is involved in the regulation of protein synthesis by mediating aminoacyl tRNA into a free site of ribosomes (...”
- More
pedE / B1N7J0 quinoprotein alcohol dehydrogenase from Pseudomonas putida (see 5 papers)
B1N7J0 alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) from Pseudomonas putida (see paper)
pedE / GI|150014701 quinoprotein phenylethanol dehydrogenase; EC 1.1.-.- from Pseudomonas putida (see paper)
24% identity, 44% coverage
- CharProtDB mutant studies suggest PedE oxidizes phenylethanol and C6 to C9 aliphatic alcohols (PMID|18177365)
NGR_b03250 alcohol dehydrogenase from Rhizobium sp. NGR234
NGR_b03250 PQQ-dependent methanol/ethanol family dehydrogenase from Sinorhizobium fredii NGR234
23% identity, 43% coverage
A0A0A8K4A4 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Methyloceanibacter caenitepidi (see paper)
GL4_1361 PQQ-dependent dehydrogenase, methanol/ethanol family from Methyloceanibacter caenitepidi
23% identity, 78% coverage
Mmol_1770 PQQ-dependent dehydrogenase, methanol/ethanol family from Methylotenera mobilis JLW8
25% identity, 46% coverage
- Lanthanide-Dependent Methanol Dehydrogenases of XoxF4 and XoxF5 Clades Are Differentially Distributed Among Methylotrophic Bacteria and They Reveal Different Biochemical Properties
Huang, Frontiers in microbiology 2018 - “...et al., 2006 XoxF4-1 mutant ( mmol_2048 ) Mustakhimov et al., 2013 XoxF4-2 mutant ( mmol_1770 ) Mustakhimov et al., 2013 XoxF4-1 XoxF4-2 double mutant ( mmol_1770 mmol_2048 ) Mustakhimov et al., 2013 XoxF4-1 XoxF4-2 double mutant expressing xoxF4-1his ( mmol_2048his ) This study XoxF4-1 XoxF4-2...”
- “...Mustakhimov et al., 2013 ) was used to express XoxF4-1 and XoxF4-2 (proteins Mmol_2048 and Mmol_1770, respectively; Lapidus et al., 2011 ). This mutant carries a kanamycin resistance gene cassette in place of xoxF4-1 and a gentamicin gene cassette in place of xoxF4-2 ( Mustakhimov et...”
- Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions
Krause, Proceedings of the National Academy of Sciences of the United States of America 2017 - “...MDH mutants xoxF1 (mmol_1170), xoxF2 (mmol_2048), and xoxF12 (mmol_1770, mmol_2048) of M. mobilis JLW8, which were created in an earlier study (38). M....”
- Insights into denitrification in Methylotenera mobilis from denitrification pathway and methanol metabolism mutants
Mustakhimov, Journal of bacteriology 2013 - “...the original pCM184based construct for mutating gene xoxF1 (mmol_1770) was replaced by a gentamicin (Gm) resistance gene, which was amplified from the vector...”
- “...(Nod; mmol_1063) and each of two xoxF genes (mmol_1770 and mmol_2048) that encode homologs of the large subunit of methanol dehydrogenase (11, 14, 19,...”
- Comparative transcriptomics in three Methylophilaceae species uncover different strategies for environmental adaptation
Vorobev, PeerJ 2013 - “...Thus the expression of these genes was of special interest. We demonstrate elevated expression of mmol_1770 in M. mobilis JLW8 in response to the in situ conditions (4 to 6-fold compared to laboratory cultures ( Fig. 4A , also highlighted in Fig. 2 ). Along with...”
- “...dissimilatory metabolism; hps encoding hexulosephosphate synthase, a key enzyme in assimilatory metabolism; Chistoserdova, 2011b ), mmol_1770 was one of the most highly expressed genes in the in situ conditions in this organism ( Tables S2 S4 ). A neighboring gene mmol_1769 predicted to encode a small...”
- An integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in Methylotenera mobilis
Beck, Journal of bacteriology 2011 - “...abundances in methanol under nitrate growth conditions (Mmol_1770, XoxF; Mmol_2290, nitrogen regulatory protein PII; Mmol_0995, PQQ biosynthesis protein C;...”
- “...XoxJ XoxF (copy 2) NADH:flavin oxidoreductase Mmol_0791 Mmol_1770 Mmol_2045 Mmol_2047 Mmol_2048 Mmol_0733 899.3 3.5 819.0 500.0 306.1 731.5 Nitrogen metabolism...”
