PaperBLAST
PaperBLAST Hits for reanno::Smeli:SM_b20890 L-arabonate dehydratase (EC 4.2.1.25) (Sinorhizobium meliloti 1021) (579 a.a., MKKKAEWPRK...)
Show query sequence
>reanno::Smeli:SM_b20890 L-arabonate dehydratase (EC 4.2.1.25) (Sinorhizobium meliloti 1021)
MKKKAEWPRKLRSQEWFGGTGKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCN
AHLRDLAERVKRGVYEAGGFPVEFPVFSTGESTLRPTAMMFRNLAAMDVEESIRGNPVDG
VVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGE
MSLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLT
GRRIVEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWD
RLGRDVPTIVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKG
VVNYNEDVILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIED
YHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIRISDARMS
GTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVK
PLTGGYGGLYIKTVMQADAGADLDFLVGARGSVVERDSH
Running BLASTp...
Found 249 similar proteins in the literature:
SM_b20890 L-arabonate dehydratase (EC 4.2.1.25) from Sinorhizobium meliloti 1021
100% identity, 100% coverage
- mutant phenotype: Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose
ARAD_RHILW / B5ZZ34 L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 from Rhizobium leguminosarum bv. trifolii (strain WSM2304) (see 2 papers)
I9XDU6 L-Arabinonate dehydratase (EC 4.2.1.25) from Rhizobium leguminosarum bv. trifolii (see 2 papers)
75% identity, 100% coverage
- function: Catalyzes the dehydration of L-arabinonate to 2-dehydro-3- deoxy-L-arabinonate during L-arabinose degradation. Can also dehydrate D-galactonate and D-fuconate with good catalytic efficiency. Has weak activity with D-xylonate and D-gluconate.
catalytic activity: L-arabinonate = 2-dehydro-3-deoxy-L-arabinonate + H2O (RHEA:20968)
catalytic activity: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O (RHEA:18649)
catalytic activity: D-fuconate = 2-dehydro-3-deoxy-D-fuconate + H2O (RHEA:12949)
cofactor: [2Fe-2S] cluster
cofactor: Mg(2+)
subunit: Homotetramer. - Structure-Guided Modulation of the Catalytic Properties of [2Fe-2S]-Dependent Dehydratases
Melse, Chembiochem : a European journal of chemical biology 2022 - “...in this study (UniProtKB); Pu DHT: A0A4R3LQ44, Ft DHAD: A0A1I2J0Y3, Ss DHAD: Q97UB2, Rl ArDT: B5ZZ34, Mt DHAD: A0A0E8UWV6, At DHAD: Q9LIR4, Cc XylDHT: Q9A9Z2. Conflict of interest The authors declare no conflict of interest. 1 Supporting information As a service to our authors and readers,...”
RL3612 putative dihydroxy-acid dehydratase from Rhizobium leguminosarum bv. viciae 3841
75% identity, 100% coverage
5j85A / I9XDU6 Ser480ala mutant of l-arabinonate dehydratase (see paper)
75% identity, 99% coverage
- Ligands: fe2/s2 (inorganic) cluster; magnesium ion (5j85A)
RLO149_c021970 L-arabinonate dehydratase from Roseobacter litoralis Och 149
73% identity, 99% coverage
- Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis
Kalhoefer, BMC genomics 2011 - “...Beside L-arabinose 1-dehydrogenase, also arabonate dehydratase of A. brasilense has an ortholog in R. litoralis (RLO149_c021970) which is also located in cluster 2 (Table 3 ). The other proteins of the pathway known in A. brasilense cannot be assigned to proteins of R. litoralis . Thus,...”
- “...protein RLO149_c021950 putative multiple sugar transport ATP-binding protein RLO149_c021960 putative multiple sugar transport permease protein RLO149_c021970 AraC: L-arabonate dehydratase (EC 4.2.1.25) RLO149_c021980 Gal: D-galactose 1-dehydrogenase (EC 1.1.1.48) Glycogen R. litoralis was not able to grow with glycogen as a carbon source, probably due to the fact...”
Q986V5 Dihydroxy-acid dehydratase from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
70% identity, 99% coverage
BPHYT_RS19730 L-arabonate dehydratase (EC 4.2.1.25) from Burkholderia phytofirmans PsJN
67% identity, 100% coverage
- mutant phenotype: Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose
C785_RS21250 IlvD/Edd family dehydratase from Herbaspirillum huttiense subsp. putei IAM 15032
66% identity, 98% coverage
- Novel non-phosphorylative pathway of pentose metabolism from bacteria
Watanabe, Scientific reports 2019 - “...of DTT-reduced C785_RS13685 at 8K (upper panel) and Na 2 S 2 O 4 -reduced C785_RS21250 at 20K (lower panel). ( h ) Effects of the substitution of cysteine to serine on activity. Values are the meansSD, n =3. The inset photograph is the purified recombinant...”
- “...doubt that C785_RS13685 is completely different from pentonate dehydratases of the ILVD/EDD type such as C785_RS21250 (see below); in fact, the g -values ( g 1 =2.047, g 2 =1.894, and g 3 =1.860, <40K) showed reasonable accordance with [2Fe-2S] protein (Fig. 2g ) 33 35...”
HSERO_RS05205 L-arabonate dehydratase (EC 4.2.1.25) from Herbaspirillum seropedicae SmR1
66% identity, 98% coverage
- mutant phenotype: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (L-ARABINONATE-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
8epzA / A0A4R3LQ44 Crystal structure of fe-s cluster-dependent dehydratase from paralcaligenes ureilyticus in complex with mn
66% identity, 98% coverage
- Ligands: fe2/s2 (inorganic) cluster; manganese (ii) ion (8epzA)
RD2015_RS13055 IlvD/Edd family dehydratase from Roseateles depolymerans
67% identity, 99% coverage
ARADA_AZOBR / Q1JUQ1 L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 from Azospirillum brasilense (see paper)
Q1JUQ1 L-Arabinonate dehydratase (EC 4.2.1.25) from Azospirillum brasilense (see paper)
66% identity, 98% coverage
- function: Catalyzes the dehydration of L-arabonate to L-2-keto-3- deoxyarabonate (L-KDA). Is involved in a degradation pathway of L- arabinose that allows A.brasilense to grow on L-arabinose as a sole carbon source. To a lesser extent, can also use D-xylonate as substrate, but not D-galactonate, D-arabonate, and D-gluconate.
catalytic activity: L-arabinonate = 2-dehydro-3-deoxy-L-arabinonate + H2O (RHEA:20968)
cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster.)
subunit: Homodimer.
PS417_11000 L-arabonate dehydratase (EC 4.2.1.25) from Pseudomonas simiae WCS417
67% identity, 98% coverage
- mutant phenotype: Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose
Pf6N2E2_609 L-arabonate dehydratase (EC 4.2.1.25) from Pseudomonas fluorescens FW300-N2E2
67% identity, 98% coverage
- mutant phenotype: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (L-ARABINONATE-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
PfGW456L13_3320 L-arabonate dehydratase (EC 4.2.1.25) from Pseudomonas fluorescens GW456-L13
67% identity, 98% coverage
- mutant phenotype: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (L-ARABINONATE-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
AO356_24585 L-arabonate dehydratase (EC 4.2.1.25) from Pseudomonas fluorescens FW300-N2C3
67% identity, 98% coverage
- mutant phenotype: Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose
Shewana3_2070 L-arabonate dehydratase (EC 4.2.1.25) from Shewanella sp. ANA-3
65% identity, 98% coverage
- mutant phenotype: Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose
ILVD1_RHIME / Q92RP0 Putative dehydratase IlvD1; EC 4.2.1.- from Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti) (see paper)
65% identity, 99% coverage
C9Z6A7 Putative dihydroxy-acid dehydratase from Streptomyces scabiei (strain 87.22)
SCAB_88411 putative dihydroxy-acid dehydratase from Streptomyces scabiei 87.22
56% identity, 98% coverage
Pan258_40810 IlvD/Edd family dehydratase from Symmachiella dynata
53% identity, 98% coverage
Mal52_42460 IlvD/Edd family dehydratase from Symmachiella dynata
53% identity, 98% coverage
CA54_38120 IlvD/Edd family dehydratase from Symmachiella macrocystis
52% identity, 98% coverage
RHE_RS23070 L-arabinonate dehydratase from Rhizobium etli CFN 42
51% identity, 98% coverage
- Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network
Taboada-Castro, Frontiers in microbiology 2022 - “...Supplementary Table 3A ), the enzyme ilvD , dihydroxy-acid dehydratase [EC:4.2.1.9], and the RHE_RS08720 and RHE_RS23070 proteins were expressed in MM and bacteroid, respectively, supporting multiplicity ( Table 1 ). Similarly, for valine, leucine, and isoleucine degradation ( Supplementary Table 2 pathway 7, and Supplementary Table...”
Atu3971 dihydroxy-acid dehydratase from Agrobacterium tumefaciens str. C58 (Cereon)
50% identity, 96% coverage
SMc04144 PUTATIVE DIHYDROXY-ACID DEHYDRATASE PROTEIN from Sinorhizobium meliloti 1021
49% identity, 97% coverage
NP_436655 putative dihydroxy-acid dehydratase protein from Sinorhizobium meliloti 1021
50% identity, 97% coverage
AT5A_22266 L-arabinonate dehydratase from Agrobacterium tumefaciens 5A
50% identity, 96% coverage
CA51_17990 L-arabinonate dehydratase from Rosistilla oblonga
47% identity, 98% coverage
Mal33_18570 L-arabinonate dehydratase from Rosistilla oblonga
47% identity, 97% coverage
Poly24_12210 L-arabinonate dehydratase from Rosistilla carotiformis
47% identity, 97% coverage
AB395_00004794 L-arabinonate dehydratase from Sinorhizobium fredii CCBAU 45436
48% identity, 97% coverage
- Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling
Contador, mSystems 2020 - “...in Bradyrhizobium sp. strain ORS278 ( 74 ). Another symbiotic gene predicted by our model, AB395_00004794, is involved in the isoleucine and valine biosynthesis pathway. Tn 5 experiments have successfully identified this pathway as being related to the symbiotic process in S. fredii HH303, but the...”
- “...) against the S. fredii genome revealed identities of 89.37%, 64%, and 31.67%, respectively, with AB395_00004794 at the amino acid level. Mutations of ilv genes have been reported to result in phenotypes ranging from no nodule formation (Nod ) ( 35 ) to being unable to...”
SGD_PSEPU / P0DOV7 6-deoxy-6-sulfo-D-gluconate dehydratase; SG dehydratase; EC 4.2.1.162 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see paper)
45% identity, 98% coverage
- function: Catalyzes the dehydration of 6-deoxy-6-sulfo-D-gluconate to 2-dehydro-3,6-dideoxy-6-sulfo-D-gluconate. Is involved in a degradation pathway of sulfoquinovose (SQ) that allows P.putida SQ1 to use SQ as the sole carbon and energy source for growth.
catalytic activity: 6-deoxy-6-sulfo-D-gluconate = 2-dehydro-3,6-dideoxy-6-sulfo-D- gluconate + H2O (RHEA:47912)
cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster.)
subunit: Homodimer.
BMEII0356 dihydroxy-acid dehydratase from Brucella melitensis 16M
50% identity, 87% coverage
BAB2_0294 Dihydroxy-acid and 6-phosphogluconate dehydratase:ATP/GTP-binding site motif A (P-loop) from Brucella melitensis biovar Abortus 2308
50% identity, 87% coverage
- Iron-dependent reconfiguration of the proteome underlies the intracellular lifestyle of Brucella abortus
Roset, Scientific reports 2017 - “...0.01 Inositol phosphate metabolism GI:82700499 BAB1_1723 inositol phosphatase/fructose-1,6-bisphosphatase C NO 0.77 0.04 Galactose metabolism GI:83269216 BAB2_0294 dihydroxy-acid dehydratase U NO 0.62 0.01 GI:83269217 BAB2_0295 2-keto-3-deoxy-galactonokinase U NO 0.57 0.04 Propanoate metabolism GI:83269853 BAB2_1009 mgsA methylglyoxal synthase C NO 0.69 0.01 a Abbreviations of assigned functional categories...”
- Intracellular adaptation of Brucella abortus
Lamontagne, Journal of proteome research 2009 - “...unchanged at this early time. Two proteins putatively involved in the galactose metabolism, galactonate dehydratase (BAB2_0294) and UDP-glucose-4-epimerase (BAB2_0694), and one galactose transporter (BAB2_0938), were also reduced within 24 hours after infection, as were other sugar metabolism enzymes and several sugar ABC transporters (BAB2_0377, BAB2_0938, BAB2_0547,...”
- “...metab Trs-ABC S 11 BAB1_0655 Stress response Anti-freeze-I 12 BAB1_0638 Central carbon metab GlnE 12 BAB2_0294 Central carbon metab IlvD 12 BAB1_2129 Stress response DnaK 13 BAB1_1808 Respiration AtpG 13 BAB1_1645 PTS system DhaK-1 13 BAB1_1131 Stress response ClpX 14 BAB2_0545 Respiration RibH 14 BAB1_1646 PTS...”
PVLB_18565 IlvD/Edd family dehydratase from Pseudomonas sp. VLB120
47% identity, 96% coverage
- Metabolic bottlenecks of Pseudomonas taiwanensis VLB120 during growth on d-xylose via the Weimberg pathway
Nerke, Metabolic engineering communications 2024 - “...up into the cell by the two transporters GntP (PVLB_13665) and PVLB_18545. Xylonate dehydratase (XAD, PVLB_18565) performs the conversion to 2-keto-3-deoxy- d -xylonate and 2-keto-3-deoxy- d -xylonate dehydratase (KDXD, PVLB_18560) to -ketoglutaric semialdehyde. Conversion to -ketoglutarate is performed by -ketoglutarate semialdehyde dehydrogenase (KGSADH, PVLB_11380/PVLB_18510/PVLB_18550). OM (outer...”
- Comparison of Three Xylose Pathways in Pseudomonas putida KT2440 for the Synthesis of Valuable Products
Bator, Frontiers in bioengineering and biotechnology 2019 - “...strand, were amplified using primers IB-63 and IB-64 and the following two genes (PVLB_18560 and PVLB_18565) were amplified using primers IB-65 and IB-66. Afterwards, the linearized pBT vector and both amplified fragments were assembled in one reaction. After that, pBT-Weimberg was used as template for pBT-Dahms....”
- “...PVLB_18555 and PVLB_18550 was amplified from pBT-Weimberg with primers IB-67 and IB-74. Amplification of gene PVLB_18565 from P. taiwanensis VLB120 was performed using primers IB-68 and IB-124 and the gene for the aldolase yagE (b0268 from E. coli DH5) was amplified using the primers IB-118 and...”
7m3kA / Q2YJ21 Crystal structure of galactonate dehydratase from brucella melitensis biovar abortus 2308
50% identity, 89% coverage
A1S_1795 dihydroxy-acid dehydratase from Acinetobacter baumannii ATCC 17978
46% identity, 93% coverage
AO356_28760 Xylonate dehydratase (EC 4.2.1.82) from Pseudomonas fluorescens FW300-N2C3
46% identity, 94% coverage
- mutant phenotype: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLONATE-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
Atu3219 dihydroxy-acid dehydratase from Agrobacterium tumefaciens str. C58 (Cereon)
48% identity, 89% coverage
Pf6N2E2_1668 Xylonate dehydratase (EC 4.2.1.82) from Pseudomonas fluorescens FW300-N2E2
45% identity, 94% coverage
- mutant phenotype: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLONATE-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
Atu2736 dihydroxy-acid dehydratase from Agrobacterium tumefaciens str. C58 (Cereon)
45% identity, 94% coverage
C785_RS00855 IlvD/Edd family dehydratase from Herbaspirillum huttiense subsp. putei IAM 15032
42% identity, 97% coverage
- Novel non-phosphorylative pathway of pentose metabolism from bacteria
Watanabe, Scientific reports 2019 - “...6a ). Among them, acid-sugar library screening and the kinetic analysis revealed that C785_RS21250 and C785_RS00855, belonging to the ILVD/EDD superfamily (COG0129), functioned as dehydratases for L-arabinonate and D-xylonate with high substrate specificities, respectively (Figs 2a and S7 ), conforming with their phylogenetic analysis (Supplementary Discussion)....”
- “...of H. huttiense IAM 15032, since D-glucose and D-gluconate were additional substrates for C785_RS00860 and C785_RS00855 (Figs 5 and S7 ), respectively, the up-regulation of these genes by D-glucose may partially metabolize its sugar through non-phosphorylative intermediates, in addition to the ED pathway, similar to Archaeon...”
CCNA_00862 Xylonate dehydratase (EC 4.2.1.82) from Caulobacter crescentus NA1000
xylD / A0A0H3C6H6 xylonate dehydratase monomer (EC 4.2.1.82) from Caulobacter vibrioides (strain NA1000 / CB15N) (see paper)
CCNA_00862, YP_002516235 xylonate dehydratase xylD from Caulobacter crescentus NA1000
43% identity, 95% coverage
5oynA / Q9A9Z2 Crystal structure of d-xylonate dehydratase in holo-form (see paper)
43% identity, 95% coverage
- Ligands: magnesium ion; fe2/s2 (inorganic) cluster (5oynA)
XYLD_CAUVC / Q9A9Z2 D-xylonate dehydratase; XyDHT; Gluconate dehydratase; EC 4.2.1.82; EC 4.2.1.39 from Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15) (Caulobacter crescentus) (see 3 papers)
Q9A9Z2 xylonate dehydratase (EC 4.2.1.82) from Caulobacter vibrioides (see 2 papers)
CC0819, CC_0819 dehydratase, IlvD/Edd family from Caulobacter crescentus CB15
43% identity, 94% coverage
- function: Catalyzes the dehydration of D-xylonate to 2-dehydro-3-deoxy- D-arabinonate during D-xylose degradation. Can also dehydrate D- gluconate, with similar catalytic efficiency. Has weak activity with D- galactonate, D-fuconate and L-arabinonate.
catalytic activity: D-xylonate = 2-dehydro-3-deoxy-D-arabinonate + H2O (RHEA:19157)
catalytic activity: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O (RHEA:21612)
cofactor: [2Fe-2S] cluster
cofactor: Mg(2+)
subunit: Homotetramer.
disruption phenotype: Deletion mutant cannot grow with D-xylose as the sole carbon source. - D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii
Johnsen, The Journal of biological chemistry 2009 - “...blue; and putative xylonolactonase (HVO_B0030) in gray. XAD (CC_0819) and XDH (CC_0821) from C. crescentus belong to different protein families. 27302 JOURNAL...”
- Genetic analysis of a novel pathway for D-xylose metabolism in Caulobacter crescentus
Stephens, Journal of bacteriology 2007 - “...xylA (CC0822), xylB (CC0821), xylC (CC0820), and xylD (CC0819). Because transposon insertions in upstream genes of the operon (which is transcribed in the order...”
- “...1 xylC (CC0820) upstream regionb xylD (CC0819) fbp (CC1385) 1 Oxidoreductase, short-chain dehydrogenase/reductase family CC0820: "SMP/Cgr family"...”
- Regulation of D-xylose metabolism in Caulobacter crescentus by a LacI-type repressor
Stephens, Journal of bacteriology 2007 - “...the expression of the five-gene xyl operon (CC0823 to CC0819) (Fig. 1) (9). A putative operator sequence in PxylX was identified by virtue of its conservation...”
- “...regulation. (A) The C. crescentus xyl operon (CC0823 to CC0819) and the surrounding region are shown on the top line. This region includes xylE (CC0814), which...”
- Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media
Hottes, Journal of bacteriology 2004 - “...f Degradation CC0788, -galactosidase, putativea,b,c CC0819, dehydratase, IlvD/Edd familyd CC0822, aldehyde dehydrogenase, aldAd CC0945, oxidoreductase,...”
- “...xylose in C. crescentus as well. The CC0823 through CC0819 genes probably form an operon, based on the close spacing of the coding regions and the coordinated...”
- Structure-Guided Modulation of the Catalytic Properties of [2Fe-2S]-Dependent Dehydratases
Melse, Chembiochem : a European journal of chemical biology 2022 - “...A0A1I2J0Y3, Ss DHAD: Q97UB2, Rl ArDT: B5ZZ34, Mt DHAD: A0A0E8UWV6, At DHAD: Q9LIR4, Cc XylDHT: Q9A9Z2. Conflict of interest The authors declare no conflict of interest. 1 Supporting information As a service to our authors and readers, this journal provides supporting information supplied by the authors....”
- Towards a Synthetic Biology Toolset for Metallocluster Enzymes in Biosynthetic Pathways: What We Know and What We Need
Shomar, Molecules (Basel, Switzerland) 2021 - “...fructosovorans P18187 1FRF [2Fe-2S] ferredoxin FdxB Pseudomonas putida Q76CS9 3AH7 D-xylonate dehydratase Caulobacter vibrioides CB15 Q9A9Z2 5OYN [2Fe-2S] and [4Fe-4S] rSAM enzyme BioB Escherichia coli P12996 1R30 Nitrogenase molybdenum-iron protein Azotobacter vinelandii P07328 6UG0 [4Fe-4S] Viperin Nematostella vectensis A7RNF3 7N7H [4Fe-4S] enzyme IspG Aquifex aeolicus O67496...”
AFUA_2G16300 dihydroxy acid dehydratase, putative from Aspergillus fumigatus Af293
45% identity, 82% coverage
- The Aspergillus fumigatus dihydroxyacid dehydratase Ilv3A/IlvC is required for full virulence
Oliver, PloS one 2012 - “...identification of four A. fumigatus proteins. Proteins encoded by the genes AFUA_2G14210, AFUA_1G03550, AFUA_1G07330 and AFUA_2G16300 were 63%, 55%, 31% and 29% identical to S. cerevisiae Ilv3p, respectively. For the purposes of clarity they shall be referred to as AfIlv3A (AFUA_2G14210), AfIlv3B (AFUA_1G03550), AfIlv3C (AFUA_1G07330) and...”
- “...pathway including the DHAD step are thought to occur, whereas AfIlv3B, AfIlv3C (AFUA_1G07330) and AfIlv3D (AFUA_2G16300) are not predicted to be mitochondrial. The phenotype of the ilv3A strain is consistent with AfIlv3A being required for branched-chain amino acid biosynthesis as it only grows when supplemented with...”