SPO1508 PQQ-dependent methanol/ethanol family dehydrogenase from Ruegeria pomeroyi DSS-3
23% identity, 44% coverage
A0A1E3VNN9 lanthanide-dependent methanol dehydrogenase (EC 1.1.2.10) from Methyloceanibacter stevinii (see paper)
23% identity, 78% coverage
boh / Q9AGW3 1-butanol dehydrogenase (EC 1.1.5.11) from Thauera butanivorans (strain ATCC 43655 / DSM 2080 / JCM 20651 / NBRC 103042 / IAM 12574 / Bu B1211) (see 2 papers)
BOH_THABB / Q9AGW3 1-butanol dehydrogenase (quinone); PQQ-containing alcohol dehydrogenase; Quinoprotein alcohol dehydrogenase; EC 1.1.5.11 from Thauera butanivorans (strain ATCC 43655 / DSM 2080 / JCM 20651 / CCUG 51053 / NBRC 103042 / IAM 12574 / Bu B1211) (Pseudomonas butanovora) (see 2 papers)
Q9AGW3 aldehyde dehydrogenase (quinone) (EC 1.2.5.2) from Thauera butanivorans (see paper)
24% identity, 44% coverage
- function: Involved in the metabolism of butane (PubMed:11889098). May function primarily in energy generation (PubMed:12142403). Catalyzes the oxidation of 1-butanol to 1-butanal (PubMed:11889098, PubMed:12142403). Also able to use 2-butanol and butyraldehyde, although the affinity is comparatively low (PubMed:12142403).
catalytic activity: butan-1-ol + a quinone = butanal + a quinol (RHEA:49808)
cofactor: pyrroloquinoline quinone (Binds 1 PQQ group per subunit. PQQ is inserted between disulfide Cys-134-Cys-135 and the plane of Trp-277.)
cofactor: Ca(2+) (Binds 2 calcium ions per subunit.)
disruption phenotype: Cells lacking this gene show a delayed growth on butane and are unable to tolerate high level of 1-butanol (PubMed:11889098, PubMed:12142403). When both bdh and boh genes are inactivated, growth on butane and 1-butanol is eliminated (PubMed:11889098).
KVC_0337 pyrroloquinoline quinone-dependent dehydrogenase from Ketogulonicigenium vulgare
24% identity, 42% coverage
- Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome
Wang, Scientific reports 2018 - “...strains, shown in Table 2 . There are 5 sdh genes (KVC_2764, KVC_2744, KVC_0718, KVC_1927, KVC_0337) and 1 sndh gene (KVC_0605) in strain SPU B805. Table 2 Genome features of different 2-KGA-producing strains of K . vulgare . Strain K. vulgare SPU B805 K. vulgare SKV...”
- “...and Rank 4. In fermentation, the FPKM of the five sdh (KVC_2764, KVC_2744, KVC_0718, KVC_1927, KVC_0337) (the average FPKM value 24691.32, 10501.89, 2078.73, 750.78, 220.99) were obviously higher than those of the central carbon degradation related genes, which partially explained that the majority of L-sorbose was...”
Q70JP0 gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 2/2) (EC 1.1.99.21) from Gluconobacter oxydans (see 2 papers)
GOX0855 D-Sorbitol dehydrogenase subunit SldB from Gluconobacter oxydans 621H
40% identity, 11% coverage
- Membrane-bound sorbitol dehydrogenase is responsible for the unique oxidation of D-galactitol to L-xylo-3-hexulose and D-tagatose in Gluconobacter oxydans
Xu, Biochimica et biophysica acta. General subjects 2023 (PubMed)- “...refer to Fusion, meaning mSldB (encoded by GOX0855) and SldA were fused to one polypeptide, yielding pET32b-FU-msldBA; (5) membrane-bound glucose dehydrogenase...”
- “...whether the transmembrane region of the mSldBA (i.e., the GOX0855 encoded small subunit SldB, 126 aa) can be replaced by the transmembrane region of the other...”
- Engineering of glycerol utilization in Gluconobacter oxydans 621H for biocatalyst preparation in a low-cost way
Yan, Microbial cell factories 2018 - “...converted into DHA by the major polyol dehydrogenase that consists of two subunits, GOX0854 and GOX0855. There is also a glycerol utilization operon that consists of glpD encoding a glycerol-3-phosphate dehydrogenase (GOX2088), glpF encoding a glycerol transporter (GOX2089), glpK encoding a glycerol kinase (GOX2090), and glpR...”
- “...(GOX1067 and GOX1068); 2, aldehyde dehydrogenase (GOX0585, GOX0586 and GOX0587); 3, polyol dehydrogenase (GOX0854 and GOX0855); 4/5, uncharacterized PQQ-depending dehydrogenase; 6, inositol dehydrogenase (GOX1857); 7, d -lactate dehydrogenase (GOX1253); 8, glucose dehydrogenase (GOX0265); 9, gluconate dehydrogenase (GOX1230, GOX1231 and GOX1232); 10, sorbitol dehydrogenase (GOX2094, GOX2095, GOX2096...”
- Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
Kranz, BMC genomics 2018 - “...membrane-bound aldehyde dehydrogenase, large subunit 9.0 31 GOX0854 polyol dehydrogenase subunit SldA 4.2 2147 | GOX0855 polyol dehydrogenase subunit SldB 4.6 5992 GOX1067 alcohol dehydrogenase cytochrome c subunit precursor 4.0 1807 | GOX1068 alcohol dehydrogenase large subunit 3.4 1706 GOX1230 gluconate 2-dehydrogenase, cytochrome c subunit 9.0...”
- “...isomerase (GOX1708); sldA , polyol dehydrogenase subunit SldA (GOX0854); sldB , polyol dehydrogenase subunit SldB (GOX0855); tal / pgi , bifunctional transaldolase (GOX1704); tkt , transketolase (GOX1703); tpi , triosephosphate isomerase (GOX2217); zwf , glucose-6-phosphate 1-dehydrogenase (GOX0145). Metabolites: 1,3-BPG, 1,3-bisphosphoglycerate; 2-KFRU, 2-ketofructose; 2-OG, 2-oxoglutarate; 2PGA, 2-phosphogylcerate;...”
- Combined fluxomics and transcriptomics analysis of glucose catabolism via a partially cyclic pentose phosphate pathway in Gluconobacter oxydans 621H
Hanke, Applied and environmental microbiology 2013 - “...by the membrane-bound major polyol dehydrogenase (GOX0854 and GOX0855) is unlikely, as this enzyme has its optimum activity for this reaction at acidic pH...”
- Mutational analysis of the pentose phosphate and Entner-Doudoroff pathways in Gluconobacter oxydans reveals improved growth of a Δedd Δeda mutant on mannitol
Richhardt, Applied and environmental microbiology 2012 - “...by the major polyol dehydrogenase SldAB (GOX0854 and GOX0855). In the second growth phase, which starts when mannitol is almost completely converted and is...”
KVC_1927, KVU_1366 pyrroloquinoline quinone-dependent dehydrogenase from Ketogulonicigenium vulgare
23% identity, 45% coverage
- Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome
Wang, Scientific reports 2018 - “...the strains, shown in Table 2 . There are 5 sdh genes (KVC_2764, KVC_2744, KVC_0718, KVC_1927, KVC_0337) and 1 sndh gene (KVC_0605) in strain SPU B805. Table 2 Genome features of different 2-KGA-producing strains of K . vulgare . Strain K. vulgare SPU B805 K. vulgare...”
- “...+6 and Rank 4. In fermentation, the FPKM of the five sdh (KVC_2764, KVC_2744, KVC_0718, KVC_1927, KVC_0337) (the average FPKM value 24691.32, 10501.89, 2078.73, 750.78, 220.99) were obviously higher than those of the central carbon degradation related genes, which partially explained that the majority of L-sorbose...”
- Characterization of a group of pyrroloquinoline quinone-dependent dehydrogenases that are involved in the conversion of L-sorbose to 2-Keto-L-gulonic acid in Ketogulonicigenium vulgare WSH-001
Gao, Biotechnology progress 2013 (PubMed)- “...were predicted, including KVU_pmdA_0245, KVU_2142, KVU_2159, KVU_1366, KVU_0203, KVU_0095, and KVU_pmdB_0115. BLAST and function domain searches showed that...”
- “...including KVU_pmdA_0245 (KVU_PA0245), KVU_2142, KVU_2159, KVU_1366, KVU_0203, KVU_0095, and KVU_pmdB_0115 (KVU_PB0115). BLAST and function domain searches...”