An15g06700 uncharacterized protein from Aspergillus niger
45% identity, 87% coverage
Q9A8D3 Dehydratase, IlvD/Edd family from Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)
46% identity, 95% coverage
- The Aspergillus fumigatus dihydroxyacid dehydratase Ilv3A/IlvC is required for full virulence
Oliver, PloS one 2012 - “...(ZP_01094431) Blastopirellula marina ; Bpar1 (NP_883684.1) Bordetella parapertussis ; Cagg1 (AOH553_9CHLR) Chloroflexus aggregans ; Cvib1 (Q9A8D3) Caulobacter vibroides ; Lint1 (Q8F219) Leptospira interrogans ; Meth1 (ZP_01850751.1) Methylobacterium sp ; Mlot1 (NP_106075.1), Mlot2 (Q986V5), Mesorhizobium loti ; Pmar1 (ZP_01852636.1) Planctomyces maris ; Rbal1 (Q7UJ69) Rhodopirelula baltica ;...”
AFUA_1G07330 dihydroxy-acid dehydratase, putative from Aspergillus fumigatus Af293
39% identity, 92% coverage
- The Aspergillus fumigatus dihydroxyacid dehydratase Ilv3A/IlvC is required for full virulence
Oliver, PloS one 2012 - “...to the identification of four A. fumigatus proteins. Proteins encoded by the genes AFUA_2G14210, AFUA_1G03550, AFUA_1G07330 and AFUA_2G16300 were 63%, 55%, 31% and 29% identical to S. cerevisiae Ilv3p, respectively. For the purposes of clarity they shall be referred to as AfIlv3A (AFUA_2G14210), AfIlv3B (AFUA_1G03550), AfIlv3C...”
- “...bulk of the pathway including the DHAD step are thought to occur, whereas AfIlv3B, AfIlv3C (AFUA_1G07330) and AfIlv3D (AFUA_2G16300) are not predicted to be mitochondrial. The phenotype of the ilv3A strain is consistent with AfIlv3A being required for branched-chain amino acid biosynthesis as it only grows...”
Q9UZ03 Dihydroxy-acid dehydratase from Pyrococcus abyssi (strain GE5 / Orsay)
42% identity, 92% coverage
Cthe_2713 dihydroxy-acid dehydratase from Clostridium thermocellum ATCC 27405
40% identity, 93% coverage
FNP_0059 dihydroxy-acid dehydratase from Fusobacterium polymorphum ATCC 10953
40% identity, 92% coverage
- Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium
Karpathy, PloS one 2007 - “...of these amino acids. The predicted products encoded by this locus include dihydroxy-acid dehydratase (IlvD, FNP_0059), threonine ammonia-lyase (IlvA, FNP_0060), acetolactate synthase (IlvB and IlvN, FNP_0061 and FNP_0062), 2-isopropyl malate synthase (LeuA, FNP_0063), 3-isopropyl malate synthase (LeuC and LeuD, FNP_0064 and FNP_0065), isopropyl malate dehydrogenase (LeuB,...”
Tsac_0569 dihydroxy-acid dehydratase from Thermoanaerobacterium saccharolyticum JW/SL-YS485
39% identity, 93% coverage
- Dynamic cell responses in Thermoanaerobacterium sp. under hyperosmotic stress
Zhu, Scientific reports 2017 - “...5.177 8.6580.311 Tsac_0104 5-Nucleotidase domain-containing protein 1.84E-03 0.137 0.0960.015 ko00290: Valine, leucine and isoleucine biosynthesis Tsac_0569 Dihydroxy-acid dehydratase 1.56E-02 4.833 4.1730.527 Tsac_0564 Ketol-acid reductoisomerase 1.58E-02 4.817 4.2160.296 Tsac_0566 3-isopropylmalate dehydratase large subunit 1.89E-02 4.649 4.2660.252 Tsac_2182 Glu/Leu/Phe/Val dehydrogenase dimerization region 2.81E-02 0.009 7.5422.795 ko00620: Pyruvate metabolism...”
ilvDD / O27498 dihydroxy-acid dehydratase subunit (EC 4.2.1.9) from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (see 4 papers)
40% identity, 93% coverage
CAC3170 Dihydroxy-acid dehydratase from Clostridium acetobutylicum ATCC 824
CA_C3170 dihydroxy-acid dehydratase from Clostridium acetobutylicum ATCC 824
40% identity, 92% coverage
- Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum
Amador-Noguez, Applied and environmental microbiology 2011 - “...biosynthesis, cac3173, cac3172, cac3169, cac3176, cac0091, cac3170, cac1479, cac0273, cac3174, and cac3171; serine biosynthesis, cac0014, cac0015, and cac0263;...”
- Meta-analysis and functional validation of nutritional requirements of solventogenic Clostridia growing under butanol stress conditions and coutilization of D-glucose and D-xylose
Heluane, Applied and environmental microbiology 2011 - “...CAC2389 CAC2390 CAC2634 CAC2708 CAC2711 CAC2712 CAC3164 CAC3170 CAC3348 CAC3462 CAC3596 CAC3680 CAC3681 0.40506 1.51803 1.07553 1.7949 2.70695 0.54094 0.61838...”
- High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11T (DSM 29698)
Patil, Standards in genomic sciences 2017 - “...was also reported for the gluconate-fermenting C. acetobutylicum ATCC 824 T , where the gene CA_C3170 was predicted to encode a 6-phosphogluconate dehydratase and BlastP analysis indicated that it is a dihydroxy acid dehydratase primarily involved in the synthesis of amino acids [ 47 , 48...”
- “...and Anaerostipes caccae DSM 14662 T , respectively, and showed only 40-60% identity with gene CA_C3170 of C. acetobutylicum ATCC 824 T . Therefore, genes Ga0116910_10068 and Ga0116910_101679 most likely encode a dihydroxy acid dehydratase that is involved in amino acid synthesis rather than in KDPG...”
- Fermentation of oxidized hexose derivatives by Clostridium acetobutylicum
Servinsky, Microbial cell factories 2014 - “...unlikely that gluconokinase is present in the organism [ 28 ]. MetaCyc also predicted that CA_C3170 encodes 6-phosphogluconate dehydratase, however the genomic context of the gene is inconsistent with that function. A BlastP analysis of the CA_C3170 translated amino acid sequence indicated it is a dihydroxyacid...”
PF0942 dihydroxy-acid dehydratase from Pyrococcus furiosus DSM 3638
42% identity, 93% coverage
Clocel_0493 dihydroxy-acid dehydratase from Clostridium cellulovorans 743B
37% identity, 96% coverage
- Clostridium cellulovorans Proteomic Responses to Butanol Stress
Costa, Frontiers in microbiology 2021 - “...lysine (Clocel_1978, Clocel_3115), methionine (Clocel_1764, Clocel_2896, Clocel_3040), and branched chain amino acids (BCAA) (Clocel_1324, Clocel_1325, Clocel_0493) ( Table 1 and Supplementary Table 2 ). In addition, up-regulated proteins include four aminotransferases (Clocel_1948, Clocel_2059, Clocel_2390, Clocel_3812). The role of amino acids in the cellular stress response is...”
- “...of branched-chain amino acids (acetolactate synthase large subunit, Clocel_1324, ketol-acid reductoisomerase, Clocel_1325, and dihydroxy-acid dehydratase, Clocel_0493) could possibly refer to additional mechanisms to modulate cell membrane fluidity ( Mansilla et al., 2004 ). In fact, branched-chain amino acids are used as primers for the synthesis of...”
Q8F219 Dihydroxy-acid dehydratase from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
38% identity, 96% coverage
- The Aspergillus fumigatus dihydroxyacid dehydratase Ilv3A/IlvC is required for full virulence
Oliver, PloS one 2012 - “...(NP_883684.1) Bordetella parapertussis ; Cagg1 (AOH553_9CHLR) Chloroflexus aggregans ; Cvib1 (Q9A8D3) Caulobacter vibroides ; Lint1 (Q8F219) Leptospira interrogans ; Meth1 (ZP_01850751.1) Methylobacterium sp ; Mlot1 (NP_106075.1), Mlot2 (Q986V5), Mesorhizobium loti ; Pmar1 (ZP_01852636.1) Planctomyces maris ; Rbal1 (Q7UJ69) Rhodopirelula baltica ; Selo1 (Q31QL1) Synechococcus elongatus ;...”
LIC11101 dihydroxy-acid dehydratase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
38% identity, 96% coverage
Dde_0116 dihydroxy-acid dehydratase from Desulfovibrio desulfuricans G20
38% identity, 95% coverage
BMMGA3_10275 dihydroxy-acid dehydratase from Bacillus methanolicus MGA3
39% identity, 93% coverage
SXYL_02469 dihydroxy-acid dehydratase from Staphylococcus xylosus
38% identity, 93% coverage
- Transcriptomic Analysis of Staphylococcus xylosus in Solid Dairy Matrix Reveals an Aerobic Lifestyle Adapted to Rind
Leroy, Microorganisms 2020 - “...SXYL_00867-69 ilvAleuDCB Leucine, valine, isoleucine biosynthesis 4.7 * 2.9 * SXYL_00870 leuB 3-isopropylmalate dehydrogenase 2.5 SXYL_02469 ilvD2 Dihydroxy-acid dehydratase 3.0 3.0 Glycine SXYL_01317-19 gcvTPAPB Glycine metabolism 4.7 * 3.1 * Tryptophan SXYL_01497 trpA Tryptophan synthase alpha chain 5.4 SXYL_01498-503 trpBFCDGE Tryptophan biosynthesis 6.3 * 6.2 *...”
- Adaptation of Staphylococcus xylosus to Nutrients and Osmotic Stress in a Salted Meat Model
Vermassen, Frontiers in microbiology 2016 - “...isoleucine SXYL_00867-75 ilvA, leuDCBA, ilvCNBD1 Valine, leucine, isoleucine biosynthesis 0.3 * 0.1 * 0.1 * SXYL_02469 ilvD2 Dihydroxy-acid dehydratase 0.2 0.1 0.1 SXYL_01337-40 lpdA, bkdA1A2 alpha-keto acid dehydrogenase complex 4.9 * 3.7 * 2.8 * Tryptophan, phenylalanine, tyrosine SXYL_01383-85 aroABC Aromatic acid biosynthesis 0.3 * 0.3...”
LBYS11_13595 dihydroxy-acid dehydratase from Lysinibacillus sp. YS11
38% identity, 92% coverage
CIBE_4586 dihydroxy-acid dehydratase from Clostridium beijerinckii
37% identity, 94% coverage
CTN_RS00550 dihydroxy-acid dehydratase from Thermotoga neapolitana DSM 4359
39% identity, 92% coverage
- CO2-Induced Transcriptional Reorganization: Molecular Basis of Capnophillic Lactic Fermentation in Thermotoga neapolitana
d'Ippolito, Frontiers in microbiology 2020 - “...). This evidence was further validated by RT-PCR that showed up-regulation of 6-phosphogluconate dehydratase (EDD CTN_RS00550) that control the key step of ED and down-regulation of 6-phosphofructokinase (PFK CTN_RS02345) that is the regulator enzyme of EMP ( Supplementary Figure 2 ). Analysis of the genes of...”
- “...Pyruvate kinase OPP and EntnerDoudoroff common enzymes CTN_RS07110 4.84 Glucose-6-phosphate 1-dehydrogenase CTN_RS07115 5.50 6-Phosphogluconolactonase EntnerDoudoroff CTN_RS00550 5.83 6-Phosphogluconate dehydratase a CTN_RS03140 1.26 2-Dehydro-3-deoxyphosphogluconate aldolase OPP CTN_RS01150 1.40 6-Phosphogluconate dehydrogenase. Decarboxylating CTN_RS04470 1.64 Ribulose-phosphate-epimerase CTN_RS07445 NDE Ribose-5-phosphate isomerase CTN_RS04700 1.81 Transketolase CTN_RS08090 1.60 Transketolase. C-terminal subunit CTN_RS08085...”
B2TIR2 Dihydroxy-acid dehydratase from Clostridium botulinum (strain Eklund 17B / Type B)
36% identity, 96% coverage
B9E299 Dihydroxy-acid dehydratase from Clostridium kluyveri (strain NBRC 12016)
36% identity, 94% coverage
F502_03482 dihydroxy-acid dehydratase from Clostridium pasteurianum DSM 525 = ATCC 6013
38% identity, 92% coverage
C4ZAW6 Dihydroxy-acid dehydratase from Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990)
39% identity, 90% coverage
SP_2126 dihydroxy-acid dehydratase from Streptococcus pneumoniae TIGR4
spr1935 Dihydroxyacid dehydratase from Streptococcus pneumoniae R6
SPD_1956 dihydroxy-acid dehydratase from Streptococcus pneumoniae D39
38% identity, 93% coverage
- Biofilm and planktonic pneumococci demonstrate disparate immunoreactivity to human convalescent sera
Sanchez, BMC microbiology 2011 - “...2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase dapH (SP_2097) 0 8 Aspartate--ammonia ligase asnA (SP_1970) 3 0 Dihydroxy-acid dehydratase ilvD (SP_2126) 0 7 ATP synthase subunit alpha atpA (SP_1510) 4 21 ATP synthase subunit beta atpD (SP_1508) 9 18 ATP synthase gamma chain atpG (SP_1509) 0 8 Phosphate import ATP-binding protein...”
- Eukaryotic-type serine/threonine protein kinase StkP is a global regulator of gene expression in Streptococcus pneumoniae
Sasková, Journal of bacteriology 2007 - “...Hypothetical genes spr0021 spr0053 spr0561 spr1324 spr1408 spr1935 spr1945 Hypothetical genes a spr1482 spr1623 spr1624 spr1625 spr1626 spr1768 The ratio of...”
- Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors
Ng, Journal of bacteriology 2003 - “...1.3 1.4 6.0 2.0 1.8 1.8 2.0 2.0 2.3 12.0 spr1935 2.5 2.2 1.8 1.8 Amino acid biosynthesis aspC ilvN ilvC metE metF ilvE asd dapA glyA metY-truncation...”
- Autoinducer 2 Signaling via the Phosphotransferase FruA Drives Galactose Utilization by Streptococcus pneumoniae, Resulting in Hypervirulence
Trappetti, mBio 2017 - “...SPD_1650 Iron compound ABC transporter 1.5 SPD_1834 adhE Bifunctional acetaldehyde-coenzyme A/alcohol dehydrogenase 2.0 0.1 0.1 SPD_1956 ilvD Dihydroxy-acid dehydratase 0.6 SPD_2012 glpO Alpha-glycerophosphate oxidase 1.7 SPD_2013 glpK Glycerol kinase 1.6 a Differential gene expression was determined by RNA-seq analysis as described in Materials and Methods. Data...”
- Sialic acid-mediated gene expression in Streptococcus pneumoniae and role of NanR as a transcriptional activator of the nan gene cluster
Afzal, Applied and environmental microbiology 2015 - “...spd_1098 spd_1099 spd_1158 spd_1514 spd_1515 spd_1516 spd_1956 Ratiob Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein ABC...”
- Characterization of central carbon metabolism of Streptococcus pneumoniae by isotopologue profiling
Härtel, The Journal of biological chemistry 2012 - “...(ilvC, SPD_0406 (EC 1.1.1.86)), dihydroxy-acid dehydratase (ilvD, SPD_1956 (EC 4.2.1.9)), and BCAA transaminase (ilvE, SPD_0749 (EC 2.6.1.42)) were identified...”
WP_010874288 dihydroxy-acid dehydratase from Synechocystis sp. PCC 6803
slr0452 dihydroxyacid dehydratase from Synechocystis sp. PCC 6803
38% identity, 96% coverage
- Plastid ancestors lacked a complete Entner-Doudoroff pathway, limiting plants to glycolysis and the pentose phosphate pathway
Evans, Nature communications 2024 - “...KDPG 28 , 48 , 49 . Chen et al. have speculated that Synechocystis DHAD (WP_010874288 or slr0452 ) might dehydrate gluconate to KDG, followed by phosphorylation to KDPG through the semi-phosphorylated pathway 11 . Our analysis indicates that Synechocystis PCC 6803, like the majority of...”
- Plastid ancestors lacked a complete Entner-Doudoroff pathway, limiting plants to glycolysis and the pentose phosphate pathway
Evans, Nature communications 2024 - “..., 48 , 49 . Chen et al. have speculated that Synechocystis DHAD (WP_010874288 or slr0452 ) might dehydrate gluconate to KDG, followed by phosphorylation to KDPG through the semi-phosphorylated pathway 11 . Our analysis indicates that Synechocystis PCC 6803, like the majority of cyanobacteria, does...”
- Sustainable production of photosynthetic isobutanol and 3-methyl-1-butanol in the cyanobacterium Synechocystis sp. PCC 6803
Xie, Biotechnology for biofuels and bioproducts 2023 - “...native acetolactate synthase (AlsS); Slr2088, large subunit of native AlsS; Sll1363, native acetohydroxy-acid isomeroreductase (IlvC); Slr0452, native dihydroxy-acid dehydratase (IlvD); LeuA, 2-isopropylmalate synthase; LeuCD, 3-isopropylmalate dehydratase; LeuB, 3-isopropylmalate dehydrogenase; Kivd S286T , -ketoisovalerate decarboxylase ( Lactococcus lactis ); Slr1192 OP , codon-optimized native alcohol dehydrogenase. Dotted...”
- “...of gene fragments kivd S286T , slr1192 OP , sll0065 , slr2088 , sll1363 , slr0452 , alsS , ilvC , ilvD , fbaA , tktA and pyk1 were codon-optimized and synthesized by GenScript. All gene sequences and all primers used for plasmid construction are listed...”
- Site-2 Protease Slr1821 Regulates Carbon/Nitrogen Homeostasis during Ammonium Stress Acclimation in Cyanobacterium Synechocystis sp. PCC 6803
Lin, International journal of molecular sciences 2023 - “...well as the downregulation of the gene for the ED pathway enzyme phosphogluconate dehydratase ( slr0452 ). Disruption of the OPP pathway was implied as the upregulation of the gene for 6-phosphogluconate dehydrogenase ( sll0329 ) and the downregulation of the gene for transketolase ( sll1070...”
- Entner-Doudoroff pathway in Synechocystis PCC 6803: Proposed regulatory roles and enzyme multifunctionalities
Bachhar, Frontiers in microbiology 2022 - “...route, consisting of only two reactions. The first one is catalyzed by 6-phosphogluconate dehydratase (EDD, slr0452 , currently annotated as ilvD dihydroxy-acid dehydratase), producing 2-keto3-deoxygluconate-6-phosphate (KDPG). The second reaction is catalyzed by keto3-deoxygluconate-6-phosphate aldolase (EDA, sll0107 ), producing pyruvate and glyceraldehyde 3-phosphate ( Figure 1 ,...”
- Enhancement of photosynthetic isobutanol production in engineered cells of Synechocystis PCC 6803
Miao, Biotechnology for biofuels 2018 - “...all the examined strains (Fig. 3 b). In addition, the expression of sll0065, slr2088, and slr0452 could not be detected using anti-Flag tag western immunoblot. Thus, two hypotheses could be made: (i) there is no other bottleneck(s) than Kivd in the isobutanol synthesis pathway. Thus, the...”
- The Entner-Doudoroff pathway is an overlooked glycolytic route in cyanobacteria and plants
Chen, Proceedings of the National Academy of Sciences of the United States of America 2016 - “...the ED pathway uncovered candidates for 6PG-dehydratase (edd, slr0452) and the key enzyme KDPG aldolase (eda, sll0107) (Table S1). The candidate KDPG aldolase...”
- “...2D). In contrast to eda (sll0107), the gene edd (slr0452) could not be completely deleted from all genome copies of Synechocystis (Fig. S2F). We hypothesize...”
- Expression profiling of the bloom-forming cyanobacterium Nodularia CCY9414 under light and oxidative stress conditions
Kopf, The ISME journal 2015 - “...59) None Ssl3364 (2e 21) Sll0877 (2e 77) Sll1937 (2e 06) Slr0452 (0.0) Sll1154 (e 112) Sll0772 (e 98) None Sll0549 (e 73) Slr2073 (3e 49) Slr1391 (e 16) None...”
- Global transcriptional profiles of the copper responses in the cyanobacterium Synechocystis sp. PCC 6803
Giner-Lamia, PloS one 2014 - “...thrA 0.37 Homoserine dehydrogenase sll0461 proA 0.35 Gamma-glutamyl phosphate reductase sll1760 thrB 0.31 Homoserine kinase slr0452 ilvD 0.29 Dihydroxyacid dehydratase sll0080 argC 0.28 N-acetyl-gamma-glutamyl-phosphate reductase sll0450 norB 0.12 Cytochrome b subunit of nitric oxide reductase Transport and binding proteins sll0064 0.18 Putative polar amino acid transport...”
Q1ILZ0 Dihydroxy-acid dehydratase from Koribacter versatilis (strain Ellin345)
36% identity, 97% coverage
- The Aspergillus fumigatus dihydroxyacid dehydratase Ilv3A/IlvC is required for full virulence.
Oliver, PloS one 2012 - “...Spom1 (ILV3_SCHPO), Schizosaccharomyces pombe ; Umay1 (UM05740.1), Umay2 (UM02980.1), Ustilago maydis . BACTERIA: ; Abac1 (Q1ILZ0) Acidobacteria bacterium ; Aura1 (ZP_01227770) Aurantimonas manganoxydans ; Bbro1 (Q7WKV5) Bordetella bronchiseptica ; Bmar1 (ZP_01094431) Blastopirellula marina ; Bpar1 (NP_883684.1) Bordetella parapertussis ; Cagg1 (AOH553_9CHLR) Chloroflexus aggregans ; Cvib1 (Q9A8D3)...”
ABO_0180 dihydroxy-acid dehydratase from Alcanivorax borkumensis SK2
39% identity, 96% coverage
Q74BW7 Dihydroxy-acid dehydratase from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)
GSU1912 dihydroxy-acid dehydratase from Geobacter sulfurreducens PCA
39% identity, 92% coverage
- Multi-instance multilabel learning with weak-label for predicting protein function in electricigens
Wu, BioMed research international 2015 - “...Case Study Table 6 presents two example results. The first protein with the UniProt ID Q74BW7 from the Geobacter sulfurreducens organism has seven ground-truth labels: {GO:0008270, GO:0046872, GO:0000287, GO:0051539, GO:0030145, GO:0005506, GO:0004160}. After training examples with 80% weak-label ratios by different MIML methods, the trained model...”
- “...examples. Organism/UniProt ID Molecular function in UniProt Methods GO molecular function list Geobacter sulfurreducens / Q74BW7 (1) 4 iron, 4 sulfur cluster binding (2) Dihydroxy-acid dehydratase activity (3) Metal ion binding Ground truth GO:0008270 GO:0046872 GO:0000287 GO:0051539 GO:0030145 GO:0005506 GO:0004160 MIMLwel GO:0005524 GO:0008270 GO:0046872 GO:0000287 GO:0030145...”
- Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes
Butler, BMC genomics 2010 - “...GSU0342 0.90 NADH dehydrogenase I, E subunit 39997952 GSU2860 0.90 translation elongation factor G 39997010 GSU1912 0.90 dihydroxy-acid dehydratase 39998398 GSU3309 0.90 hypothetical protein GSU3309 Identifying genes encoding cytochromes After the electron donors have been oxidized and the electrons have been transferred into the inner membrane,...”
ilvD / Q0K7F8 dihydroxyacid dehydratase (EC 4.2.1.9) from Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337) (see paper)
Q0K7F8 dihydroxy-acid dehydratase (EC 4.2.1.9) from Cupriavidus necator (see paper)
38% identity, 96% coverage
PMM0774 Dihydroxy-acid dehydratase from Prochlorococcus marinus sp. MED4
35% identity, 96% coverage
- Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus
Ofaim, Frontiers in genetics 2021 - “...( Altschul et al., 1990 ) from which we identified 6PG-dehydratase (EC: 4.2.1.12) encoded by PMM0774, thereby completing this pathway in the model reconstruction. (iv) The revised model was checked for redox and elemental balance. Since the biomass function was based on experimental data ( Casey...”
- “...Supplementary Material 1 Results from the BLAST-search used to identify 6PG-dehydratase (EC: 4.2.1.12) encoded by PMM0774 in P. marinus MED4. Click here for additional data file. Supplementary Material 2 Memote snapshot report of i SO595. Click here for additional data file. References Aharonovich D. Sher D....”
MRA_0197 dihydroxy-acid dehydratase from Mycobacterium tuberculosis H37Ra
39% identity, 95% coverage
- Genetic basis of virulence attenuation revealed by comparative genomic analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv
Zheng, PloS one 2008 - “...transmembrane protein MRA_0105 peptide synthetase SNV Rv0101 peptide syntherase Nrp MRA_0131 PE-PGRS SNV Rv0124 PE-PGRS MRA_0197 dihydroxy-acid dehydratase SNV Rv0189c dihydroxy-acid dehydratase MRA_0288 PE-PGRS family protein insertion+deletion+SNV Rv0279c PE-PGRS MRA_0391 up conserved secreted protein deletion Rv0383c up Conserved secreted protein MRA_0585 PE-PGRS SNV Rv0578c PE-PGRS MRA_0646...”
- “...this nrdHIEF2 operon might impact exit from dormancy or survival in vivo . The ilvD (MRA_0197, Rv0189c) gene encoding dihydroxy-acid dehydratase, an essential enzyme for branch chain amino acid and pantothenate (coenzyme A) biosynthesis, has a highly conserved Val284 (GTA) being substituted by Gly284 (GGA) in...”
CD2014 dihydroxy-acid dehydratase from Clostridium difficile 630
37% identity, 93% coverage
6ovtA / P9WKJ5 Crystal structure of ilvd from mycobacterium tuberculosis (see paper)
39% identity, 95% coverage
- Ligands: magnesium ion; fe2/s2 (inorganic) cluster (6ovtA)
ILVD_MYCTU / P9WKJ5 Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
Rv0189c dihydroxy-acid dehydratase from Mycobacterium tuberculosis H37Rv
NP_214703 dihydroxy-acid dehydratase from Mycobacterium tuberculosis H37Rv
39% identity, 95% coverage
- function: Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo- 3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3- dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. Is specific for the (R) isomer of 2,3-dihydroxy-3-methylbutanoate, with no catalytic activity against the (S) isomer.
catalytic activity: (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (RHEA:24809)
catalytic activity: (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2- oxopentanoate + H2O (RHEA:27694)
cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor.)
cofactor: Mg(2+)
subunit: Homodimer.
disruption phenotype: Cells lacking this gene display impaired growth. - Unraveling tuberculosis patient cluster transmission chains: integrating WGS-based network with clinical and epidemiological insights
Sadovska, Frontiers in public health 2024 - “...by isolates of the cases F4 (SIT254) and B2 (SIT42), respectively; p.Gly35Ser in the locus Rv0189c ( ilvD gene) was detected in J1 and J2 (SIT53) isolates, and synonymous variant g.221163G>T in the codon Val187 was found in case O1 Mtb isolates. No recently acquired variants...”
- The active site of the Mycobacterium tuberculosis branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster
Bashiri, The Journal of biological chemistry 2019 (secret) - Novel T7 Phage Display Library Detects Classifiers for Active Mycobacterium Tuberculosis Infection
Talwar, Viruses 2018 - “...2614 2619 10.1128/JB.00224-12 22427625 34. Singh V. Chandra D. Srivastava B.S. Srivastava R. Downregulation of Rv0189c, encoding a dihydroxyacid dehydratase, affects growth of Mycobacterium tuberculosis in vitro and in mice Microbiology 2011 157 38 46 10.1099/mic.0.042358-0 20864475 35. Kolly G.S. Sala C. Vocat A. Cole S.T....”
- “...Rv2007c 1.36 10 9 7.27 10 7 0.92 0.91 0.89 P51_BP3_131 Dihydroxy acid dehydratase ilvD Rv0189c 2.15 10 8 3.84 10 6 0.95 0.92 0.98 P51_BP3_137 Transketolase TKT Rv1449c 7.14 10 8 9.72 10 6 0.95 1 0.81 P197_BP4_1078 Signal peptidase lepB Rv2903 1.44 10 7...”
- A systematic review of East African-Indian family of Mycobacterium tuberculosis in Brazil
Duarte, The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases 2017 - “...Rv0041 Rv0041_384a>G S 34 92199 Rv0083 Rv0083_188t>G S 34 157292 Rv0129c Rv0129c_309g>A S 33 220050 Rv0189c Rv0189c_1674g>A S 34 311613 Rv0260c Rv0260c_1047c>A S 34 720863 Rv0629c Rv0629c_870c>A S 13 797736 Rv0697 Rv0697_804c>T S 34 918316 Rv0824c Rv0824c_435a>G S 34 923065 Rv0831c Rv0831c_645a>T S 34 1047683 Rv0938...”
- SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis
Elghraoui, BMC genomics 2017 - “...our Assembly Rv0037c Rv0037c Probable conserved integral membrane protein Rv0124 PE_PGRS2 PE-PGRS family protein PE_PGRS2 Rv0189c ilvD Probable dihydroxy-acid dehydratase IlvD (dad) [ 48 , 58 ] Rv0279c PE_PGRS4 PE-PGRS family protein PE_PGRS4 Rv0383c Rv0383c Possible conserved secreted protein masks sequencing error in H37Rv [ 8...”
- Bacterial Branched-Chain Amino Acid Biosynthesis: Structures, Mechanisms, and Drugability
Amorim, Biochemistry 2017 - “...262 274 4933736 83 Singh V Chandra D Srivastava BS Srivastava R 2011 Downregulation of Rv0189c, encoding a dihydroxyacid dehydratase, affects growth of Mycobacterium tuberculosis in vitro and in mice Microbiology 157 38 46 20864475 84 Kiritani K Narise S Wagner RP 1966 The dihydroxy acid...”
- “...isomeroreductase ilv C 1.1.1.86 4YPO, 1QMG, 1YRL, 1SR9 Rv3001c herbicides dihydroxyacid dehydratase ilv D 4.2.1.9 Rv0189c a isopropylmalate synthase leu A 2.3.3.13 3U6W, 3FIG, 4OV9 Rv3710 a isopropylmalate isomerase leu CD 4.2.1.33 3Q3W, 3H5E, 3H5H, 3H5J, 2HCU (C); 3H5H (D) Rv2988c (C), Rv2987c (D) a isopropylmalate...”
- Development of a T7 Phage Display Library to Detect Sarcoidosis and Tuberculosis by a Panel of Novel Antigens
Talwar, EBioMedicine 2015 - “...TKT 2.710 6 0.86 82 76 P51-BP4_563 (BAL) Dihydroxy acid dehydratase ( Mycobacterium tuberculosis ) Rv0189C 1.0410 6 0.85 76 86 Clone Decreased in TB vs sarcoidosis subjects P51_BP3_113 (BAL) Chain A Mycobacterium tuberculosis BfrA 1.210 10 0.9 88 85 P51_BP3_200 (BAL) Disabled homologue 2 isoform...”
- Equal opportunity for low-degree network nodes: a PageRank-based method for protein target identification in metabolic graphs
Bánky, PloS one 2013 - “...0.0030 Rv2607 pdxH R00277 0.0061 3 2 0.0030 Rv2607 pdxH R01209 0.0025 7 1 0.0025 Rv0189c ilvD R03051 0.0028 3 2 0.0014 Rv3001c ilvC R06905 0.0013 1 1 0.0013 bnsG R03968 0.0020 4 2 0.0010 Rv2987c(leuD) Rv2988c(leuC) R04942 0.0020 3 2 0.0010 Rv1077 cysM R04440 0.0020...”
- “...reported [33] that the downregulation of the third largest scoring protein with gene name ilvD (Rv0189c, a dihydroxyacid dehydratase) affects the growth of Mycobacterium tuberculosis in vitro and in mice. The sixth highest scoring hit, the leuD gene (Rv2987c) is shown to be essential in Mycobacterium...”
- More
- Downregulation of Rv0189c, encoding a dihydroxyacid dehydratase, affects growth of Mycobacterium tuberculosis in vitro and in mice.
Singh, Microbiology (Reading, England) 2011 (PubMed)- GeneRIF: It may be concluded that the DHAD encoded by Rv0189c is essential for the survival of Mycobacterium tuberculosis and could be a potential drug/vaccine target, as it is absent in mammals.
Q97UB2 dihydroxy-acid dehydratase (EC 4.2.1.9) from Saccharolobus solfataricus (see 2 papers)
SSO3107 Dihydroxy-acid dehydratase (ilvD) from Sulfolobus solfataricus P2
36% identity, 96% coverage
- Metabolic reconstruction and experimental verification of glucose utilization in Desulfurococcus amylolyticus DSM 16532
Reischl, Folia microbiologica 2018 - “...in S. solfataricus , e.g., SSO3124, SSO3117 and SSO3118 (Peng et al. 2011 ) or SSO3107, SSO1303 (Brouns et al. 2006 ), could not be detected in the genome of D. amylolyticus . Only a homolog of the 2-keto-3-deoxy-D-arabinonate dehydratase (COG3970), which is responsible for arabinose...”
- Structure-Guided Modulation of the Catalytic Properties of [2Fe-2S]-Dependent Dehydratases
Melse, Chembiochem : a European journal of chemical biology 2022 - “...of enzymes discussed in this study (UniProtKB); Pu DHT: A0A4R3LQ44, Ft DHAD: A0A1I2J0Y3, Ss DHAD: Q97UB2, Rl ArDT: B5ZZ34, Mt DHAD: A0A0E8UWV6, At DHAD: Q9LIR4, Cc XylDHT: Q9A9Z2. Conflict of interest The authors declare no conflict of interest. 1 Supporting information As a service to our...”
- The Aspergillus fumigatus dihydroxyacid dehydratase Ilv3A/IlvC is required for full virulence.
Oliver, PloS one 2012 - “...Synechococcus elongatus ; Smut1 (Q8DRT7) Streptococcus mutans ; Srub1 (Q2SOM3) Salinabacter ruber ; ARCHAEBACTERIA: Ssol1 (Q97UB2) Sulfolobus solfataricus . The scale bar corresponds to the branch length for an expected number of 0.1 substitutions per site. Group 1, which contained S. cerevisiae ILV3 also contained A....”
SMU_RS09725 dihydroxy-acid dehydratase from Streptococcus mutans UA159
Q8DRT7 Dihydroxy-acid dehydratase from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
37% identity, 93% coverage
WP_011692381 dihydroxy-acid dehydratase from Arthrobacter sp. FB24
37% identity, 93% coverage
Q8XWR1 Dihydroxy-acid dehydratase from Ralstonia nicotianae (strain ATCC BAA-1114 / GMI1000)
37% identity, 96% coverage
ACIAD3636 putative dihydroxyacid dehydratase (ilvD-like) from Acinetobacter sp. ADP1
37% identity, 93% coverage
alr2771 dihydroxyacid dehydratase from Nostoc sp. PCC 7120
37% identity, 93% coverage
- The Anabaena sp. PCC 7120 Exoproteome: Taking a Peek outside the Box
Oliveira, Life (Basel, Switzerland) 2015 - “...2 Transport and binding proteins - Alr2709 Alr2709 protein N 2 Conserved hypothetical protein - Alr2771 Dihydroxy-acid dehydratase NO 3 Amino acid biosynthesis Anabaena Alr2877 Bicarbonate transport bicarbonate-binding protein N 2 , NO 3 , NH 4 + Transport and binding proteins - Alr2887 Alr2887 protein...”
- “...acid biosynthesis and processing (All2533, Alr0237, Alr0880, Alr0996, Alr1381, All4287, Alr1742, Alr4853, All2315, Alr1004, Alr1313, Alr2771, Alr0608, Alr1080, Alr2328 Alr4907, All1683, All4464), sugar breakdown and processing (Alr3608, Alr4448, All3964, All0167, All0168, All0875, Alr0169, Alr2190, All4539) and phosphor scavenge and transport (All0207, All2843, All4575, Alr4238, Alr4976). Detection...”
GYMC52_2001 dihydroxy-acid dehydratase from Geobacillus sp. Y412MC52
35% identity, 92% coverage
LMON_2054, LMRG_RS10020 dihydroxy-acid dehydratase from Listeria monocytogenes 10403S
lmo1983 similar to dihydroxy-acid dehydratase from Listeria monocytogenes EGD-e
LMRG_01131 dihydroxy-acid dehydratase from Listeria monocytogenes 10403S
36% identity, 90% coverage
- Genome-wide identification of Listeria monocytogenes CodY-binding sites
Biswas, Molecular microbiology 2020 - “...LMRG_01636) (K D 5 nM), glnK (lmo1517, LMRG_RS07550, LMRG_01453) (K D 5 nM), ilvD (lmo1983, LMRG_RS10020, LMRG_01131) (K D 10 nM), ilvE (lmo0978, LMRG_RS04930, LMRG_02078) (K D 12.5 nM), mfd (lmo0214, LMRG_RS01035, LMRG_02636) (K D 12.5 nM), and lmo0849 ( LMRG_RS04250, LMRG_02272) (K D 12.5 nM)...”
- Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
Hingston, PloS one 2017 - “...-0.01 LMON_1932 Predicted membrane protein hemolysin III + lmo1864 14 2.21 1.58 1.78 1.84 1.06 LMON_2054 Dihydroxy-acid dehydratase ilvD + lmo1983 4 * 3.52 3.89 3.34 4.29 3.62 LMON_2055 Acetolactate synthase large subunit ilvB + lmo1984 3/15 3.67 4.17 3.41 4.41 4.37 LMON_2056 Acetolactate synthase small...”
- “...5.06 2.55 -0.95 0.67 LMON_1936 Pyruvate,phosphate dikinase + lmo1867 20 4.31 2.17 1.90 0.47 2.16 LMON_2054 Dihydroxy-acid dehydratase ilvD + lmo1983 4 * 3.52 3.89 3.34 4.29 3.62 LMON_2055 Acetolactate synthase large subunit ilvB + lmo1984 3/15 3.67 4.17 3.41 4.41 4.37 LMON_2056 Acetolactate synthase small...”
- Genome-wide identification of Listeria monocytogenes CodY-binding sites
Biswas, Molecular microbiology 2020 - “...LMRG_RS11140, LMRG_01636) (K D 5 nM), glnK (lmo1517, LMRG_RS07550, LMRG_01453) (K D 5 nM), ilvD (lmo1983, LMRG_RS10020, LMRG_01131) (K D 10 nM), ilvE (lmo0978, LMRG_RS04930, LMRG_02078) (K D 12.5 nM), mfd (lmo0214, LMRG_RS01035, LMRG_02636) (K D 12.5 nM), and lmo0849 ( LMRG_RS04250, LMRG_02272) (K D 12.5...”
- Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
Boonmee, Frontiers in microbiology 2019 - “...LMRG_00826 lmo1375 Peptidase M20 2.07 0.00 LMRG_00942 lmo1489 LMRG_00945-LMRG_00939 RNA binding protein 2.22 0.00 LMRG_01131 lmo1983 ilvD ilv-leu Dihydroxy-acid dehydratase 2.62 0.01 LMRG_01132 lmo1984 ilvB Acetolactate synthase large subunit 3.12 0.00 LMRG_01134 lmo1986 ilvC Ketol-acid reductoisomerase 2.91 0.00 LMRG_01453 lmo1517 LMRG_01454-LMRG_01453 Nitrogen regulatory protein P-II 2.07...”
- Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
Hingston, PloS one 2017 - “...hemolysin III + lmo1864 14 2.21 1.58 1.78 1.84 1.06 LMON_2054 Dihydroxy-acid dehydratase ilvD + lmo1983 4 * 3.52 3.89 3.34 4.29 3.62 LMON_2055 Acetolactate synthase large subunit ilvB + lmo1984 3/15 3.67 4.17 3.41 4.41 4.37 LMON_2056 Acetolactate synthase small subunit ilvH + lmo1985 15/1...”
- “...Pyruvate,phosphate dikinase + lmo1867 20 4.31 2.17 1.90 0.47 2.16 LMON_2054 Dihydroxy-acid dehydratase ilvD + lmo1983 4 * 3.52 3.89 3.34 4.29 3.62 LMON_2055 Acetolactate synthase large subunit ilvB + lmo1984 3/15 3.67 4.17 3.41 4.41 4.37 LMON_2056 Acetolactate synthase small subunit ilvH + lmo1985 15/1...”
- The multicopy sRNA LhrC controls expression of the oligopeptide-binding protein OppA in Listeria monocytogenes
Sievers, RNA biology 2015 - “...2.40 1.50 1.002 0.452 2.63 lmo1584 lmo1585 lmo1983 / ilvD hypothetical transport protein transcriptional regulator CD4C T cell-stimulating antigen, lipoprotein...”
- Pyruvate carboxylase plays a crucial role in carbon metabolism of extra- and intracellularly replicating Listeria monocytogenes
Schär, Journal of bacteriology 2010 - “...lmo1298 (glnR)e lmo1299 (glnAe lmo1516d lmo1517d lmo1634 lmo1983 (ilvD) lmo1984 (ilvB)b lmo1985 (ilvN)b lmo2064 lmo2192d lmo2193d lmo2195d lmo2360 lmo2374...”
- Intracellular gene expression profile of Listeria monocytogenes
Chatterjee, Infection and immunity 2006 - “...(encoded by ilv and leu) was highly enhanced (lmo1983 to lmo1991). The TnrA protein, a negative regulator of branched-chain-amino-acid expression in B....”
- Genome-wide identification of Listeria monocytogenes CodY-binding sites
Biswas, Molecular microbiology 2020 - “...(K D 5 nM), glnK (lmo1517, LMRG_RS07550, LMRG_01453) (K D 5 nM), ilvD (lmo1983, LMRG_RS10020, LMRG_01131) (K D 10 nM), ilvE (lmo0978, LMRG_RS04930, LMRG_02078) (K D 12.5 nM), mfd (lmo0214, LMRG_RS01035, LMRG_02636) (K D 12.5 nM), and lmo0849 ( LMRG_RS04250, LMRG_02272) (K D 12.5 nM) genes...”
- Listeria monocytogenes σA Is Sufficient to Survive Gallbladder Bile Exposure
Boonmee, Frontiers in microbiology 2019 - “...0.00 LMRG_00826 lmo1375 Peptidase M20 2.07 0.00 LMRG_00942 lmo1489 LMRG_00945-LMRG_00939 RNA binding protein 2.22 0.00 LMRG_01131 lmo1983 ilvD ilv-leu Dihydroxy-acid dehydratase 2.62 0.01 LMRG_01132 lmo1984 ilvB Acetolactate synthase large subunit 3.12 0.00 LMRG_01134 lmo1986 ilvC Ketol-acid reductoisomerase 2.91 0.00 LMRG_01453 lmo1517 LMRG_01454-LMRG_01453 Nitrogen regulatory protein P-II...”
- Controlled branched-chain amino acids auxotrophy in Listeria monocytogenes allows isoleucine to serve as a host signal and virulence effector
Brenner, PLoS genetics 2018 - “...and ilvD transcription pattern under varying BCAA concentrations. (A) Schematic representation of rli60 and ilvD (LMRG_01131 ) genomic region. A single promoter is indicated upstream to rli60 (-10 and -35 are marked as white boxes). Two putative CodY binding sites are indicated upstream to rli60 and...”
SAUSA300_RS11035, USA300HOU_RS11060 dihydroxy-acid dehydratase from Staphylococcus aureus subsp. aureus USA300_TCH1516
SAUSA300_2006 dihydroxy-acid dehydratase from Staphylococcus aureus subsp. aureus USA300_FPR3757
35% identity, 92% coverage
- Metabolic diversity of human macrophages: potential influence on Staphylococcus aureus intracellular survival
Bertrand, Infection and immunity 2024 - “...). Among the top 10 essential genes that were unique to IL-10-treated HMDMs were ilvD (SAUSA300_RS11035), gudB (SAUSA300_RS04645), hemX (SAUSA300_RS08820), miaA (SAUSA300_RS06455), and ndh2 (SAUSA300_RS04560) ( Fig. 3A ; Table 1 ). In terms of untreated HMDMs, unique genes included itaA (SAUSA300_RS04930), pckA (SAUSA300_RS09470), katA (SAUSA300_RS06680),...”
- Absence of Protoheme IX Farnesyltransferase CtaB Causes Virulence Attenuation but Enhances Pigment Production and Persister Survival in MRSA
Xu, Frontiers in microbiology 2016 - “...protein S17 USA300HOU_RS04900 oppD1 1.91 4.92E-03 Oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein USA300HOU_RS11060 ilvD 1.89 1.79E-02 Dihydroxy-acid dehydratase USA300HOU_RS07110 dapB 1.84 1.91E-02 Dihydrodipicolinate reductase USA300HOU_RS13735 1.82 1.46E-02 Transcriptional regulator USA300HOU_RS08760 rplU 1.79 1.10E-02 Ribosomal protein L21 USA300HOU_RS07115 dapD 1.75 2.17E-02 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase USA300HOU_RS07100...”
- Cigarette Smoke Extract-Exposed Methicillin-Resistant Staphylococcus aureus Regulates Leukocyte Function for Pulmonary Persistence
Kulkarni, American journal of respiratory cell and molecular biology 2016 - “...SAUSA300_2521 SAUSA300_0204 SAUSA300_0083 SAUSA300_2008 SAUSA300_2006 leuD SAUSA300_0084 SAUSA300_0310 SAUSA300_0438 SAUSA300_0107 SAUSA300_1726 SAUSA300_0846...”
- The DUF59 Containing Protein SufT Is Involved in the Maturation of Iron-Sulfur (FeS) Proteins during Conditions of High FeS Cofactor Demand in Staphylococcus aureus
Mashruwala, PLoS genetics 2016 - “...] NE892 SAUSA300_2012( leuC ):: TN ( ermB ) LAC NARSA [ 105 ] NE718 SAUSA300_2006( ilvD ):: TN ( ermB ) LAC NARSA [ 105 ] JMB1432 fur :: tet LAC [ 106 ] JMB1163 acnA :: tet LAC [ 107 ] JMB3537 acnA ::...”
- Differential gene expression in Staphylococcus aureus exposed to Orange II and Sudan III azo dyes
Pan, Journal of industrial microbiology & biotechnology 2015 - “...SAUSA300_1231 SAUSA300_0864 SAUSA300_2538 SAUSA300_1808 SAUSA300_1916 SAUSA300_0914 SAUSA300_2006 ilvD EG Amino acid permease family protein Amino acid ABC...”
- “...cytoplasmic argininosuccinate synthase and ilvD (SAUSA300_2006) encoding dihydroxy-acid dehydratase were observed to be significantly up-regulated (3.14...”
- Bacillithiol has a role in Fe-S cluster biogenesis in Staphylococcus aureus
Rosario-Cruz, Molecular microbiology 2015 - “...NE892 SAUSA300_2013( leuD )::Tn( ermB ) JE2 ( Fey et al. , 2013 ) NE718 SAUSA300_2006( ilvD )::Tn( ermB ) JE2 ( Fey et al. , 2013 ) NE861 SAUSA300_1246( acnA )::Tn( ermB ) JE2 ( Fey et al. , 2013 ) NE1932 SASUA300_1513( sodA )::Tn(...”
- “...( ermB ) LAC JMB5272 SAUSA300_1349 ::kanR , 2013( leuD )::Tn( ermB ) LAC JMB3804 SAUSA300_2006( ilvD )::Tn( ermB ) LAC JMB4417 SAUSA300_1071( bshC ) , 2006( ilvD )::Tn( ermB ) LAC JMB3702 SAUSA300_1246( acnA )::Tn( ermB ) LAC JMB5225 SAUSA300_1349( bshA ) ::kanR , 1246(...”
- Nfu facilitates the maturation of iron-sulfur proteins and participates in virulence in Staphylococcus aureus
Mashruwala, Molecular microbiology 2015 - “...SAUSA300_0380( ahpC ):: TN ( ermB ) NARSA( Fey et al. , 2013 ) NE718 SAUSA300_2006 (ilvD)::TN(ermB) NARSA( Fey et al. , 2013 ) NE1175 SAUSA300_0839( nfu ):: TN ( ermB ) NARSA( Fey et al. , 2013 ) NE1932 sodA::TN(ermB) (SAUSA300_1513) NARSA( Fey et al....”
- “...al. , 2002 ) pEPSA5_ nfu SAUSA300_0839 pEPSA5_ acnA SAUSA300_1246 pEPSA5_FLAG_ leuCD SAUSA300_2012-3 pEPSA5_ IlvD SAUSA300_2006 pEPSA5_ ahpCF SAUSA300_0379-80 pCM11 Transcriptional fusion containing promoterless gfp ( Malone et al. , 2009 ) pCM11_ acnA p SAUSA300_1246 promoter pCM11_ dps p pCM11_ recA p SAUSA300_1178 promoter pET20b...”
A8IX80 dihydroxy-acid dehydratase from Chlamydomonas reinhardtii
38% identity, 86% coverage
SE1654 dihydroxy-acid dehydratase from Staphylococcus epidermidis ATCC 12228
35% identity, 92% coverage
GBAA_1853 dihydroxy-acid dehydratase from Bacillus anthracis str. 'Ames Ancestor'
BAS1717 dihydroxy-acid dehydratase from Bacillus anthracis str. Sterne
35% identity, 93% coverage
SAV2053 dihydroxy-acid dehydratase from Staphylococcus aureus subsp. aureus Mu50
SA1858 dihydroxy-acid dehydratase from Staphylococcus aureus subsp. aureus N315
SAOUHSC_02281 dihydroxy-acid dehydratase from Staphylococcus aureus subsp. aureus NCTC 8325
35% identity, 92% coverage
- Two novel point mutations in clinical Staphylococcus aureus reduce linezolid susceptibility and switch on the stringent response to promote persistent infection
Gao, PLoS pathogens 2010 - “...protease HtrA 3.34 SAV1083 argJ bifunctional ornithine acetyltransferase/N-acetylglutamate synthase, ArgJ 2.61 SAV1085 ornithine aminotransferase 2.69 SAV2053 ilvD dihydroxy-acid dehydratase 6.03 SAV2054 ilvB acetolactate synthase large subunit 4.54 SAV2057 leuA 2-isopropylmalate synthase 7.07 SAV2058 leuB 3-isopropylmalate dehydrogenase 2.58 SAV2059 leuC isopropylmalate isomerase large subunit 4.81 SAV2060 leuD...”
- Determination of essentiality and regulatory function of staphylococcal YeaZ in branched-chain amino acid biosynthesis
Lei, Virulence 2015 - “...YeaZ a ORF (N315) Gene Fold Change Sa0512 Sa1098 Sa1557 Sa1858 Sa1862 Sa1866 ilvE codY ccpA ilvD leuA ilvA 0.97 0.64 1.16 17.45 133.9 289.01 Note: aThe fold...”
- The essentiality of staphylococcal Gcp is independent of its repression of branched-chain amino acids biosynthesis
Lei, PloS one 2012 - “...ORF (N315) Gene Fold Change a Sa0512 ilvE 0.97 Sa1098 codY 0.78 Sa1557 ccpA 3.24 Sa1858 ilvD 5.45 Sa1862 leuA 68.59 Sa1866 ilvA 111.37 a The fold change represents the transcription levels of genes with the depletion of Gcp compared with those during the induction of...”
- Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism
Bohn, Nucleic acids research 2010 - “...) 0.37 0.48 14.80 Methylcitrate synthase SA1553 ( fhs ) 0.30 f 14.08 Formatetetrahydrofolate ligase SA1858 ( ilvD ) 3.45 1.90 Dihydroxy-acid dehydratase SA1859 ( ilvB ) 2.75 Acetolactate synthase large subunit SA1860 ( ilvH ) 3.12 Acetolactate synthase 1 regulatory subunit SA1861 ( ilvC )...”
- “...and total RNA were extracted. a SA0845 to SA849, SA1088-SA1089, SA1367-SA1365, SA1435 to SA1432, SA1518-SA1517, SA1858 to SA1865, likely organized in six distinct operons, respectively (genes for the same operon are expected to have a RsaE-dependent coordinated regulation). b Gene expression ratios between strains containing pAT12-RsaE...”
- Transcriptional signature following inhibition of early-stage cell wall biosynthesis in Staphylococcus aureus
O'Neill, Antimicrobial agents and chemotherapy 2009 - “...SA1254 SA1255 SA1256 SA1257 SA1532 SA1545 SA1546 SA1691 SA1858 SA1859 SA1860 SA1861 SA1862 SA1863 SA1864 SA1865 SA1866 SA2112 SA2221 SA2235 SA2236 SA2237 SA2240...”
- Microarray analysis of toxicogenomic effects of ortho-phenylphenol in Staphylococcus aureus
Jang, BMC genomics 2008 - “...SA1211 0.000158 -2.3 ATP-binding ABC transporter protein opp -2F Amino acid transport and metabolism sa_c4209s3561_a_at SA1858 0.000144 -6.2 dihydroxy-acid dehydratase (DAD) ilv D Amino acid transport and metabolism, Coenzyme metabolism sa_c4213s3565_a_at SA1859 0.000431 -8.0 acetolactate synthase isozyme III large subunit (AHAS-III) ilv B Amino acid transport...”
- “..."amino acid transport and metabolism", which contained half of the genes in that group. Further, SA1858 ( ilv D)-SA1859 ( ilv B) and SA1861 ( ilv C)-SA1862 ( leu A)-SA1863 ( leu B)-SA1864 ( leu C)-SA1865 ( leu D)-SA1866 ( ilv A) which were downregulated (table...”
- The roles of cell wall inhibition responsive protein CwrA in the pathogenicity of <i>Staphylococcus aureus</i>
Han, Virulence 2024 - “...SAOUHSC_00899 argG Argininosuccinate synthase; ArgG 6.8 SAOUHSC_00898 argH Argininosuccinate lyase; ArgH 6.3 2-Oxocarboxylic acid metabolism SAOUHSC_02281 Dihydroxy-acid dehydratase 1.7 Nitrogen metabolism SAOUHSC_02671 narK Putative nitrate transporter; NarK 1.9 SAOUHSC_02679 narJ Probable nitrate reductase molybdenum cofactor assembly chaperone; NarJ 1.2 SAOUHSC_02684 nasD Assimilatory nitrite reductase; NasD 1.1...”
- An extensively validated whole-cell biosensor for specific, sensitive and high-throughput detection of antibacterial inhibitors targeting cell-wall biosynthesis
Galarion, The Journal of antimicrobial chemotherapy 2023 - “...former case as candidates for generating CWBI-responsive biosensors: gltB (SAOUHSC_00435), oppB (SAOUHSC_00923), sgtB (SAOUHSC_02012), ilvD (SAOUHSC_02281) and ORF2768 (SAOUHSC_03021). To our knowledge, only one of these ( sgtB ) has previously been employed as the basis for a staphylococcal CWBI biosensor. 9 For each of these,...”
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...also significantly downregulated (0.132-fold to 0.331-fold) ( p < 0.05), including a dihydroxy-acid dehydratase ( SAOUHSC_02281 ), an acetolactate synthase large subunit biosynthetic type ( SAOUHSC_02282 ), a conserved hypothetical protein ( SAOUHSC_02283 ), a ketol-acid reductoisomerase ( SAOUHSC_02284 ), a 2-isopropylmalate synthase ( SAOUHSC_02285 ),...”
- “...Ketol-acid reductoisomerase SAOUHSC_02283 0.184 Conserved hypothetical protein SAOUHSC_02282 0.208 Acetolactate synthase large subunit biosynthetic type SAOUHSC_02281 0.331 Dihydroxy-acid dehydratase ABC transporters SAOUHSC_00634 0.012 ABC transporter substrate-binding protein putative SAOUHSC_00636 0.014 Iron (chelated) ABC transporter permease protein putative SAOUHSC_00637 0.015 Conserved hypothetical protein SAOUHSC_01945 0.095 Membrane protein...”
- Teg58, a small regulatory RNA, is involved in regulating arginine biosynthesis and biofilm formation in Staphylococcus aureus
Manna, Scientific reports 2022 - “...3.41 SAOUHSC_02564 Urease accessory protein, ureG 4811 1747 2.75 Valine, leucine, and isoleucine biosynthesis pathway SAOUHSC_02281 Dihydroxy-acid dehydratase, ilvD 147 501 3.41 SAOUHSC_02282 Acetolactate synthase large subunit, ilvB 246 804 3.27 SAOUHSC_02284 2-dehydropantoate 2-reductase, ilvC 315 906 2.88 SAOUHSC_02283 Acetolactate synthase small subunit, ilvH 283 671...”
- The Staphylococcus aureus KdpDE two-component system couples extracellular K+ sensing and Agr signaling to infection programming
Xue, Infection and immunity 2011 - “...SAOUHSC_01389 SAOUHSC_00113 SAOUHSC_01619 SAOUHSC_01825 SAOUHSC_02281 SAOUHSC_02282 SAOUHSC_02283 SAOUHSC_02671 SAOUHSC_02679 SAOUHSC_02680 SAOUHSC_02682...”
G7IRL3 dihydroxy-acid dehydratase from Medicago truncatula
36% identity, 87% coverage
- Label-free quantitative proteomic analysis of alfalfa in response to microRNA156 under high temperature
Arshad, BMC genomics 2020 - “...MTR_5g096970 3.13 0.0035 Carboxy-terminal TIM barrel domain enolase G7JMP4 MTR_4g104300 3.10 0.0345 F-box/RNI/FBD-like domain protein G7IRL3 MTR_2g089340 2.95 0.0127 Dihydroxyacid dehydratase G7KG90 MTR_5g012030 2.86 0.0127 Putative Heat shock chaperonin-binding A0A072VBG9 MTR_2g084715 2.84 0.0018 Putative transcription factor C3H family G7L4S2 MTR_7g088490 2.77 0.0327 Proteasome subunit beta A0A072UGC6...”
- “...0.0157 Sterol regulatory element-binding protein G7IF74 MTR_1g088640 4.31 0.0048 Putative universal stress protein A a G7IRL3 MTR_2g089340 3.60 0.0076 Dihydroxyacid dehydratase G7LGJ8 MTR_8g095680 3.33 0.0173 Calnexin 2 a G7KWU8 MTR_7g024390 3.24 0.0160 Heat shock cognate 70kDa protein a G7L491 MTR_7g012820 2.70 0.0080 Casein lytic proteinase B3...”
HD73_2029 dihydroxy-acid dehydratase from Bacillus thuringiensis serovar kurstaki str. HD73
35% identity, 93% coverage
NWMN_1960 dihydroxy-acid dehydratase from Staphylococcus aureus subsp. aureus str. Newman
SACOL2042 dihydroxy-acid dehydratase from Staphylococcus aureus subsp. aureus COL
35% identity, 92% coverage
- (p)ppGpp/GTP and Malonyl-CoA Modulate Staphylococcus aureus Adaptation to FASII Antibiotics and Provide a Basis for Synergistic Bi-Therapy
Pathania, mBio 2021 - “...triggers (p)ppGpp synthesis ( 24 ) ( Fig.1A and data not shown). P ilvD -lacZ (NWMN_1960) and P oppB -lacZ (NWMN_0856) were upregulated, and P cshA -lacZ (NWMN_1985) was downregulated by mupirocin. Nutrient starvation during stationary phase induces the stringent response in E. coli ( 16...”
- “...used to transform DNA in S. aureus ( 45 ). (p)ppGpp sensors. The genes ilvD (NWMN_1960) and oppB (NWMN_0856) are upregulated, while the cshA (NWMN_1985) gene is downregulated, upon stringent response induction ( 24 , 40 , 46 ). The corresponding stringent response sensors P ilvD...”
- CodY in Staphylococcus aureus: a regulatory link between metabolism and virulence gene expression
Pohl, Journal of bacteriology 2009 - “...NWMN_1348 NWMN_1616 NWMN_1617 NWMN_1749 NWMN_1750 NWMN_1960 NWMN_1961 NWMN_1962 NWMN_1963 NWMN_1964 NWMN_1965 NWMN_1966 NWMN_2347 NWMN_2500 NWMN_2501 NWMN_2571...”
- In vitro and in vivo models of Staphylococcus aureus endophthalmitis implicate specific nutrients in ocular infection
Sadaka, PloS one 2014 - “...5.0 (1.9) 5.6 (1.2) ig_SACOL2041-2 Intergenic region upstream ofSACOL2042 ilvD ( ilvD promoterregion) 23.4 (4.3) SACOL2042 ilvD Dihydroxy-acid dehydratase 48.5 (1.4) 11.3 (5.4) 26.4 (1.4) SACOL2043 ilvB Acetolactate synthase large subunit 80.2 (1.2) 39.4 (1.2) SACOL2044 Acetolactate synthase 1 regulatory subunit 157.6 (1.7) 8.6 (3.1) 85.9...”
- Global analysis of the Staphylococcus aureus response to mupirocin
Reiss, Antimicrobial agents and chemotherapy 2012 - “...typA SACOL1136 SACOL1206 ileS SACOL1272 codY SACOL1759 SACOL2042 ilvD SACOL2054 sigB SACOL2058 SACOL2131 SACOL2379 SACOL2484 csb7 SACOL2511 fnbA SACOL2597 a b...”
- “...Asp23 IleS SACOL2050 SACOL2043 IlvA2 IlvB SACOL2045 IlvC SACOL2042 IlvD SACOL2049 LeuD Asp23-4 IleS-2 IleS-3 IlvA2-1 IlvB-1 IlvB-2 IlvC-1 IlvC-3 IlvD-1 IlvD-2...”
- A new oxidative sensing and regulation pathway mediated by the MgrA homologue SarZ in Staphylococcus aureus
Chen, Molecular microbiology 2009 - “...5.2 Fructose permiase SACOL2525 gntK 6.5 + Gluconokinase SACOL2516 gntR 5.6 + Gluconate operon repressor SACOL2042 ilvD 3.2 -2.3 Dihydroxy-acid dehydrates SACOL2183 lacD 2.0 Tagatose 1, 6-diphosphate aldrase SACOL0248 lrgB 3.2 Holinlike protein SACOL1428 lysC 4.4 Aspartokinase, and subunits SACOL1551 malA 4.7 -glucosidase SACOL0192 msmX 2.1...”
A0A481UJA7 dihydroxy-acid dehydratase (EC 4.2.1.9) from Hevea brasiliensis (see paper)
36% identity, 89% coverage
Ssal_00131 dihydroxy-acid dehydratase from Streptococcus salivarius 57.I
34% identity, 90% coverage
VDAG_04620 dihydroxy-acid dehydratase from Verticillium dahliae VdLs.17
35% identity, 89% coverage
- The Transcription Factor VdHapX Controls Iron Homeostasis and Is Crucial for Virulence in the Vascular Pathogen Verticillium dahliae
Wang, mSphere 2018 - “...homoaconitase; hemA ( VDAG_06343 ), encoding aminolevulinic acid synthase; VDAG_00564 , encoding isopropylmalate dehydratase; and VDAG_04620 , encoding dihydroxy acid dehydratase. After a 45-min shift from iron-limiting to iron-replete conditions, deletion of VdHapX impairs the transcriptional activation of VDAG_02332 , VDAG_08540 , VDAG_06343 , and VDAG_04620...”
- “...+Fe). Transcript levels of acoA , lysF , hemA , cycA , VDAG_00564 , and VDAG_04620 were analyzed under the different iron conditions shown. Averages of the gene expression values were normalized against the V. dahliae -tubulin gene. Error bars represent standard deviations. Asterisks represent signicant...”
ILVD_ARATH / Q9LIR4 Dihydroxy-acid dehydratase, chloroplastic; AthDHAD; DAD; EC 4.2.1.9 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Q9LIR4 dihydroxy-acid dehydratase (EC 4.2.1.9) from Arabidopsis thaliana (see 2 papers)
NP_189036 dehydratase family from Arabidopsis thaliana
AT3G23940 dehydratase family from Arabidopsis thaliana
36% identity, 89% coverage
- function: Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo- 3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3- dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively.
catalytic activity: (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (RHEA:24809)
catalytic activity: (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2- oxopentanoate + H2O (RHEA:27694)
cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit.)
cofactor: Mg(2+) - Dihydroxyacid dehydratase is important for gametophyte development and disruption causes increased susceptibility to salinity stress in Arabidopsis.
Zhang, Journal of experimental botany 2015 - GeneRIF: Dihydroxyacid dehydratase (DHAD) is highly expressed in most vegetative and reproductive tissues. It is an essential gene, and complete disruption caused partial sterility in both male and female gametophyte phases. In addition, reduced expression of DHAD in knockdown mutants resulted in a reduction in the accumulation of all three BCAAs in roots and, as a consequence, led to a shorter root phenotype.[DHAD]
- Structure-Guided Modulation of the Catalytic Properties of [2Fe-2S]-Dependent Dehydratases
Melse, Chembiochem : a European journal of chemical biology 2022 - “...A0A4R3LQ44, Ft DHAD: A0A1I2J0Y3, Ss DHAD: Q97UB2, Rl ArDT: B5ZZ34, Mt DHAD: A0A0E8UWV6, At DHAD: Q9LIR4, Cc XylDHT: Q9A9Z2. Conflict of interest The authors declare no conflict of interest. 1 Supporting information As a service to our authors and readers, this journal provides supporting information supplied...”
- Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria
Grabsztunowicz, BMC plant biology 2020 - “...decarboxylase 2 56 Q94A94, At5g11880 Diaminopimelate epimerase 86 Q9LFG2, At3g53580 Dihydroxy-acid dehydratase 30, 43, 45 Q9LIR4, At3g23940 Glutamine synthetase 55 Q43127, At5g35630 Homoserine kinase 83, 85 Q8L7R2, At2g17265 Imidazole glycerol phosphate synthase hisHF 4346, 56 Q9SZ30, At4g26900 Ketol-acid reductoisomerase 36, 37 Q05758, At3g58610 Ornithine carbamoyltransferase 85...”
- Proteomic Analysis of Arabidopsis pldα1 Mutants Revealed an Important Role of Phospholipase D Alpha 1 in Chloroplast Biogenesis
Takáč, Frontiers in plant science 2019 - “...At5g47840 Adenylate kinase 2, chloroplastic mutant unique mutant unique n.a. n.a. 11.01/8.51 3/2 19.43/14.49 3/4 Q9LIR4 At3g23940 Dihydroxy-acid dehydratase, chloroplastic Unique in Col-0 0.31 n.a. 0.04 7.31/7.59 2/2 6.09/6.09 3/5 Q8L940 At5g01410 Pyridoxal 5'-phosphate synthase subunit PDX1.3 1.49 1.85 0.053 0.018 23.65/23.94 6/6 29.77/29.77 28/28 Q9LEU8...”
- Involvement of a universal amino acid synthesis impediment in cytoplasmic male sterility in pepper
Fang, Scientific reports 2016 - “...peptide fragments were derived from the conserved protein sequences of the UniProt accessions Q9C5U8 (HDH), Q9LIR4 (DAD), Q9SIE1 (ATAAT), P47999 (CS), P54887 (P5CS), Q9LV03 (GS), and CAC80377 (GAPDH). Each peptide, along with an additional N-terminal cysteine (not part of the protein sequence), was synthesized and purified...”
- “...1.850.22 P54887 Delta-1-pyrroline-5-carboxylate synthase A 98.41 2 717 5.89 77.70 1 0.910.11 0.330.09 0.420.03 0.360.03 Q9LIR4 Dihydroxy-acid dehydratase 109.82 2 608 5.44 61.06 1 1.530.33 0.620.08 0.420.05 0.440.04 Q9SI75 Elongation factor G 430.06 4 783 5.06 77.67 1 3.240.12 1.350.23 1.840.20 2.600.15 Q9C9C4 Enolase 1 125.74...”