WP_116701676 glycerol dehydrogenase from Komagataeibacter melaceti
44% identity, 10% coverage
KVC_2744 pyrroloquinoline quinone-dependent dehydrogenase from Ketogulonicigenium vulgare
33% identity, 15% coverage
- Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome
Wang, Scientific reports 2018 - “...among all the strains, shown in Table 2 . There are 5 sdh genes (KVC_2764, KVC_2744, KVC_0718, KVC_1927, KVC_0337) and 1 sndh gene (KVC_0605) in strain SPU B805. Table 2 Genome features of different 2-KGA-producing strains of K . vulgare . Strain K. vulgare SPU B805...”
- “...as Rank +6 and Rank 4. In fermentation, the FPKM of the five sdh (KVC_2764, KVC_2744, KVC_0718, KVC_1927, KVC_0337) (the average FPKM value 24691.32, 10501.89, 2078.73, 750.78, 220.99) were obviously higher than those of the central carbon degradation related genes, which partially explained that the majority...”
B0W47_01005 glycerol dehydrogenase from Komagataeibacter nataicola
40% identity, 12% coverage
- Complete genome sequence of the cellulose-producing strain Komagataeibacter nataicola RZS01
Zhang, Scientific reports 2017 - “...K. nataicola RZS01. Family Cofactor Genes Glucose dehydrogenase PQQ B0W47_01230, B0W47_02520, B0W47_10950 Glycerol dehydrogenase PQQ B0W47_01005, B0W47_01010 Alcohol dehydrogenase PQQ B0W47_13410 Aldehyde dehydrogenase PQQ B0W47_16410 2-Keto- d -gluconate dehydrogenase FAD B0W47_11030, B0W47_11035, B0W47_11040 Gluconate 2-dehydrogenase FAD B0W47_05395, B0W47_05400, B0W47_05405, B0W47_13405 Adaptation to extreme conditions K. nataicola...”
4mh1B Crystal structure and functional studies of quinoprotein l-sorbose dehydrogenase from ketogulonicigenium vulgare y25 (see paper)
31% identity, 14% coverage
- Ligand: pyrroloquinoline quinone (4mh1B)
KVU_2159 pyrroloquinoline quinone-dependent dehydrogenase from Ketogulonicigenium vulgare WSH-001
22% identity, 45% coverage
- Characterization of a group of pyrroloquinoline quinone-dependent dehydrogenases that are involved in the conversion of L-sorbose to 2-Keto-L-gulonic acid in Ketogulonicigenium vulgare WSH-001
Gao, Biotechnology progress 2013 (PubMed)- “...dehydrogenases were predicted, including KVU_pmdA_0245, KVU_2142, KVU_2159, KVU_1366, KVU_0203, KVU_0095, and KVU_pmdB_0115. BLAST and function domain searches...”
- “...WSH-001, including KVU_pmdA_0245 (KVU_PA0245), KVU_2142, KVU_2159, KVU_1366, KVU_0203, KVU_0095, and KVU_pmdB_0115 (KVU_PB0115). BLAST and function domain...”
KVC_2764 pyrroloquinoline quinone-dependent dehydrogenase from Ketogulonicigenium vulgare
31% identity, 14% coverage
- Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome
Wang, Scientific reports 2018 - “...different among all the strains, shown in Table 2 . There are 5 sdh genes (KVC_2764, KVC_2744, KVC_0718, KVC_1927, KVC_0337) and 1 sndh gene (KVC_0605) in strain SPU B805. Table 2 Genome features of different 2-KGA-producing strains of K . vulgare . Strain K. vulgare SPU...”
- “...defined as Rank +6 and Rank 4. In fermentation, the FPKM of the five sdh (KVC_2764, KVC_2744, KVC_0718, KVC_1927, KVC_0337) (the average FPKM value 24691.32, 10501.89, 2078.73, 750.78, 220.99) were obviously higher than those of the central carbon degradation related genes, which partially explained that the...”
KVC_0718, KVU_0203 pyrroloquinoline quinone-dependent dehydrogenase from Ketogulonicigenium vulgare
21% identity, 45% coverage
- Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome
Wang, Scientific reports 2018 - “...all the strains, shown in Table 2 . There are 5 sdh genes (KVC_2764, KVC_2744, KVC_0718, KVC_1927, KVC_0337) and 1 sndh gene (KVC_0605) in strain SPU B805. Table 2 Genome features of different 2-KGA-producing strains of K . vulgare . Strain K. vulgare SPU B805 K....”
- “...Rank +6 and Rank 4. In fermentation, the FPKM of the five sdh (KVC_2764, KVC_2744, KVC_0718, KVC_1927, KVC_0337) (the average FPKM value 24691.32, 10501.89, 2078.73, 750.78, 220.99) were obviously higher than those of the central carbon degradation related genes, which partially explained that the majority of...”