- Structural Bases of Dihydroxy Acid Dehydratase Inhibition and Biodesign for Self-Resistance
Zang, Biodesign research 2024 (no snippet) - Molecular mechanisms of resistance to Myzus persicae conferred by the peach Rm2 gene: A multi-omics view
Le, Frontiers in plant science 2022 - “...2.60E-02 ALS; Acetolactate synthase Prupe_3G094300 AT1G80560 82 Yes -1.5 4.30E-07 IMDH2; 3-isopropylmalate dehydrogenase 2 Prupe_1G003100 AT3G23940 82 Yes -3.2 7.70E-21 DHAD; Dihydroxy-acid dehydratase Prupe_1G416900 AT3G49680 59 No 3.0 1.70E-03 BCAT3; Branched-chain-amino-acid aminotransferase 3 Lysine metabolism Prupe_8G007000 AT1G31230 80 Yes -2.7 8.60E-10 AKHSDH1;Aspartokinase/homoserine dehydrogenase 1 Prupe_1G334400 AT1G14810...”
- Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria
Grabsztunowicz, BMC plant biology 2020 - “...2 56 Q94A94, At5g11880 Diaminopimelate epimerase 86 Q9LFG2, At3g53580 Dihydroxy-acid dehydratase 30, 43, 45 Q9LIR4, At3g23940 Glutamine synthetase 55 Q43127, At5g35630 Homoserine kinase 83, 85 Q8L7R2, At2g17265 Imidazole glycerol phosphate synthase hisHF 4346, 56 Q9SZ30, At4g26900 Ketol-acid reductoisomerase 36, 37 Q05758, At3g58610 Ornithine carbamoyltransferase 85 O50039,...”
- “...parallel pathway towards L-valine and L-isoleucine biosynthesis [ 22 , 29 ]. Dihydroxyacid dehydratase (DHAD, At3g23940), performing the third step in synthesis of L-isoleucine from 2-oxobutanoate or synthesis of L-valine from two molecules of pyruvate [ 30 ], was identified in spots 30, 43 and 45....”
- A Global Proteomic Approach Sheds New Light on Potential Iron-Sulfur Client Proteins of the Chloroplastic Maturation Factor NFU3
Berger, International journal of molecular sciences 2020 - “...J protein C82 At4g29890 CMO n.d. n.q. rieske 2Fe/2S Glycine betaine biosynthesis Choline monooxygenase (putative) At3g23940 DHAD n.v. n.v. 2Fe2S Branched chain amino acid biosynthesis Dihydroxyacid dehydratase At1g03055 DWARF27.1 n.d. n.q. 4Fe4S (?) Strigolactone biosynthesis DWARF27.1 At1g64680 DWARF27.2 1.05 * n.q. 4Fe4S (?) Unknown DWARF27.2 At4g01995...”
- Redox Conformation-Specific Protein-Protein Interactions of the 2-Cysteine Peroxiredoxin in Arabidopsis
Liebthal, Antioxidants (Basel, Switzerland) 2020 - “...60S ribosomal protein L26-1 (AT3G49910) Glutathione S-transferase F8 (AT2G47730) ATPase alpha subunit (AtCg00120) Dihydroxy-acid dehydratase (AT3G23940) PLAT domain-containing protein 1 (AT4G39730) Photosystem I reaction center subunit II-1 (AT4G02770) Monodehydroascorbate reductase 6 (AT1G63940) E-Z type HEAT repeat- protein (AT3G62530) Chlorophyll a-b binding protein 2 (AT1G29920) Protease Do-like...”
- Proteomic Analysis of Arabidopsis pldα1 Mutants Revealed an Important Role of Phospholipase D Alpha 1 in Chloroplast Biogenesis
Takáč, Frontiers in plant science 2019 - “...Adenylate kinase 2, chloroplastic mutant unique mutant unique n.a. n.a. 11.01/8.51 3/2 19.43/14.49 3/4 Q9LIR4 At3g23940 Dihydroxy-acid dehydratase, chloroplastic Unique in Col-0 0.31 n.a. 0.04 7.31/7.59 2/2 6.09/6.09 3/5 Q8L940 At5g01410 Pyridoxal 5'-phosphate synthase subunit PDX1.3 1.49 1.85 0.053 0.018 23.65/23.94 6/6 29.77/29.77 28/28 Q9LEU8 At5g10920...”
- Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action
Yan, Nature 2018 - “...we expressed and purified housekeeping DHAD from both A. terreus (XP_001208445.1, fDHAD) and A. thaliana (AT3G23940, pDHAD), as well as the putative self-resistance enzyme AstD ( Supplementary Fig. 6 ). Both housekeeping DHAD enzymes converted dihydroxyisovalerate to ketoisovalerate (pDHAD: k cat = 1.2 sec 1 ,...”
- “...primers pDHAD-pET-F and pDHAD-pET-R were used to amplify a 1.7 kb DNA fragment containing pdhad (AT3G23940). The PCR product was cloned into pET28a using Nhe I and Not I restriction sites. The resulting plasmid pDHAD-pET was transformed into E.coli BL21 (DE3) to give TY08. To express...”
- Function and maturation of the Fe-S center in dihydroxyacid dehydratase from Arabidopsis
Gao, The Journal of biological chemistry 2018 - “...purchased from GE Healthcare. Plasmid construction The AtDHAD (At3g23940) coding sequence was amplified by PCR from rosette cDNAs using the following primers:...”
- More
SXYL_00875 dihydroxy-acid dehydratase from Staphylococcus xylosus
34% identity, 92% coverage
PADG_07241 dihydroxy-acid dehydratase from Paracoccidioides brasiliensis Pb18
36% identity, 85% coverage
PAAG_00014 dihydroxy-acid dehydratase from Paracoccidioides lutzii Pb01
36% identity, 85% coverage
- Hemoglobin uptake by Paracoccidioides spp. is receptor-mediated
Bailão, PLoS neglected tropical diseases 2014 - “...Methionine biosynthesis 1 PAAG_08166 4-hydroxyphenylpyruvate dioxygenase 203.44 3.00 *** 1.13.11.27 Tyrosine and phenylalanine degradation 1 PAAG_00014 dihydroxy-acid dehydratase 312.52 10.83 0.73 4.2.1.9 Valine and isoleucine biosynthesis 2 PAAG_02554 3-hydroxyisobutyryl-CoA hydrolase 402.87 9.75 0.58 3.1.2.4 Valine degradation 2 PAAG_01194 2-oxoisovalerate dehydrogenase subunit beta 219.86 6.00 *** 1.2.4.4...”
MGL_3741 uncharacterized protein from Malassezia globosa CBS 7966
36% identity, 89% coverage
- Production and Quantification of Virulence Factors in Malassezia Species
Hadrich, Polish journal of microbiology 2022 - “...of Aghaei Gharehbolagh et al. (2018), RT-PCR was used to investigate the contribution of the MGL_3741 gene to the pathogenicity of M. globosa in pityriasis versicolor. These authors revealed that this gene can be related to the yeasts pathogenicity and is a candidate for the new...”
- “...Hashemi SJ Daie Ghazvini R Asgari Y Agha Kuchak Afshari S Seyedmousavi S Rezaie S MGL_3741 gene contributes to pathogenicity of Malassezia globosa in pityriasis versicolor Mycoses 2018 Dec 61 12 938 944 10.1111/myc.12840 30106184 Angiolella L Leone C Rojas F Mussin J de Los Angeles...”
- Malassezia-Associated Skin Diseases, the Use of Diagnostics and Treatment
Saunte, Frontiers in cellular and infection microbiology 2020 - “...in lesions. But the reasons for hyphal growth are still unknown. The activation of the MGL_3741 gene which encodes the enzyme Dihydroxy acid dehydratase (DHAD) in M. globosa has been implicated as it is present in lesional but not non-lesional skin (Aghaei Gharehbolagh et al., 2018...”
- “...S. J. Daie Ghazvini R. Asgari Y. Agha Kuchak Afshari S. . ( 2018 ). MGL_3741 gene contributes to pathogenicity of Malassezia globosa in pityriasis versicolor . Mycoses 61 , 938 944 . 10.1111/myc.12840 30106184 Akaza N. Akamatsu H. Sasaki Y. Kishi M. Mizutani H. Sano...”
- MGL_3741 gene contributes to pathogenicity of Malassezia globosa in pityriasis versicolor
Aghaei, Mycoses 2018 (PubMed)- “...2018 DOI: 10.1111/myc.12840 ORIGINAL ARTICLE MGL_3741 gene contributes to pathogenicity of Malassezia globosa in pityriasis versicolor Sanaz Aghaei...”
- “...PCR to investigate the differentially expressed of the MGL_3741 gene in healthy and pathogenic states. Our results indicate a significant difference between two...”
8hs0A / Q9LIR4 The mutant structure of dhad v178w
36% identity, 94% coverage
- Ligands: fe2/s2 (inorganic) cluster; magnesium ion (8hs0A)
Caur_2851 dihydroxy-acid dehydratase from Chloroflexus aurantiacus J-10-fl
37% identity, 93% coverage
- Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
Tang, BMC genomics 2011 - “...ilvA (Caur_2585, Caur_3892), isoleucine/leucine/valine biosynthesis (Caur_0041, Caur_0163 - 0169, Caur_0329 - 0331, Caur_0488, Caur_1435, and Caur_2851) Sulfur metabolism Sulfur reduction operon (Caur_0686 - 0692), a sulfate adenylyl-transferase/adenylylsulfate kinase (Caur_2113), cysK (Caur_1341), cysM (Caur_3489), sqr (Caur_3894, type II SQR), sulfotransferase (Caur_2114). B808-866 light-harvesting complex Caur_2090 (-subunit) and...”
ABH19_09600 dihydroxy-acid dehydratase from Leptospirillum sp. Group II 'CF-1'
36% identity, 93% coverage
- A novel gene from the acidophilic bacterium Leptospirillum sp. CF-1 and its role in oxidative stress and chromate tolerance
Javier, Biological research 2022 - “...contained in an operon, here named the och operon, that also contains ABH19_09585, ABH19_09595 and ABH19_09600 genes. The expression of the och operon was significantly up-regulated in Leptospirillum sp. CF-1 exposed to 5mM K 2 CrO 4 for 15 and 30min. Genes of this operon potentially...”
- “...are found, while downstream, genes encoding a hypothetical protein (ABH19_09595), a possible dihydroxy-acid dehydratase (DHAD, ABH19_09600) and the translational factor Sua5 (ABH19_09605) were detected. The six candidate genes were analyzed to evaluate co-transcription using RT-PCR, in order to define whether ABH19_09590 is contained in an operon....”
FOIG_06470 dihydroxy-acid dehydratase, mitochondrial from Fusarium odoratissimum NRRL 54006
35% identity, 89% coverage
PHYSODRAFT_557322 hypothetical protein from Phytophthora sojae
36% identity, 87% coverage
- Insights into the adaptive response of the plant-pathogenic oomycete Phytophthora capsici to the fungicide flumorph
Pang, Scientific reports 2016 - “...protein PHYSODRAFT_349787 Others 348683892 hypothetical protein PHYSODRAFT_353864 Others 348683825 putative dehydratase Others 348681277 hypothetical protein PHYSODRAFT_557322 Others 348673004 hypothetical protein PHYSODRAFT_354913 Others 348673003 hypothetical protein PHYSODRAFT_354912 Others 262105863 aldo/keto reductase family Others 262103226 succinate semialdehyde dehydrogenase Others 262099089 succinate dehydrogenase iron-sulfur protein Others 262098735 alcohol dehydrogenase,...”
PITG_22685 dihydroxy-acid dehydratase, putative from Phytophthora infestans T30-4
36% identity, 87% coverage
BBA_09252 dihydroxy-acid dehydratase from Beauveria bassiana ARSEF 2860
35% identity, 85% coverage
- Unveiling a Novel Role of Cdc42 in Pyruvate Metabolism Pathway to Mediate Insecticidal Activity of Beauveria bassiana
Guan, Journal of fungi (Basel, Switzerland) 2022 - “...implicated an increase in pyruvate accumulation in the cdc42 mutant. Moreover, several upregulated genes (BBA_00790, BBA_09252, BBA_01687, BBA_04309, and BBA_08608) were involved in the participation of pyruvate in tricarboxylic acid (TCA) cycle and/or valine, leucine, and isoleucine biosynthesis. Three other upregulated genes (BBA_ 08607, BBA_02336, and...”
SPAC17G8.06c dihydroxy-acid dehydratase from Schizosaccharomyces pombe
35% identity, 87% coverage
- Response to leucine in Schizosaccharomyces pombe (fission yeast)
Ohtsuka, FEMS yeast research 2022 - “.... 1974 ). In S. pombe , this enzyme is predicted to be encoded by SPAC17G8.06c, but this prediction has not been confirmed. Therefore, we investigated whether S. cerevisiae ILV3 encoding dihydroxy-acid dehydratase can complement this gene (Fig. 2 ). The deletion mutant of SPAC17G8.06c can...”
- “...also essential for the growth of S. pombe in EMM. The defective growth of the SPAC17G8.06c mutant was complemented not only by the expression of S. pombe SPAC17G8.06c itself but also by the S. cerevisiae ILV3 . This finding suggests that S. pombe SPAC17G8.06c is a...”
- Posttranslational Arginylation Enzyme Arginyltransferase1 Shows Genetic Interactions With Specific Cellular Pathways in vivo
Wiley, Frontiers in physiology 2020 - “...protein L18 RPL18B,RPL18A RPL18 rpl3702 SPCC1223.05c 0.00161788 3.15266 60S ribosomal protein L37 (predicted) RPL37B,RPL37A RPL37 SPAC17G8.06c 0.00198848 3.09195 Dihydroxy-acid dehydratase (predicted) ILV3 his7 SPBC29A3.02c 0.0021838 3.06403 Phosphoribosyl-AMP cyclohydrolase/phosphoribosyl- ATP pyrophosphohydrolase His7 HIS4 lys9 SPBC3B8.03 0.0023364 3.04376 Saccharopine dehydrogenase LYS9 AASS his5 SPBC21H7.07c 0.002481 3.02565 Imidazoleglycerol-phosphate dehydratase...”
- “...hits list Mitochondrion (mitochondria) GO:0005739 428 19 mpn1, SPACUNK4.13c, lip2, gor2, hmt2, sod2, SPAC14C4.01c, qcr8, SPAC17G8.06c, cox6, oma1, cys2, SPBC1271.14, SPBC1703.13c, atp3, atp15, coq7, rps1802, ppr5 Mitochondria inner membrane GO:0005743 71 4 oma1, SPBC1703.13c, coq7, atp15 The numbers of those genes in the effective library (non-sterile)...”
- Php4 Is a Key Player for Iron Economy in Meiotic and Sporulating Cells
Brault, G3 (Bethesda, Md.) 2016 - “...synthase Glt1 (predicted) 2.982 3.254 913 a , 881 a , 266 a , 199 SPAC17G8.06c Dihydroxy-acid dehydratase (predicted) 2.781 3.534 327, 284 a SPBC21H7.07c his5 + Imidazoleglycerol-phosphate dehydratase His5 2.636 2.623 994, 269, 165 a SPAC13G7.06 met16 + Phosphoadenosine phosphosulfate reductase 2.463 2.461 820 a...”
- Metabolic remodeling in iron-deficient fungi
Philpott, Biochimica et biophysica acta 2012 - “...GLT1 Afu1g07380 glt1 -isopropylmalate isomerase (Leu) LEU1 Afu2g11260 leu2 dihydroxy acid dehydratase (Ile/Val) ILV3 Afu2g14210 SPAC17G8.06C Homoaconitase (Lys) LYS4 lysF lys2 Fe-S cluster biosynthesis iron sulfur assembly protein ISA1 Afu4g10690 isa1 TCA cycle succinate dehydrogenase, flavoprotein subunit SDH1 Afu3g07810 sdh1 succinate dehydrogenase, cytochrome b560 subunit SDH3...”
- Key function for the CCAAT-binding factor Php4 to regulate gene expression in response to iron deficiency in fission yeast
Mercier, Eukaryotic cell 2008 - “...516, 387, 236 16.8 3.5 21.9 3.1 SPAC17G8.06c SPAC343.16 SPBC21H7.07c SPAC1782.11 SPBC27.08c SPBC1709.19c Fe related SPBC1683.10c SPAC23E2.01 pcl1 fep1 Ferrous...”
CNH01530 dihydroxy-acid dehydratase, putative from Cryptococcus neoformans var. neoformans JEC21
34% identity, 89% coverage
- Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets
Tezcan, Frontiers in bioinformatics 2023 - “...Glycine, Serine and Threonine Metabolism CND03580 Amino Sugar and Nucleotide Sugar Metabolism CNA02570, CNN01460, CNF02480, CNH01530 CNH01520, CNA02270, CNH03010 Valine, Leucine and Isoleucine Biosynthesis and Degradation CND01200, CNK00580, CND03850, CNG00170, CND06290 Lysine Biosynthesis CNJ01640 Transport CNM00100 Terpenoid Backbone Biosynthesis CNB02610, CNH03390, CNN02320 Starch and Sucrose Metabolism...”
Cj0013 dihydroxy-acid dehydratase from Campylobacter jejuni subsp. jejuni NCTC 11168
34% identity, 93% coverage
- A Systematic Review of Campylobacter jejuni Vaccine Candidates for Chickens
Pumtang-On, Microorganisms 2021 - “...26 ] 60 10 8 CFU of Salmonella Enteritidis (SE) vectored vaccine expressing Omp18 protein (Cj0013), peptidoglycan associated lipoprotein of Salmonella (PAL of Salmonella ), and high mobility group box 1 protein (HMGB1), orally C. jejuni field strain (6.8) and Day 7 43 7.14 0.29 7.70...”
- “...61 10 8 CFU of SE vectored vaccine expressing HMGB1, PAL of Salmonella , and Cj0013, orally C. jejuni field strain (6.8) and Day 7 43 7.5 3 7.70 0.29 Non-significant 0.2 log10 reduction (non-significant) Yang et al. [ 58 ] 62 10 8 CFU of...”
- Identification of Campylobacter jejuni genes contributing to acid adaptation by transcriptional profiling and genome-wide mutagenesis
Reid, Applied and environmental microbiology 2008 - “...(nuoI) (nuoG) (gltA) Amino acid biosynthesis and transport Cj0007 (gltB) Cj0013 (ilvD) Cj1015c (livG) DOWN (2, 12) ND UP (4) DOWN (4) DOWN (5.5) UP (12, 20) UP...”
- Signature-tagged transposon mutagenesis studies demonstrate the dynamic nature of cecal colonization of 2-week-old chickens by Campylobacter jejuni
Grant, Applied and environmental microbiology 2005 - “...Intergenic cj1191-dctA cj1194 HS41.24a cj0337c cj0631c cj0970 cj1471c cj0013 cj1544c cj0948c --b cj1716c cj0893c --c cj1633 Unmatched cj1468 cj1256c cj1565c a b...”
ILVC_ASPFU / Q4X099 Dihydroxy-acid dehydratase ilvC, mitochondrial; DHAD ilvC; EC 4.2.1.9 from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) (Neosartorya fumigata) (see paper)
AFUA_2G14210, Afu2g14210 dihydroxy acid dehydratase Ilv3, putative from Aspergillus fumigatus Af293
35% identity, 85% coverage
- function: Dihydroxyacid dehydratase that catalyzes the third step in the common pathway leading to biosynthesis of branched-chain amino acids (PubMed:23028460). Catalyzes the dehydration of (2R,3R)-2,3- dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2- oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3- dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3- methylbutanoate (2-oxoisovalerate), the penultimate precursor to L- isoleucine and L-valine, respectively (By similarity). IlvC and the branched-chain amino acid biosynthesis are crucial for virulence and may be a potential target to develop antifungal agents (PubMed:23028460).
catalytic activity: (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (RHEA:24809)
catalytic activity: (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2- oxopentanoate + H2O (RHEA:27694)
cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit.)
cofactor: Mg(2+)
disruption phenotype: Requires supplementation with isoleucine and valine for growth (PubMed:23028460). Results in considerably lower kidney tissue burden in murine infection models (PubMed:23028460). - Assembly and disassembly of Aspergillus fumigatus conidial rodlets
Valsecchi, Cell surface (Amsterdam, Netherlands) 2019 - “...AFUB_043810 AFUA_3G04160 B0XZB5 Ser/Thr protein phosphatase family Yes 0.51 14.40 626 71.262 377700 1.3 AFUB_029830 AFUA_2G14210 B0XTT1 Mitochondrial dihydroxy acid dehydratase, putative No 0.51 12.60 642 68.256 371027 5.0 AFUB_098310 AFUA_4G04690 B0YE87 Uncharacterized protein No 0.73 18.70 209 22.594 333057 1.0 AFUB_025060 AFUA_2G09180 B0XRW4 Coatomer subunit...”
- The Aspergillus fumigatus dihydroxyacid dehydratase Ilv3A/IlvC is required for full virulence
Oliver, PloS one 2012 - “...the filamentous fungus Aspergillus fumigatus by homology to Saccharomyces cerevisiae ILV3. Two of these genes, AFUA_2G14210 and AFUA_1G03550, initially designated AfIlv3A and AfIlv3B for this study, clustered in the same group as S. cerevisiae ILV3 following phylogenetic analysis. To investigate the functions of these genes, AfIlv3A...”
- “...for branched-chain amino acid synthesis in A. fumigatus . A recombinant AfIlv3A protein derived from AFUA_2G14210 was shown to have DHAD activity in an in vitro assay, confirming that AfIlv3A is a DHAD. In addition we show that mutants lacking AfIlv3A and ilv3B exhibit reduced levels...”
- Metabolic remodeling in iron-deficient fungi
Philpott, Biochimica et biophysica acta 2012 - “...(Glu) GLT1 Afu1g07380 glt1 -isopropylmalate isomerase (Leu) LEU1 Afu2g11260 leu2 dihydroxy acid dehydratase (Ile/Val) ILV3 Afu2g14210 SPAC17G8.06C Homoaconitase (Lys) LYS4 lysF lys2 Fe-S cluster biosynthesis iron sulfur assembly protein ISA1 Afu4g10690 isa1 TCA cycle succinate dehydrogenase, flavoprotein subunit SDH1 Afu3g07810 sdh1 succinate dehydrogenase, cytochrome b560 subunit...”
B0XTT1 dihydroxy-acid dehydratase from Aspergillus fumigatus (strain CBS 144.89 / FGSC A1163 / CEA10)
35% identity, 81% coverage
- Assembly and disassembly of Aspergillus fumigatus conidial rodlets
Valsecchi, Cell surface (Amsterdam, Netherlands) 2019 - “...AFUA_3G04160 B0XZB5 Ser/Thr protein phosphatase family Yes 0.51 14.40 626 71.262 377700 1.3 AFUB_029830 AFUA_2G14210 B0XTT1 Mitochondrial dihydroxy acid dehydratase, putative No 0.51 12.60 642 68.256 371027 5.0 AFUB_098310 AFUA_4G04690 B0YE87 Uncharacterized protein No 0.73 18.70 209 22.594 333057 1.0 AFUB_025060 AFUA_2G09180 B0XRW4 Coatomer subunit zeta,...”
- A murine inhalation model to characterize pulmonary exposure to dry Aspergillus fumigatus conidia
Buskirk, PloS one 2014 - “...Putative, Mitochondrial aconitate hydratase Q4WLN1 85.48/6.25 8 9.91 3 a) Putative, Mitochondrial dihydroxy acid dehydratase B0XTT1 68.21/7.78 10 13.08 b) Phosphoglucomutase PgmA B0XXA2 60.46/6.30 14 16.58 c) Putative, Pyruvate decarboxylase PdcA B0XXN9 62.96/6.07 3 10.72 d) Putative, GMC oxidoreductase Q4WFN7 72.10/7.08 3 7.58 4 a) Putative,...”
FPSE_05147 hypothetical protein from Fusarium pseudograminearum CS3096
35% identity, 87% coverage
- Histone H3 N-Terminal Lysine Acetylation Governs Fungal Growth, Conidiation, and Pathogenicity through Regulating Gene Expression in Fusarium pseudograminearum
Jiang, Journal of fungi (Basel, Switzerland) 2024 - “...and FpH3 K18R mutants ( Supplementary Tables S4S6 ) [ 38 ]. Additionally, dihydroxyacid dehydratase (FPSE_05147, FpILV3A ), hexokinase (FPSE_04405, FpHXK1 ), and acetohydroxyacid synthase (FPSE_00996, FpILV6 ), which play vital roles in growth, conidiation, and pathogenicity, are all downregulated in the FpH3 K9R , FpH3...”
FGSG_02056 dihydroxy-acid dehydratase from Fusarium graminearum PH-1
35% identity, 86% coverage
ZP_01094431 dihydroxy-acid dehydratase from Blastopirellula marina DSM 3645
36% identity, 89% coverage
- The Aspergillus fumigatus dihydroxyacid dehydratase Ilv3A/IlvC is required for full virulence
Oliver, PloS one 2012 - “...(Q1ILZ0) Acidobacteria bacterium ; Aura1 (ZP_01227770) Aurantimonas manganoxydans ; Bbro1 (Q7WKV5) Bordetella bronchiseptica ; Bmar1 (ZP_01094431) Blastopirellula marina ; Bpar1 (NP_883684.1) Bordetella parapertussis ; Cagg1 (AOH553_9CHLR) Chloroflexus aggregans ; Cvib1 (Q9A8D3) Caulobacter vibroides ; Lint1 (Q8F219) Leptospira interrogans ; Meth1 (ZP_01850751.1) Methylobacterium sp ; Mlot1 (NP_106075.1),...”
XP_958280 dihydroxy-acid dehydratase from Neurospora crassa OR74A
34% identity, 93% coverage
rrnAC0302 dihydroxy-acid dehydratase from Haloarcula marismortui ATCC 43049
36% identity, 92% coverage
NMB1150 dihydroxy-acid dehydratase from Neisseria meningitidis MC58
35% identity, 83% coverage
- Cationic antimicrobial peptide resistance in Neisseria meningitidis
Tzeng, Journal of bacteriology 2005 - “...in NMB1052 (dedA), and XZS17 with an insertion in NMB1150 (ilvD; dihydroxy acid dehydratase). All three of these genes are predicted (TopPred II [8] and PSORT...”
- “...mtrR-mtrC mtrD mtrD, NMB1052 mtrD, NMB0355 mtrD, NMB0355 mtrD, NMB1150 mtrD, lptA mtrD, lptA mtrD, lptA FIG. 2. Silver staining of whole-cell PK digestion of...”
Sb07g024070 No description from Sorghum bicolor
35% identity, 88% coverage
B4FWX5 dihydroxy-acid dehydratase from Zea mays
35% identity, 88% coverage
- Quantitative iTRAQ-based proteomic analysis of phosphoproteins and ABA-regulated phosphoproteins in maize leaves under osmotic stress
Hu, Scientific reports 2015 - “...and ribosome, which had the second greatest number of proteins (B8A367, C0HHU2, B6TS38, C0HIV2, B4FRM3, B4FWX5, C0PKN2, B6TPG2, B4FCE7, O04014, B4FCK4, B4FWI0), and only B4FWI0 was not regulated by ABA under osmotic stress. Moreover, the signaling pathways related to photosynthesis, such as carbon fixation in photosynthetic...”
An14g03280 uncharacterized protein from Aspergillus niger
35% identity, 85% coverage
Q7UJ69 Dihydroxy-acid dehydratase from Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
35% identity, 90% coverage
ILV3_YEAST / P39522 Dihydroxy-acid dehydratase, mitochondrial; DAD; EC 4.2.1.9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 13 papers)
NP_012550, YJR016C Dihydroxyacid dehydratase, catalyzes third step in the common pathway leading to biosynthesis of branched-chain amino acids from Saccharomyces cerevisiae
34% identity, 95% coverage
- function: Dihydroxyacid dehydratase that catalyzes the third step in the common pathway leading to biosynthesis of branched-chain amino acids (PubMed:20008079, PubMed:21798060, PubMed:21987576, PubMed:22954227, PubMed:25280745, PubMed:26543501, PubMed:27532773, PubMed:28505306, PubMed:30850698, PubMed:31303893, PubMed:33620449, PubMed:8299945). Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3- methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3- methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3- methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L- valine, respectively (PubMed:20008079, PubMed:27532773). Required for the synthesis of alpha-isopropylmalate which modulates the activity of LEU3 and subsequently regulates the expression of LEU1 (PubMed:20008079).
catalytic activity: (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (RHEA:24809)
catalytic activity: (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2- oxopentanoate + H2O (RHEA:27694)
cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit.)
cofactor: Mg(2+)
disruption phenotype: Strongly reduces the iron responsiveness of expression of LEU1 by affecting the synthesis of alpha-isopropylmalate. - Combinatorial library design for improving isobutanol production in Saccharomyces cerevisiae
Gambacorta, Frontiers in bioengineering and biotechnology 2022 - “...ID: A0A0G9FA99), KARI from Pfam families PF01450 and PF07991, DHAD from S. cerevisiae (Uniprot ID: P39522), KDC from S. cerevisiae (Uniprot ID: Q06408), and ADH from S. cerevisiae (Uniprot ID: P38113). A diverse set of variants was chosen from the resulting network by 1) gathering homologs...”
- Identification of in vivo substrates of the yeast mitochondrial chaperonins reveals overlapping but non-identical requirement for hsp60 and hsp10
Dubaquié, The EMBO journal 1998 - “...RHO1 HSP60 SSC1 2,3-dihydroxy acid hydrolase P39522 ketol-acid reductoisomerase P06168 isocitrate dehydrogenase P28834 aconitase homolog P39533 aconitase P19414...”
- Commonalities and Differences in the Transcriptional Response of the Model Fungus Saccharomyces cerevisiae to Different Commercial Graphene Oxide Materials
Laguna-Teno, Frontiers in microbiology 2020 - “...in the pathway ( Ihrig et al., 2010 ). One of them, the dihydroxyacid dehydratase YJR016C ( ILV3 ), which catalyzes the third step in the common pathway leading to biosynthesis of leucine, isoleucine and valine, was downregulated upon exposure to both nanomaterials. The transcriptional changes...”
- tRNA Genes Affect Chromosome Structure and Function via Local Effects
Hamdani, Molecular and cellular biology 2019 - “...YER073w YER091c YGL009c YHR208w YJR010w YJR016c 0.030966243 0.039894621 0.015662463 0.045197971 0.042003857 0.009117145 0.007776891 0.042003857 0.017736878...”
- Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae
Chen, Biotechnology for biofuels 2016 - “...YNL160W, YOL058W, YOL086C, YOR184W, YOR375C YCL030C, YDR007W, YDR502C , YER091C , YGL245W, YGL256W , YJL200C, YJR016C, YLR142W , YMR169C , YMR250W YCL030C, YCR005C, YDL168W, YDL182W, YDR007W, YDR135C, YDR502C , YDR513W, YEL046C, YER043C, YER091C , YFL030W, YGL009C, YGL256W , YGR209C, YGR267C, YIL074C, YJL101C, YJR010W, YJR137C, YJR139C, YKL001C,...”
- Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism
Wildenhain, Scientific data 2016 - “...human familial dysautonomia (FD) protein Null mutant is viable, insensitive tokiller toxin, G1 delay S000004376 YJR016C ILV3 + Dihydroxyacid dehydratase, catalyzes third step in the common pathway leading to biosynthesis of branched-chain amino acids Null mutant is viable, isoleucine and valine auxotroph S000003777 YPL209C IPL1 +...”
- Genome-Wide Transcription Study of Cryptococcus neoformans H99 Clinical Strain versus Environmental Strains
Movahed, PloS one 2015 - “...3.0 3.2 2.6 0.0002 CNAG_00484T0_1473 2.9 3.0 2.4 0.0186 CNAG_04346T0_968 2.9 3.4 2.9 0.0076 CNAG_06540T1_1679 NP_012550 ILV3 Dihydroxy-acid dehydratase, mitochondrial 2.8 2.0 3.9 0.0038 CNAG_04122T0_1086 NP_013755 ARA2 D-arabinose 1-dehydrogenase 2.7 2.7 2.4 0.0100 CNAG_02336T0_1615 NP_013031 VBA5 Vacuolar basic amino acid transporter 5 2.6 2.6 4.7 0.0096...”
- Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance
Shah, Physiological genomics 2011 - “...gi 809587 YGL234W YGL156W YAL038W YNL118C YHR132C YMR108W YJR016C YKL103C YGL009C YBL091C YGR240C YDL185W YPR074C YOL057W YPR022C ADE5,7 AMS1 CDC19 DCP2 ECM14...”
- Comparative transcriptomic and proteomic profiling of industrial wine yeast strains
Rossouw, Applied and environmental microbiology 2010 - “...MCR1 MDH1 MET10 MET17 MET22 MET3 MET6 YMR108W YJR016C YLR355C YCL009C YHR216W YLR432W YML056C YBR011C YCL018W YNL104C YFL018C YIR034C YIL094C YDL131W YDR234W...”
- “...YDR035W YBR249C YPR145W YHR208W YOR375C YDL022W YPR160W YJR016C YLR355C YCL018W YIL094C YDL131W YDR234W YNR050C YLR044C YGR240C YMR205C YMR105C YDR502C YLR058C...”
- Combined analysis of expression data and transcription factor binding sites in the yeast genome
Nagaraj, BMC genomics 2004 - “...ALD6 0.597 0.018 0.009 - YBR028C 0.793 0.046 0.036 - YOL022C 0.563 0.023 0.013 - YJR016C ILV3 0.248 0.025 0.006 - YBR218C PYC2 0.324 0.027 0.008 - YFR040W SAP155 0.234 0.165 0.038 - YMR269W 0.332 0.049 0.016 - YJL129C TRK1 0.297 0.083 0.024 - YCR053W THR4...”
- More
Q5F8G6 Dihydroxy-acid dehydratase from Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)
35% identity, 83% coverage
- Comparative Proteomics of Extended-Spectrum Cephalosporin-Resistant Neisseria gonorrhoeae Isolates Demonstrates Altered Protein Synthesis, Metabolism, Substance Transport, and Membrane Permeability
Diao, Frontiers in microbiology 2020 - “...Ethanolactive dehydrogenase/acetaldehydeactive reductase G 0 N 4.18 Q5F873 gltA Citrate synthase C 0 N 2.13 Q5F8G6 ilvD Dihydroxyacid dehydratase EG 0 N 1.73 Q5F9V2 NGO_0286 Uncharacterized protein S 0 N 1.75 A0A0M3GXE9 M736_02645 Conjugal transfer protein TrbB UW 0 N 2.36 A0A0M3GXY6 M736_02455 Phosphoribosyltransferase F 0...”
- “...and degradation (ngk00280) ( P < 0.05) ( Table 3 ). Six differentially expressed proteins (Q5F8G6, Q5F873, D6H9Y3, A0A1D3IB26, A0A1D3FF29, and D6HBH4) were involved in the three enrichment pathways, and all of the 6 proteins were downregulated. The function of Q5F873 (citrate synthase) was associated with...”
CHLNCDRAFT_58991 hypothetical protein from Chlorella variabilis
E1ZPZ3 dihydroxy-acid dehydratase from Chlorella variabilis
37% identity, 44% coverage
- Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae
Rai, Scientific reports 2017 - “...15. E1ZQQ9 Proteasome subunit alpha type CHLNCDRAFT_27583 2 0.8640.49 1.6760.58 2.0300.85 16. E1ZPZ3 Dihydroxy-acid dehydratase CHLNCDRAFT_58991 2 1.4190.57 2.1591.25 2.1170.78 Photosynthesis 17 E1Z6S6 Putative uncharacterized protein (photosystem II assembly) CHLNCDRAFT_140330 1 1.4510.19 2.3460.38 2.6840.55 18 E1ZBP9 FerredoxinNADP reductase CHLNCDRAFT_35035 3 1.3120.12 1.8530.19 2.1210.17 19 E1ZQR2 Putative...”
- Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae
Rai, Scientific reports 2017 - “...1.5320.02 1.6660.14 2.5990.33 15. E1ZQQ9 Proteasome subunit alpha type CHLNCDRAFT_27583 2 0.8640.49 1.6760.58 2.0300.85 16. E1ZPZ3 Dihydroxy-acid dehydratase CHLNCDRAFT_58991 2 1.4190.57 2.1591.25 2.1170.78 Photosynthesis 17 E1Z6S6 Putative uncharacterized protein (photosystem II assembly) CHLNCDRAFT_140330 1 1.4510.19 2.3460.38 2.6840.55 18 E1ZBP9 FerredoxinNADP reductase CHLNCDRAFT_35035 3 1.3120.12 1.8530.19 2.1210.17...”
- “...maintain the intracellular nitrogen homeostasis. 6 , 49 , 50 2 Amino acid biosynthesis 9 E1ZPZ3, E1Z4T9, E1ZF33, A0A087SJX6, A0A087SKJ2, E1ZEF2, E1ZIW5, E1Z357, E1ZP71 To maintain the overall intracellular levels of nitrogen, amino acid biosynthesis particularly of aspartate, glutamate and arginine is elevated. Accumulation of arginine...”
HI0738 dihydroxyacid dehydratase (ilvD) from Haemophilus influenzae Rd KW20
35% identity, 86% coverage
BCAM1262 dihydroxyacid dehydratase from Burkholderia cenocepacia J2315
34% identity, 88% coverage
APL_0097 Dihydroxy-acid dehydratase from Actinobacillus pleuropneumoniae L20
34% identity, 84% coverage
- Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
Labrie, Veterinary research 2010 - “...APL_0099 ilvG Acetolactate synthase isozyme II large subunit (AHAS-II) 3.915 APL_1499 thrC Threonine synthase 3.198 APL_0097 ilvD Dihydroxy-acid dehydratase 3.142 APL_0393 leuA 2-isopropylmalate synthase 3.000 APL_0098 ilvM Acetolactate synthase isozyme II small subunit (AHAS-II) 2.934 APL_2027 hisF Imidazole glycerol phosphate synthase subunit hisF 2.833 APL_0702 serC...”
Q31QL1 Dihydroxy-acid dehydratase from Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)
Synpcc7942_0626 dihydroxy-acid dehydratase from Synechococcus elongatus PCC 7942
34% identity, 83% coverage
ABO_2312 dihydroxy-acid dehydratase from Alcanivorax borkumensis SK2
35% identity, 77% coverage
CC77DRAFT_1063831 dihydroxy-acid dehydratase-like protein from Alternaria alternata
32% identity, 90% coverage
- Combination of Bacillus tequilensis with difenoconazole to control pear black spot and the related synergistic mechanism
Bi, Frontiers in microbiology 2024 - “...CACACACGTTCACCACTCAG CAGAGTCAGCAGATTGTCGC CC77DRAFT_942416 (down) ATP-dependent RNA helicase TCATTTTCGTCAGGACCCGA TTGATGACCATGGTGACGGA CC77DRAFT_938423 (down) ADP-ribose pyrophosphatase CTCCTCGGATGCAAAATGGG ACGGGTGGTCTGAATTGGAT CC77DRAFT_1063831 (down) Valine, leucine, and isoleucine biosynthesis CACTGTGAGTAGACGCATGC ACCAGCATACCTTCTCCACC CC77DRAFT_1061793(down) Glycine, serine, and threonine metabolism TGGAAGCTGCTGGATCTCAA TTCACCCTTTGCGACCTTTG 2.4.2 Verification of the main metabolic components involved in the synergistic effect 2.4.2.1 Detection...”
CA_C3604, WP_010966867 dihydroxy-acid dehydratase from Clostridium acetobutylicum ATCC 824
33% identity, 87% coverage
- The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family
Rahman, Scientific reports 2018 - “...Corynebacterium glutamicum (GeneBank: BAV23085), Ca DHADHT is a dihydroxy acid dehydratase from Clostridium acetobutylicum (GeneBank: WP_010966867), and Zm 6PGDHT and So 6PGDHT are 6-phosphogluconate dehydratasesfrom Zymomonas mobilis (GeneBank: WP_013934127) and Shewanella oneidensis (GeneBank: WP_011072452). The N- and C-terminal domain are shown in red and blue, connecting...”
- Elucidation of the roles of adhE1 and adhE2 in the primary metabolism of Clostridium acetobutylicum by combining in-frame gene deletion and a quantitative system-scale approach
Yoo, Biotechnology for biofuels 2016 (no snippet) - Fermentation of oxidized hexose derivatives by Clostridium acetobutylicum
Servinsky, Microbial cell factories 2014 - “...2-keto-3-deoxygluconokinase, CA_C0395; 27) 2-keto-3-deoxygluconate 6-phosphate aldolase, CA_C0394, CA_C2973; 28) gluconate symporter, CA_C3605; 29) gluconate dehydratase, CA_C3604. The pathway for gluconate metabolism in MetaCyc proceeded via the ED pathway, where phosphorylation of gluconate to 6-phosphogluconate by gluconokinase was followed by dehydration to KDPG by 6-phosphogluconate dehydratase. KDPG...”
- “...been identified in C. acetobutylicum. Upstream of the putative gluconate symporter gene is a gene, CA_C3604, annotated as encoding a putative IlvD type dihydroxyacid dehydratase. This class of enzymes includes gluconate dehydratase; the only other enzyme in this class for C. acetobutylicum is the xylulose kinase...”
MS2219 dihydroxy-acid dehydratase from [Mannheimia] succiniciproducens MBEL55E
34% identity, 86% coverage
salH / B0L7G4 dihydroxy-acid dehydratase from Salinispora tropica (see paper)
34% identity, 90% coverage
MS2219 IlvD protein from Mannheimia succiniciproducens MBEL55E
34% identity, 85% coverage
ACIAD1266 dihydroxy-acid dehydratase from Acinetobacter sp. ADP1
35% identity, 84% coverage
PFLU5797 dihydroxy-acid dehydratase from Pseudomonas fluorescens SBW25
35% identity, 84% coverage
NP_879169 dihydroxy-acid dehydratase from Bordetella pertussis Tohama I
BP0289 dihydroxy-acid dehydratase from Bordetella pertussis Tohama I
35% identity, 83% coverage
8imuA / Q9LIR4 Dihydroxyacid dehydratase (dhad) mutant-v497f
34% identity, 94% coverage
- Ligand: fe2/s2 (inorganic) cluster (8imuA)
WP_007877043 dihydroxy-acid dehydratase from Herbaspirillum sp. CF444
33% identity, 83% coverage
BB0431 dihydroxy-acid dehydratase from Bordetella bronchiseptica RB50
35% identity, 83% coverage
PFL_5877 dihydroxy-acid dehydratase from Pseudomonas fluorescens Pf-5
35% identity, 84% coverage
llmg_1280 dihydroxy-acid dehydratase from Lactococcus lactis subsp. cremoris MG1363
33% identity, 90% coverage
- Transcriptional response of Lactococcus lactis during bacterial emulsification
Tarazanova, PloS one 2019 - “...1.2e-10 llmg_1298 hisC histidinol-phosphate aminotransferase 8.6 1.2e-10 llmg_1279 ilvB acetolactate synthase catalytic subunit 4.9 1.9e-7 llmg_1280 ilvD dihydroxy-acid dehydratase 4.9 3.6e-8 llmg_1183 gltB glutamate synthase. large subunit 4.3 3.4e-4 llmg_1290 hisF imidazole glycerol phosphate synthase subunit HisF 4.9 1.9e-4 llmg_1291 hisA 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase 4.3...”
Atu1918 dihydroxy-acid dehydratase from Agrobacterium tumefaciens str. C58 (Cereon)
34% identity, 84% coverage
PITG_20759 dihydroxy-acid dehydratase from Phytophthora infestans T30-4
36% identity, 81% coverage
A1S_3455 dihydroxy-acid dehydratase from Acinetobacter baumannii ATCC 17978
35% identity, 85% coverage
VC0028 dihydroxy-acid dehydratase from Vibrio cholerae O1 biovar eltor str. N16961
34% identity, 84% coverage
- Transcriptomics reveals a cross-modulatory effect between riboflavin and iron and outlines responses to riboflavin biosynthesis and uptake in Vibrio cholerae
Sepúlveda-Cisternas, Scientific reports 2018 - “...portion 1.809 VC0018 ibpA 16kDa heat shock protein A 1.740 VC0027 threonine dehydratase 1.226 1.191 VC0028 dihydroxy-acid dehydratase 1.087 VC0030 ilvM acetolactate synthase II small subunit 1.116 VC0053 hypothetical protein 1.074 VC0089 cytochrome c551 peroxidase 1.076 VC0102 hypothetical protein 1.160 VC0138 hypothetical protein 1.564 VC0139 DPS...”
- Pyomelanin produced by Vibrio cholerae confers resistance to predation by Acanthamoeba castellanii
Noorian, FEMS microbiology ecology 2017 - “...VC2643, and VC2508 (arginine metabolism and biosynthesis), VC1704 (cysteine and methionine metabolism), VC0162, VC0031 and VC0028 (isoleucine biosynthesis) and VC0392, VCA0604 and VCA0605 (aminotransferases). The increase in metabolism and energy production might be related to an increase in available nutrient resources since feeding will result in...”
- Genomic and phenotypic characterization of Vibrio cholerae non-O1 isolates from a US Gulf Coast cholera outbreak
Haley, PloS one 2014 - “...A A CDP-diacylglycerolserine O-phosphatidyltransferase VC1899 C C C C T C C C hypothetical protein VC0028 C C C C C C T C Dihydroxy-acid dehydratase VC0031 C C C C C C C A Acetolactate synthase large subunit VC1359 T T T T C C...”
- Host-induced epidemic spread of the cholera bacterium
Merrell, Nature 2002 - “...genes differentially expressed in the stool samples are VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350 and VCA0583, all of which were recently...”
IlvD / b3771 dihydroxy-acid dehydratase (EC 4.2.1.9) from Escherichia coli K-12 substr. MG1655 (see paper)
ilvD / P05791 dihydroxy-acid dehydratase (EC 4.2.1.9) from Escherichia coli (strain K12) (see 14 papers)
ILVD_ECOLI / P05791 Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 from Escherichia coli (strain K12) (see 4 papers)
ilvD / EW|b3771 dihydroxyacid dehydratase from Escherichia coli K12 (see 2 papers)
YP_026248 dihydroxy-acid dehydratase from Escherichia coli str. K-12 substr. MG1655
b3771 dihydroxy-acid dehydratase from Escherichia coli str. K-12 substr. MG1655
34% identity, 83% coverage
- function: Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo- 3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3- dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively.
catalytic activity: (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (RHEA:24809)
catalytic activity: (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2- oxopentanoate + H2O (RHEA:27694)
cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor.)
cofactor: Mg(2+)
subunit: Homodimer. - Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli.
Hyduke, Proceedings of the National Academy of Sciences of the United States of America 2007 - GeneRIF: This approach identified the comprehensive E. coli NO response network and evinced that nitric oxide (NO) halts bacterial growth via inhibition of the branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase.
- The role and properties of the iron-sulfur cluster in Escherichia coli dihydroxy-acid dehydratase.
Flint, The Journal of biological chemistry 1993 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Protein-based biorefining driven by nitrogen-responsive transcriptional machinery
Ma, Biotechnology for biofuels 2020 - “...dihydroxy acid dehydratase are encoded by alsS (UniProt: Q04789), ilvC (UniProt: P05793), and ilvD (UniProt: P05791), respectively, together, these enzymes convert pyruvate to 2-ketoisovalerate (KIV) and 2-keto-3-methyl-valerate (KMV), which are the direct precursors of valine and isoleucine, respectively. A substantial proportion of the produced KIV, KMV,...”
- A Multiplex Enzymatic Machinery for Cellular Protein S-nitrosylation
Seth, Molecular cell 2018 - “...P0AG67 2.6 1.9 1.4 HybC Hydrogenase-2 large chain P0ACE0 2.4 1.9 1.3 IlvD Dihydroxy-acid dehydratase P05791 4.0 3.3 1.2 NirB Nitrite reductase (NADH) large subunit P08201 3.1 2.6 1.2 Y Hcr NADH oxidoreductase HCR P75824 3.3 2.7 1.2 Y Table 2 GAPDH-dependent S-nitrosylation of Proteins Proteins...”
- Characterization of D-xylonate dehydratase YjhG from Escherichia coli
Jiang, Bioengineered 2015 - “...accession numbers are as follows: E. coli (ILvD), P05791; E. coli (EDD), AAB59053; Z. mobilis, P21909. sequences with several IlvD/EDD proteins demonstrated...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...(DIGE 4.5-6.5) 5.29/51,264 (DIGE 4.5-6.5) IlvD P05791 Dihydroxy-acid dehydratase 5.59/65,400.37 5.54/62,065 (DIGE 4.5-6.5) IlvE P0AB80 Branched-chain amino acid...”
- Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Xu, BMC bioinformatics 2009 - “...b0159 b0074 b0088 b0182 b2472 b0173, b0174, b0369 b3770 b0090 b0524 b2478 b0414, b0415, b0417 b3771 b0091 b0914 b2838 b0420, b0421, b0423 b3774 b0954 b0915 b3359 b0475, b0750, b0907 b1093 b0918 b3433 b1096, b1208, b1210 b1094 b1094 b3809 b1277, b1662, b1740 b1288 b1215 s0001 b1812, b2103,...”
- Experimental and computational assessment of conditionally essential genes in Escherichia coli
Joyce, Journal of bacteriology 2006 - “...hisI (b2026) ilvA (b3772) ilvB (b3671) ilvC (b3774) ilvD (b3771) leuA (b0074) leuB (b0073) leuC (b0072) leuD (b0071) lysA (b2838) metA (b4013) metB (b3939) metC...”
- Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
Smulski, Journal of bacteriology 2001 - “...b2507 b2508 b1615 b2231 b1619 b4348 b4018 b3671 b3774 b3771 b3770 b3767 b3769 b3168 b0275 b0274 b0051 b2568 b0072 b0071 b3455 b3460 b3458 b4024 b4033 b1620...”
NJ56_05450 dihydroxy-acid dehydratase from Yersinia ruckeri
34% identity, 84% coverage
- Genome Sequence of the Fish Pathogen Yersinia ruckeri SC09 Provides Insights into Niche Adaptation and Pathogenic Mechanism
Liu, International journal of molecular sciences 2016 - “...transport exists exclusively in bacteria [ 58 ]. PTS for transport and metabolism of N-acetyl-glucosamine (NJ56_05450), sucrose (NJ56_16635), cellobiose (NJ56_09805, NJ56_09815-20), mannitol (NJ56_13600), ascorbate (NJ56_08600-05, NJ56_15455-65), glucose (NJ56_07070, NJ56_15910), fructose (NJ56_15025-35), nitrogen (NJ56_11960, NJ56_11970, NJ56_10665), mannose (NJ56_09565-75), trehalose (NJ56_11995, NJ56_15910), glucitol/sorbitol (NJ56_11140-50), and N -acetylga-lactosamine (NJ56_02695-10)...”
SAV_4716 dihydroxy-acid dehydratase from Streptomyces avermitilis MA-4680
32% identity, 85% coverage
- SAV742, a Novel AraC-Family Regulator from Streptomyces avermitilis, Controls Avermectin Biosynthesis, Cell Growth and Development
Sun, Scientific reports 2016 - “...the large subunit of acetolactate synthase), ilvC (sav_2731 , encoding a putative ketol-acid reductoisomerase), ilvD1 (sav_4716 , encoding a putative dihydroxy-acid dehydratase) and ilvE (sav_2717 , encoding a putative branched-chain amino acid aminotransferase); in oxidative phosphorylation: ndh1 (sav_1892 , encoding a putative NADH dehydrogenase) and ctaD2...”
KPN_04270 dihydroxy-acid dehydratase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
A6TGF8 Dihydroxy-acid dehydratase from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
33% identity, 83% coverage
ECs4705 dihydroxyacid dehydratase from Escherichia coli O157:H7 str. Sakai
34% identity, 83% coverage
AB395_RS15445 dihydroxy-acid dehydratase from Sinorhizobium fredii CCBAU 45436
33% identity, 84% coverage
AFUA_1G03550 mitochondrial dihydroxy acid dehydratase, putative from Aspergillus fumigatus Af293
33% identity, 90% coverage
- The Aspergillus fumigatus dihydroxyacid dehydratase Ilv3A/IlvC is required for full virulence
Oliver, PloS one 2012 - “...fungus Aspergillus fumigatus by homology to Saccharomyces cerevisiae ILV3. Two of these genes, AFUA_2G14210 and AFUA_1G03550, initially designated AfIlv3A and AfIlv3B for this study, clustered in the same group as S. cerevisiae ILV3 following phylogenetic analysis. To investigate the functions of these genes, AfIlv3A and AfIlv3B...”
- “...leading to the identification of four A. fumigatus proteins. Proteins encoded by the genes AFUA_2G14210, AFUA_1G03550, AFUA_1G07330 and AFUA_2G16300 were 63%, 55%, 31% and 29% identical to S. cerevisiae Ilv3p, respectively. For the purposes of clarity they shall be referred to as AfIlv3A (AFUA_2G14210), AfIlv3B (AFUA_1G03550),...”
PP_5128 dihydroxy-acid dehydratase from Pseudomonas putida KT2440
34% identity, 84% coverage
- Functional characterization of the dbu locus for D-branched-chain amino acid catabolism in Pseudomonas putida
Fulton, Applied and environmental microbiology 2024 (secret) - A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
Nogales, BMC systems biology 2008 - “...ilvA-2 SER_AL, THRD_L (+/-)* PP_4680 ilvB (ilvI) ACHBS, ACLS (-/-) PP_4678 ilvC KARA1, KARA2 (-/-) PP_5128 ilvD DHAD1, DHAD2 (-/-) PP_3511 ilvE VALTA, LEUTA, ILETA (-/-) PP_4679 ilvN(ilvH) ACHBS, ACLS (-/-) Leucine PP_1025 leuA IPPS (-/-) PP_1988 leuB IPMDr (-/-) PP_1985 leuC IPPMIa, IPPMIb (-/-) PP_1986...”
PVLB_01425 dihydroxy-acid dehydratase from Pseudomonas sp. VLB120
34% identity, 84% coverage
PA0353 dihydroxy-acid dehydratase from Pseudomonas aeruginosa PAO1
PA14_04630 dihydroxy-acid dehydratase from Pseudomonas aeruginosa UCBPP-PA14
34% identity, 84% coverage
- Massively parallel mutant selection identifies genetic determinants of <i>Pseudomonas aeruginosa</i> colonization of <i>Drosophila melanogaster</i>
Miles, mSystems 2024 - “...Amino acids [E] + PA0036 trpB Amino acids [E] PA0649 trpG Amino acids [E] + PA0353 ilvD Amino acids [E] + PA4695 ilvH Amino acids [E] + PA4694 ilvC Amino acids [E] PA4696 ilvI Amino acids [E] PA5013 ilvE Amino acids [E] PA5204 argA Amino acids...”
- Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics
Yung, NPJ biofilms and microbiomes 2019 - “...factor NR NR NR HemN PA1546 Oxygen-independent coproporphyrinogen-III oxidase NR NR NR NR NR IlvD PA0353 Dihydroxy-acid dehydratase NR NR NR NR NR KatA PA4236 Catalase NR o NR MtnB PA1683 Methylthioribulose-1-phosphate dehydratase NR NR NR NR NfuA PA1847 Fe/S biogenesis protein NR NR NR NR...”
- A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm
Sigurdsson, PloS one 2012 - “...capsule UppS (PA3652) Biotin biosynthesis AccC (PA4848) Branched chain amino acid biosynthesis IlvC (PA4694), IlvD (PA0353) Cell envelope biosynthesis GlmU (PA5552), GlmS (PA5549), MurI (PA4662), MraY (PA4415), MurE (PA4417), MurC (PA4411), MurB (PA2977) DdlB (PA4410), DdlA (PA4201), MurA (PA4450),MurD (PA4414) Cell envelope biosynthesis- O-antigen RmlA (PA5163)...”
- Role of lon, an ATP-dependent protease homolog, in resistance of Pseudomonas aeruginosa to ciprofloxacin
Brazas, Antimicrobial agents and chemotherapy 2007 - “...73_D6 75_D3 81_D2 6_G1 80_B7 22_C5 53_F11 16_G12 PA0353 PA0836 PA1803 PA1803 PA1803 PA3082 PA3294 PA3617 PA3777 PA3965 PA4163 PA4316 PA4316 PA4422 PA4466 PA4700...”
- Genetics of Pseudomonas
Holloway, Bacteriological reviews 1969 - Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence
Panayidou, Scientific reports 2020 - “...( aroB ) 29 Valine, leucine and isoleucine biosynthesis (pau00290) PA14_62130 ( ilvC ) 30 PA14_04630 ( ilvD ) 31 PA14_62150 ( ilvH ) 32 PA14_62160 ( ilvI ) 33 PA14_23790 ( leuB ) 34 PA14_23750 ( leuC ) 35* Pyrimidine metabolism (pau00240) PA14_18710 ( pyrC...”
bll6092 dihydroxy-acid dehydratase from Bradyrhizobium japonicum USDA 110
33% identity, 96% coverage
Q8NQZ9 dihydroxy-acid dehydratase (EC 4.2.1.9) from Corynebacterium glutamicum (see 2 papers)
NCgl1219 dihydroxy-acid dehydratase from Corynebacterium glutamicum ATCC 13032
cg1432 dihydroxy-acid dehydratase from Corynebacterium glutamicum ATCC 13032
33% identity, 85% coverage
- Understanding the high L-valine production in Corynebacterium glutamicum VWB-1 using transcriptomics and proteomics
Zhang, Scientific reports 2018 - “...0.00 1295.30 2.6 25 NCgl0368 cg0454 TetR family transcriptional regulator 5.41/24817.09 0.00 571.02 NC 32 NCgl1219 cg1432 ilvD Dihydroxy-acid dehydratase 5.18/64674.11 4354.80 1888.03 2.8 33 NCgl1219 cg1432 ilvD Dihydroxy-acid dehydratase 5.18/64674.11 0.00 667.12 2.8 34 NCgl2930 cg3362 trpCF Indole-3-glycerol phosphate synthase 5.15/50477.16 1290.96 0.00 3.4 38...”
- High-throughput screening of a Corynebacterium glutamicum mutant library on genomic and metabolic level
Reimer, PloS one 2014 - “...NCgl1536 encoding the ribulose-phosphate 3-epimerase, EC 5.1.3.1) or the valine, leucine and isoleucine pathway ( NCgl1219 encoding the dihydroxy-acid dehydratase, EC 4.2.1.9 and NCgl0245 encoding the 2-isopropylmalate synthase, EC 2.3.3.13). Also an intergenic mutation (mutant P21E12), that did not hit a gene directly was found within...”
- Understanding the high L-valine production in Corynebacterium glutamicum VWB-1 using transcriptomics and proteomics
Zhang, Scientific reports 2018 - “...1295.30 2.6 25 NCgl0368 cg0454 TetR family transcriptional regulator 5.41/24817.09 0.00 571.02 NC 32 NCgl1219 cg1432 ilvD Dihydroxy-acid dehydratase 5.18/64674.11 4354.80 1888.03 2.8 33 NCgl1219 cg1432 ilvD Dihydroxy-acid dehydratase 5.18/64674.11 0.00 667.12 2.8 34 NCgl2930 cg3362 trpCF Indole-3-glycerol phosphate synthase 5.15/50477.16 1290.96 0.00 3.4 38 NCgl1023...”
- Ciprofloxacin triggered glutamate production by Corynebacterium glutamicum
Lubitz, BMC microbiology 2016 - “...of glutamate production by C. glutamicum . The mechanosensitive channel protein MscS encoded by yggB (cg1432) is involved in the export of glutamate and in its absence glutamate production is reduced about four to five fold [ 26 ]. To test whether YggB is important for...”
- Exploring the role of sigma factor gene expression on production by Corynebacterium glutamicum: sigma factor H and FMN as example
Taniguchi, Frontiers in microbiology 2015 - “...trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase 1.5 1.7 6.6E-4 4.8E-3 cg1398 Conserved hypothetical protein 1.7 2.4 1.9E-2 2.3E-2 cg1432 ilvD Dihydroxy-acid dehydratase 1.9 1.9 2.0E-4 6.7E-4 cg1628 Putative hydrolase, alpha/beta superfamily 2.5 1.9 4.8E-2 9.1E-3 cg1671 Putative membrane-associated GTPase 1.7 1.3 3.9E-2 1.4E-2 cg1687 Putative transcriptional regulatory protein 1.4...”
- “...( http://www.uniprot.org/ ) identified putative iron sulfur cluster-containing proteins encoded by cg0616 ( fdhD ), cg1432 ( ilvD ), cg2206 ( ispG ) and cg2423 ( lipA ), proteins predicted to contain NAD(P)H binding sites encoded by cg0184, cg0616 ( fdhD ), cg1778 ( zwf ),...”
- Transcriptional regulation of the operon encoding stress-responsive ECF sigma factor SigH and its anti-sigma factor RshA, and control of its regulatory network in Corynebacterium glutamicum
Busche, BMC genomics 2012 - “...Conserved hypothetical protein 6.19 cg0617* Hypothetical protein 4.20 cg1288 Putative multidrug efflux permease, MFS-type 3.94 cg1432 ilvD Dihydroxy-acid dehydratase 3.84 cg1398 Conserved hypothetical protein 3.78 cg0614 Hypothetical protein 3.71 cg0616 fdhD Putative formate dehydrogenase, FdhD-family 3.71 cg1397* trmU tRNA (5-methylaminomethyl-2-thiouridylate) -methyltransferase 3.71 cg2423 lipA Lipoyl synthetase...”
BIF_00467 dihydroxy-acid dehydratase from Bifidobacterium animalis subsp. lactis BB-12
33% identity, 82% coverage
- Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12
Jensen, Microbiology resource announcements 2021 - “...Intergenic(+236/+53) BIF_00072 / BIF_00341 1360042 19bp35bp Intergenic(+28/+7) BIF_00368 / BIF_01760 1376069 14bp33bp Intergenic(+38/+27) BIF_01846 / BIF_00467 1414041 CA A373D(G C CG A C) BIF_00934 1414072 1bp Coding(1,149/1,152nt) BIF_00934 1414079 +G Intergenic(+4/+74) BIF_00934 / BIF_00718 1414090 8bp28bp Intergenic(+15/+56) BIF_00934 / BIF_00718 1419213 +G Intergenic(+37/+331) BIF_00332 / BIF_02065...”
AO090009000414 No description from Aspergillus oryzae RIB40
32% identity, 90% coverage
DR1132, DR_1132 dihydroxy-acid dehydratase from Deinococcus radiodurans R1
34% identity, 84% coverage
IYO_025960 dihydroxy-acid dehydratase from Pseudomonas syringae pv. actinidiae ICMP 18884
33% identity, 83% coverage
- Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae
Mesarich, PloS one 2017 - “...in Fig 2B . Of the 13 genes identified, IYO_007210 , IYO_008330 , IYO_008720 and IYO_025960 , which putatively encode the phosphoribosylformylglycinamidine synthase enzyme PurL (purine biosynthesis), the quinolinate synthase enzyme NadA (NAD biosynthesis), the phosphoribosylglycinamide formyltransferase enzyme PurN (purine biosynthesis), and the dihydroxy-acid dehydratase enzyme...”
- “...red arrows at positions P96-A9, P96-B10 and P96-G2, respectively; (B) Schematic of the IYO_007210 , IYO_025960 and IYO_025885 genes disrupted in the auxotrophic mutants retrieved from positions P96-A9, P96-B10 and P96-G2, respectively in (A). Arrow colors correspond to the mutants highlighted in (A), and show the...”
NP_386934 PROBABLE DIHYDROXY-ACID DEHYDRATASE PROTEIN from Sinorhizobium meliloti 1021
34% identity, 84% coverage
BL1788 dihydroxy-acid dehydratase from Bifidobacterium longum NCC2705
32% identity, 81% coverage
ILVD_CAUVC / P55186 Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 from Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15) (Caulobacter crescentus) (see paper)
CC3044, CC_3044 dihydroxy-acid dehydratase from Caulobacter crescentus CB15
CCNA_03139 dihydroxy-acid dehydratase from Caulobacter crescentus NA1000
34% identity, 84% coverage
- function: Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo- 3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3- dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively.
catalytic activity: (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (RHEA:24809)
catalytic activity: (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2- oxopentanoate + H2O (RHEA:27694)
cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor.)
cofactor: Mg(2+)
subunit: Homodimer. - Global transcriptional response of Caulobacter crescentus to iron availability
da, BMC genomics 2013 - “...(CC3667), NADH ubiquinone oxidoreductase ( nuo genes CC1946, CC1944-43-42), glutamate synthase (CC3606) and dihydroxy-acid dehydratase (CC3044) (Table 4 ). In some cases, at least part of the operons ( nuo and CC3607) was downregulated by both iron limitation and fur mutation (Figure 2 B). A possible...”
- “...CCNA_02223 Beta-lactamase, type II (Zinc) 2.83 CC_2140 CCNA_02224 Methylenetetrahydrofolate reductase 2.39 CC_2840 CCNA_02933 Aminopeptidase 2.14 CC_3044 CCNA_03139 Dihydroxy-acid dehydratase (Fe-S cluster) 3.35 CC_3246 CCNA_03355 Acylamino-acid-releasing enzyme 2.20 CC_3606 CCNA_03721 Glutamate synthase (NADPH) small chain 2.30 CC_3607 b CCNA_03722 Glutamate synthase (NADPH) large chain (Fe-S cluster) 2.51...”
- Global transcriptional response of Caulobacter crescentus to iron availability
da, BMC genomics 2013 - “...Beta-lactamase, type II (Zinc) 2.83 CC_2140 CCNA_02224 Methylenetetrahydrofolate reductase 2.39 CC_2840 CCNA_02933 Aminopeptidase 2.14 CC_3044 CCNA_03139 Dihydroxy-acid dehydratase (Fe-S cluster) 3.35 CC_3246 CCNA_03355 Acylamino-acid-releasing enzyme 2.20 CC_3606 CCNA_03721 Glutamate synthase (NADPH) small chain 2.30 CC_3607 b CCNA_03722 Glutamate synthase (NADPH) large chain (Fe-S cluster) 2.51 Chemotaxis...”
SC3809 dihydroxyacid dehydratase from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
33% identity, 83% coverage
- FlbT couples flagellum assembly to gene expression in Caulobacter crescentus
Mangan, Journal of bacteriology 1999 - “...SC3802 SC3803 SC3804 SC3805 SC3806 SC3807 SC3808 SC3809 SC3843 Plasmids pJBZ282 pfljK::lacZ pfljK1::lacZ pfljK2::lacZ pfljK3::lacZ pfljK-lacZ/290 This work This...”
- “...Transduction of SC508 to Kanr recA Phage SC3809 SC276 fliL::Tn5 str-140 flbT650 fliL179::Tn5 flbT650 flhA608::Tn5 flbT650 flaN176::Tn5 flbT650 flbD198::Tn5...”
- A new class of Caulobacter crescentus flagellar genes
Leclerc, Journal of bacteriology 1998 - “...SC1117 SC1127 SC1128 SC1132 SC1134 SC1135 SC2663 SC3090 SC3809 SC3898 SC3899 SC3971 SC3973 SC3975 SC4016 SC4250 Wild type syn-1000 bla-6 syn-1000 ctrA401...”
- “...flmE::cat flmG::cat SC1029 SC1032 SC1055 SC1066 SC1132 SC2663 SC3809 SC1117 SC1134 SC1135 SC1128 flhB (II) flbD (II) rpoN (II) fliL (II) flhA (II) fliM...”
SCO3345 dihydroxy-acid dehydratase from Streptomyces coelicolor A3(2)
33% identity, 83% coverage
- The Onset of Tacrolimus Biosynthesis in Streptomyces tsukubaensis Is Dependent on the Intracellular Redox Status
Pires, Antibiotics (Basel, Switzerland) 2020 - “...subunit (SdhB) 0.50 1 STSU_30056 SCO1391 Phosphoenolpyruvate-protein phosphotransferase (EI component) 0.45 Amino acid metabolism STSU_14552 SCO3345 Dihydroxy-acid dehydratase (IlvD) 0.29 STSU_24776 SCO2528 2-isopropylmalate synthase (LeuA) 0.21 1 STSU_26189 SCO2198 Glutamine synthetase I (GlnA) 0.23 Hypothetical/uncharacterized proteins/not classified STSU_10084 SCO5389 Hypothetical protein 2.00 STSU_13630 SCO4637 Hypothetical protein...”
- Genome-Wide Mutagenesis Links Multiple Metabolic Pathways with Actinorhodin Production in Streptomyces coelicolor
Xu, Applied and environmental microbiology 2019 - “...genes involved in branched-chain amino acid metabolism, including three ACT upmodulators, SCO2528 ( leuA ), SCO3345 ( ilvD ), and SCO5512 ( ilvB ), and three ACT downmodulators, SCO5513 ( ilvN ), SCO5514 ( ilvC ), and SCO5522 ( leuB ); five genes involved in the...”
- “...SCO5522 ( leuB ) had increased ACT production, whereas mutants of SCO5512 ( ilvB ), SCO3345 ( ilvD ), and SCO2528 ( leuA ) had decreased ACT production. The ilvB , ilvC , ilvD , and leuA mutants were bald (deficient in developing aerial hyphae). Branched-chain...”
- Large-Scale Transposition Mutagenesis of Streptomyces coelicolor Identifies Hundreds of Genes Influencing Antibiotic Biosynthesis
Xu, Applied and environmental microbiology 2017 - “...amino acids affected RED production. Mutants of SCO3345 (ilvD), SCO2528 (leuA), and SCO5529 (leuA2) increased RED production, while mutants of SCO5553...”
- Genome-scale analysis reveals a role for NdgR in the thiol oxidative stress response in Streptomyces coelicolor
Kim, BMC genomics 2015 - “...* SCO2999 gdhB Glutamate dehydrogenase 0.0.2 Conserved in organism other than Escherichia coli *, I SCO3345 ilvD Dihydroxy acid dehydratase 3.1.21 Valine * SCO4164 cysA Putative thiosulfate sulfurtransferase 3.3.19 Sulfur metabolism * SCO4165 Hypothetical protein 0.0.2 Conserved in organism other than Escherichia coli SCO4193 Putative ATP/GTP-binding...”
- “...upstream region between two divergent genes is denoted as D. Five genes, metF (SCO2103), ilvD (SCO3345), ilvB (SCO5512), leuB (SCO5522), and ndgR - leuC intergenic region (SCO5552-SCO5553) were previously annotated as direct regulatory targets of NdgR by in vitro experiments such as electrophoretic mobility shift assay...”
- Genome-wide dynamics of a bacterial response to antibiotics that target the cell envelope
Hesketh, BMC genomics 2011 - “...branched chain amino acid (leucine, isoleucine and valine), lysine and methionine biosynthesis. Indeed, the ilvD (SCO3345), leuB (SCO5522) and leuC (SCO5553) genes for the biosynthesis of the branched chain amino acids leucine, valine and isoleucine were up to 7-fold up-regulated by moenomycin treatment (Additional file 14...”
MSMEG_1290 dihydroxy-acid dehydratase from Mycobacterium smegmatis str. MC2 155
32% identity, 81% coverage
RHE_RS08720 dihydroxy-acid dehydratase from Rhizobium etli CFN 42
34% identity, 84% coverage
- Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network
Taboada-Castro, Frontiers in microbiology 2022 - “...6, and Supplementary Table 3A ), the enzyme ilvD , dihydroxy-acid dehydratase [EC:4.2.1.9], and the RHE_RS08720 and RHE_RS23070 proteins were expressed in MM and bacteroid, respectively, supporting multiplicity ( Table 1 ). Similarly, for valine, leucine, and isoleucine degradation ( Supplementary Table 2 pathway 7, and...”
ILVD_RHIJ3 / Q1MIB2 Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 from Rhizobium johnstonii (strain DSM 114642 / LMG 32736 / 3841) (Rhizobium leguminosarum bv. viciae) (see paper)
RL1803 putative dihydroxy-acid dehydratase from Rhizobium leguminosarum bv. viciae 3841
34% identity, 84% coverage
- function: Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo- 3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3- dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively.
catalytic activity: (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O (RHEA:24809)
catalytic activity: (2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2- oxopentanoate + H2O (RHEA:27694)
cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor.)
cofactor: Mg(2+)
subunit: Homodimer.
disruption phenotype: Does not nodulate the roots of pea plants. - Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis
Wheatley, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret)
A9KL28 Dihydroxy-acid dehydratase from Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)
34% identity, 87% coverage
EAMY_0161 dihydroxy-acid dehydratase from Erwinia amylovora CFBP1430
34% identity, 83% coverage
ZMO1792 dihydroxy-acid dehydratase from Zymomonas mobilis subsp. mobilis ZM4
33% identity, 83% coverage
- Systematic investigation of TetR-family transcriptional regulators and their roles on lignocellulosic inhibitor acetate tolerance in Zymomonas mobilis
Xiao, Frontiers in bioengineering and biotechnology 2024 - “...after ZMO0281 knockout may be also related to the repression of sucrose hydrolysis. In addition, ZMO1792 ( ilvD ) which related to amino acid metabolism was found to be repressed as well ( Supplementary Table S3 ). However, about 20 of the downregulated genes by ZM...”
- A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4
Nouri, Scientific reports 2020 - “...genes/inconsistent Up-regulated metabolic genes/inconsistent ZMO0172 Thiamine biosynthesis protein ZMO1853 Dihydrodipicolinate synthase ZMO0889 Aldose 1-epimerase precursor ZMO1792 Dihydroxy-acid dehydratase ZMO0239 ATP synthase alpha subunit ZMO1887 Isochorismatase ZMO0241 ATP synthase beta subunit ZMO1879 Delta-aminolevulinic acid dehydratase ZMO0367 Glucose-6-phosphate dehydrogenase ZMO1489 3-deoxy-D-manno-octulosonate cytidylyltransferase ZMO0465 Triosephosphate isomerase ZMO1496 Phosphoenolpyruvate carboxylase...”
- Metabolic engineering of Zymomonas mobilis for anaerobic isobutanol production
Qiu, Biotechnology for biofuels 2020 - “...Based on gene homology search results, Z. mobilis possesses four genes ZMO01139, ZMO1140, ZMO1141, and ZMO1792 encoding the enzymes Als, IlvC, and IlvD, respectively. ZMO01139 and ZMO1140 encode the large and small (regulatory) subunits of Als, respectively. These enzymes are the first three enzymes in the...”
Psyr_0469 Dihydroxy-acid dehydratase from Pseudomonas syringae pv. syringae B728a
33% identity, 83% coverage
Rru_A1786 Dihydroxy-acid dehydratase from Rhodospirillum rubrum ATCC 11170
34% identity, 83% coverage
Q2RTF9 Dihydroxy-acid dehydratase from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
34% identity, 84% coverage
NP_462432 putative dihydroxyacid dehydratase from Salmonella typhimurium LT2
34% identity, 84% coverage
HSM_0213 dihydroxy-acid dehydratase from Haemophilus somnus 2336
HSM_0213 dihydroxy-acid dehydratase from Histophilus somni 2336
32% identity, 84% coverage
DIP1096 dihydroxy-acid dehydratase from Corynebacterium diphtheriae NCTC 13129
32% identity, 85% coverage
- Corynebacterium diphtheriae Proteome Adaptation to Cell Culture Medium and Serum
Möller, Proteomes 2021 - “...expression level in serum compared to BHI and RPMI 1640. Cluster four comprises eight proteins (DIP1096, DIP0409, DIP0745, DIP0009, DIP0154, DIP0948, DIP0833, and DIP1131). Significantly increased abundance of proteins from bacteria grown in BHI medium are represented in cluster five. This cluster includes 15 proteins (DIP1636,...”
Q2YNW9 Dihydroxy-acid dehydratase from Brucella abortus (strain 2308)
BAB1_0096 Dihydroxy-acid and 6-phosphogluconate dehydratase:Dihydroxy-acid dehydratase from Brucella melitensis biovar Abortus 2308
33% identity, 84% coverage
BMEI1848 DIHYDROXY-ACID DEHYDRATASE from Brucella melitensis 16M
33% identity, 84% coverage
- Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics
He, Frontiers in cellular and infection microbiology 2012 - “...macrophages, HeLa 14979322 47 gluP BMEII1053 Mice 12414147 48 gnd BMEII1124 Mice 12761078 49 ilvD BMEI1848 Mice, macrophages 15271960 50 malK BMEI1713 Macrophages 14979322 51 manB BMEII0899 Mice, macrophages, HeLa 14979322 52 mocC BMEII0570 Mice, HeLa 14979322 53 ndvB BMEI1837 Mice, HeLa 14979322 54 pgi BMEI1636...”
- Intact purine biosynthesis pathways are required for wild-type virulence of Brucella abortus 2308 in the BALB/c mouse model
Alcantara, Infection and immunity 2004 - “...BMEI1905 BMEII0606 BMEI2034 BMEII0428 BMEII0783 BMEI1123 BMEI0233 BMEI1848 BMEI0296 a Open reading frame designation in the B. melitensis genome. pected, the...”
XHV734_0458 dihydroxy-acid dehydratase from Xanthomonas hortorum pv. vitians
34% identity, 84% coverage
PXO_03941 dihydroxy-acid dehydratase from Xanthomonas oryzae pv. oryzae PXO99A
34% identity, 84% coverage
PMI3302 dihydroxy-acid dehydratase from Proteus mirabilis HI4320
PMI_RS16415 dihydroxy-acid dehydratase from Proteus mirabilis HI4320
34% identity, 84% coverage
- Organ agar serves as physiologically relevant alternative for in vivo bacterial colonization
Pearson, Infection and immunity 2023 - “...PMI3301 ilvE PMI_RS16410 207 B4 1.016 U Branched-chain amino acid aminotransferase Amino acid metabolism Y PMI3302 ilvD PMI_RS16415 207 D2 0.913 U Dihydroxy-acid dehydratase Amino acid metabolism n/a PMI3316 wecA/ rfe PMI_RS16480 219 D6 0.351 U Undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphate transferase Lipopolysaccharide biosynthesis Y PMI3319 rffD PMI_RS16495...”
- Pathogenesis of Proteus mirabilis Infection
Armbruster, EcoSal Plus 2018 - “...efflux protein Y ( 129 ) pldA PMI3344 Phospholipase A N ( 129 ) ilvD PMI3302 Dihydroxy-acid dehydratase (branched chain amino acid biosynthesis protein) Y f ( 129 ) lon PMI0117 ATP-dependent proteinase, serine peptidase Y ( 129 ) argR PMI3399 Transcriptional regulator, repressor of the...”
- Organ agar serves as physiologically relevant alternative for in vivo bacterial colonization
Pearson, Infection and immunity 2023 - “...PMI_RS16410 207 B4 1.016 U Branched-chain amino acid aminotransferase Amino acid metabolism Y PMI3302 ilvD PMI_RS16415 207 D2 0.913 U Dihydroxy-acid dehydratase Amino acid metabolism n/a PMI3316 wecA/ rfe PMI_RS16480 219 D6 0.351 U Undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphate transferase Lipopolysaccharide biosynthesis Y PMI3319 rffD PMI_RS16495 219 C5...”
VF_2559 dihydroxy-acid dehydratase from Vibrio fischeri ES114
32% identity, 84% coverage
Cp258_0893 dihydroxy-acid dehydratase from Corynebacterium pseudotuberculosis 258
33% identity, 85% coverage
Q8A608 Dihydroxy-acid dehydratase from Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)
31% identity, 89% coverage
NCU05683 dihydroxy-acid dehydratase from Neurospora crassa OR74A
30% identity, 87% coverage
- Coordinated Regulation of Protoperithecium Development by MAP Kinases MAK-1 and MAK-2 in Neurospora crassa
Lan, Frontiers in microbiology 2021 - “...and fsd-1 , and several genes with unknown functions, such as NCU07743 , NCU09716 , NCU05683 , and NCU05789 , were also selected for RT-qPCR analysis. In wild type, the transcript levels of these genes were dramatically increased during protoperithecium formation, but these increases were abolished...”
- “...continuous light for 7 days. However, the mutant phenotype of NCU09716, NCU05104, NCU01383, NCU03530, NCU05789, NCU05683, NCU08131, and NCU07180 did not co-segregate well with hygromycin resistance ( Chinnici et al., 2014 ), indicating that additional genetic modifications are likely the cause of the observed deficiencies. Therefore,...”
Q64PS6 Dihydroxy-acid dehydratase from Bacteroides fragilis (strain YCH46)
31% identity, 92% coverage
Q5L9I8 Dihydroxy-acid dehydratase from Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)
31% identity, 89% coverage
BU600 dihydroxy-acid dehydratase from Buchnera aphidicola str. APS (Acyrthosiphon pisum)
30% identity, 83% coverage
- A substrate ambiguous enzyme facilitates genome reduction in an intracellular symbiont
Price, BMC biology 2014 - “...ilvM x EG10501 2.2.1.6 acetolactate synthase (ALS) ilvC BU599 EG10495 1.1.1.86 ketol-acid reductoisomerase (KARI) ilvD BU600 EG10496 4.2.1.9 dihydroxyacid dehydratase (DHAD) panB BU197 EG11675 2.1.2.11 ketopantoate hydroxymethltransferase (KPHMT) panE x EG13271 1.1.1.169 ketopantoate reductase (KPR) panD x EG11747 4.1.1.11 L-aspartate--decarboxylase (ADC) panC BU196 EG11746 6.3.2.1 pantothenate...”
MSMEG_0482 dihydroxy-acid dehydratase from Mycobacterium smegmatis str. MC2 155
32% identity, 94% coverage
edd / CAE53634.1 6-phosphogluconate dehydratase from Nonomuraea gerenzanensis (see paper)
32% identity, 77% coverage
Rmet_5802 phosphogluconate dehydratase from Cupriavidus metallidurans CH34
31% identity, 80% coverage
Rmet_5802 phosphogluconate dehydratase from Ralstonia metallidurans CH34
31% identity, 70% coverage
YjhG / b4297 KpLE2 phage-like element; D-xylonate dehydratase (EC 4.2.1.82) from Escherichia coli K-12 substr. MG1655 (see 8 papers)
yjhG / P39358 KpLE2 phage-like element; D-xylonate dehydratase (EC 4.2.1.82) from Escherichia coli (strain K12) (see 7 papers)
YJHG_ECOLI / P39358 D-xylonate dehydratase YjhG; EC 4.2.1.82 from Escherichia coli (strain K12) (see 2 papers)
P39358 xylonate dehydratase (EC 4.2.1.82) from Escherichia coli (see paper)
yjhG / RF|NP_418717 uncharacterized protein yjhG from Escherichia coli K12 (see paper)
b4297 KpLE2 phage-like element; predicted dehydratase from Escherichia coli str. K-12 substr. MG1655
NP_418717 D-xylonate dehydratase from Escherichia coli str. K-12 substr. MG1655
32% identity, 67% coverage
PMI2760 6-phosphogluconate dehydratase from Proteus mirabilis HI4320
29% identity, 79% coverage
- Pathogenesis of Proteus mirabilis Infection
Armbruster, EcoSal Plus 2018 - “...dehydrogenase, decarboxylating Y ( 166 ) talB PMI0006 Transaldolase B Y ( 166 ) edd PMI2760 6-phosphogluconate dehydratase Y ( 166 ) sdhB PMI0568 Succinate dehydrogenase iron-sulfur protein Y ( 166 ) frdA PMI3588 Fumarate reductase flavoprotein subunit Y ( 166 ) fumC PMI1296 Fumarate hydratase,...”
- “...K, O B, K PMI2575 36D2 B, O PMI2605 nrpG A18 U, K, O K PMI2760 edd 11D4 U, K B, K PMI2823 ppiA 6D1 U, K, O PMI2828 dsbA F437 U, B, K B, K PMI2893 pstS H434 U, B, K B, K PMI2894 pstC...”
- Proteus mirabilis and Urinary Tract Infections
Schaffer, Microbiology spectrum 2015 - “...branched TCA cycle. Mutations in gluconeogenesis ( pckA PMI3015) or the Entner-Doudoroff pathway ( edd PMI2760) had no effect on swarming patterns, nor did a mutation in the fumarate reductase subunit gene frdA (PMI3588) which is involved in anaerobic respiration using the branched TCA pathway (...”
- “...( aceE PMI2046), the TCA cycle ( sdhC PMI0565), and the Entner-Doudoroff pathway ( edd PMI2760). Genes associated with amino acid metabolism and transport were identified, including D-methionine transporter metN (PMI2259), dihydrouridine synthase dusB (PMI3623), carbamoyl phosphate synthetase carA (PMI0020), and L-serine deaminase sdaA (PMI1607) (...”
Q1PAG1 phosphogluconate dehydratase (EC 4.2.1.12) from Pseudomonas chlororaphis (see paper)
29% identity, 80% coverage
RHA1_ro02368 phosphogluconate dehydratase from Rhodococcus sp. RHA1
29% identity, 79% coverage
- Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis
Gilmore, mBio 2020 - “...nature. However, despite success identifying multiple eda homologs, no identifiable E. faecalis homolog to edd (RHA1_ro02368) (or to the putative gluconokinase encoded by RHA1_02362) was found. Collectively, this indicates that E. faecalis must have an alternative to the Edd enzyme for processing gluconate or 6-phosphogluconate to...”
- Nutrient starvation leading to triglyceride accumulation activates the Entner Doudoroff pathway in Rhodococcus jostii RHA1
Juarez, Microbial cell factories 2017 - “...52 Glucose-6-phosphate 1-dehydrogenase RHA1_ro04138 1740 89,076 51 Possible hydratase RHA1_ro02367 2703 133,001 49 KHG/KDPG aldolase RHA1_ro02368 2874 126,594 44 Phosphogluconate dehydratase RHA1_ro06059 569 22,385 39 Hypothetical protein RHA1_ro04137 702 20,726 30 Reductase RHA1_ro04278 2020 49,893 25 Glucokinase RHA1_ro04140 3796 86,218 23 Probable phosphoglycerate dehydrogenase RHA1_ro02361 2216...”
Pput_1048 phosphogluconate dehydratase from Pseudomonas putida F1
PP1010, PP_1010 6-phosphogluconate dehydratase from Pseudomonas putida KT2440
29% identity, 80% coverage
- iTRAQ-based quantitative proteomic analysis of the global response to 17β-estradiol in estrogen-degradation strain Pseudomonas putida SJTE-1
Xu, Scientific reports 2017 - “...gi|148545429 Acetyl-CoA hydrolase Pput_0172 1.94 0.029 gi|148550398 Acetylglutamate kinase Pput_5198 0.63 0.004 gi|148546291 6-phosphogluconate dehydratase Pput_1048 0.44 0.000 gi|148549733 Methylmalonate-semialdehyde dehydrogenase Pput_4531 1.57 0.002 gi|148550491 Glutaminefructose-6-phosphate aminotransferase Pput_5291 1.66 0.028 gi|148549700 Acetyl-CoA acetyltransferase Pput_4498 2.24 0.029 gi|148546692 Branched-chain alpha-keto acid dehydrogenase E1 component Pput_1452 2.23 0.047...”
- Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Dvořák, Nature communications 2024 - “...(PP_2114 - PP_2219) in chromosome 18 PD505 EM42 gcd with additional deletion of gene edd (PP_1010) encoding phosphogluconate dehydratase, with pSEVA2213_ xylABE plasmid This study PD506 EM42 gcd with additional deletion of gene gnd (PP_4043) encoding 6-phosphogluconate dehydrogenase, with pSEVA2213_ xylABE plasmid This study PD507 EM42...”
- “...growth of PD310 on xylose. Genes encoding Pgi-I (PP_1808), Pgi-II (PP_4701), Gnd (PP_4043), and Edd (PP_1010) were knocked out in P. putida EM42 gcd and the growth of the resulting mutants with inserted pSEVA2213_ xylABE plasmid (named PD505, PD506, PD507, Table 1 ) was tested on...”
- UEG Week 2024 Poster Presentations
, United European gastroenterology journal 2024 - UEG Week 2023 Poster Presentations
, United European gastroenterology journal 2023 - Refactoring the Conjugation Machinery of Promiscuous Plasmid RP4 into a Device for Conversion of Gram-Negative Isolates to Hfr Strains
Silbert, ACS synthetic biology 2021 - “...in uracil synthesis, so deletion mutants display uracil auxotrophy. 34 Deletion of the edd gene (PP_1010), on the other hand, gives rise to mutants with impaired growth on glycolytic carbon sources since it encodes the first enzyme of the Entner-Doudoroff pathway of P. putida . 35...”
- CRISPR/Cas9-enhanced ssDNA recombineering for Pseudomonas putida
Aparicio, Microbial biotechnology 2019 - “...the transformation of 6phosphoDgluconate (6PG) to 2keto3deoxy6phosphoDgluconate (KDPG). This enzyme is encoded by the edd (PP_1010) gene. A disruption of this gene prevents the growth of those clones in glycolytic carbon sources but not in gluconeogenic ones or rich media (Nikel etal ., 2015 ). For...”
- Transcriptome remodeling of Pseudomonas putida KT2440 during mcl-PHAs synthesis: effect of different carbon sources and response to nitrogen stress
Mozejko-Ciesielska, Journal of industrial microbiology & biotechnology 2018 - “...pyruvate and glyceraldehyde 3-phosphate via the ED route. The latter pathway involves two genes: edd (PP_1010) and eda (PP_1021), which encode gluconate 6-P dehydrogenase and 2-keto-3-deoxygluconate-6-P aldolase, respectively. Our results confirm that the edd and eda genes are also active when Pseudomonas putida KT2440 is cultivated...”
- Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol
Beckers, Microbial cell factories 2016 - “...0.28 0.29 0.10 0.46 tal PP2168 Transaldolase B 0.6 0.07 0.10 0.70 Entner-Doudoroff pathway edd PP1010 6-Phosphogluconate dehydratase 0.9 0.22 0.03 0.71 eda PP1024 KDPG aldolase 1.24 0.29 1.65 0.98 Pyruvate metabolism acoA PP0555 Pyruvate dehydrogenase 1.16 1.86 1.03 0.33 acoB PP0554 Pyruvate dehydrogenase 1.5 1.88...”
- Pseudomonas putida KT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways
Nikel, The Journal of biological chemistry 2015 - “...(PP1024, 2-keto-3-deoxy-6-phosphogluconate aldolase), edd (PP1010, 6-phosphogluconate dehydratase), gnd (PP4043, 6-phosphogluconate dehydrogenase), and zwf-1...