- Characterization of a group of pyrroloquinoline quinone-dependent dehydrogenases that are involved in the conversion of L-sorbose to 2-Keto-L-gulonic acid in Ketogulonicigenium vulgare WSH-001
Gao, Biotechnology progress 2013 (PubMed)- “...predicted, including KVU_pmdA_0245, KVU_2142, KVU_2159, KVU_1366, KVU_0203, KVU_0095, and KVU_pmdB_0115. BLAST and function domain searches showed that enzymes...”
- “...KVU_pmdA_0245 (KVU_PA0245), KVU_2142, KVU_2159, KVU_1366, KVU_0203, KVU_0095, and KVU_pmdB_0115 (KVU_PB0115). BLAST and function domain searches showed...”
Q83X81 Probable polyvinylalcohol dehydrogenase from Streptomyces rochei
26% identity, 44% coverage
7wmkA / A0A6B8QJ68 Pqq-dependent alcohol dehydrogenase complexed with pqq (see paper)
38% identity, 10% coverage
- Ligands: pyrroloquinoline quinone; calcium ion (7wmkA)
7wmdA / A0A6B8QJ68 Pqq-dependent alcohol dehydrogenase detoxifying don (see paper)
38% identity, 10% coverage
- Ligand: calcium ion (7wmdA)
Q93RE9 alcohol dehydrogenase (quinone) (EC 1.1.5.5) from Pseudogluconobacter saccharoketogenes (see paper)
34% identity, 13% coverage
4cvbA / Q93RE9 Crystal structure of quinone-dependent alcohol dehydrogenase from pseudogluconobacter saccharoketogenenes (see paper)
34% identity, 13% coverage
- Ligands: calcium ion; pyrroloquinoline quinone; zinc ion (4cvbA)
sldB / Q8L1D5 D-sorbitol dehydrogenase small subunit (EC 1.1.99.21) from Gluconobacter thailandicus (see 4 papers)
sldB / BAC02908.1 SldB from Gluconobacter oxydans (see paper)
NBRC3255_0236, NBRC3257_1135 glycerol dehydrogenase small subunit from Gluconobacter thailandicus NBRC 3257
47% identity, 8% coverage
- Draft genome sequence of Gluconobacter thailandicus NBRC 3257
Matsutani, Standards in genomic sciences 2014 - “...paralogous copies of the PQQ-glycerol dehydrogenase sld AB operon (NBRC3257_0924 to NBRC3257_0925 and NBRC3257_1134 to NBRC3257_1135) were identified. It has been thought that the respiratory chains of Gluconobacter species play key roles in respiratory energy metabolism [ 48 - 51 ]. Therefore, the gene repertoires of...”
- Draft Genome Sequence of Dihydroxyacetone-Producing Gluconobacter thailandicus Strain NBRC 3255
Matsutani, Genome announcements 2013 - “...dehydrogenase 1, while two paralogous sets of sldAB operons (NBRC3255_0025 to NBRC3255_0026 and NBRC3255_0235 to NBRC3255_0236) were identified. One of the two paralogs, the NBRC3255_0235 operon, is responsible for dihydroxyacetone production from glycerol as a glycerol dehydrogenase ( 9 ), and NBRC 3255 was shown to...”
NBRC3255_0025, NBRC3257_0924 hypothetical protein from Gluconobacter thailandicus NBRC 3255
44% identity, 8% coverage
- Draft genome sequence of Gluconobacter thailandicus NBRC 3257
Matsutani, Standards in genomic sciences 2014 - “...(NBRC3257_1743), were identified. In addition, two paralogous copies of the PQQ-glycerol dehydrogenase sld AB operon (NBRC3257_0924 to NBRC3257_0925 and NBRC3257_1134 to NBRC3257_1135) were identified. It has been thought that the respiratory chains of Gluconobacter species play key roles in respiratory energy metabolism [ 48 - 51...”
- Draft Genome Sequence of Dihydroxyacetone-Producing Gluconobacter thailandicus Strain NBRC 3255
Matsutani, Genome announcements 2013 - “...compared. NBRC 3255 lacks the PQQ-dependent dehydrogenase 1, while two paralogous sets of sldAB operons (NBRC3255_0025 to NBRC3255_0026 and NBRC3255_0235 to NBRC3255_0236) were identified. One of the two paralogs, the NBRC3255_0235 operon, is responsible for dihydroxyacetone production from glycerol as a glycerol dehydrogenase ( 9 ),...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory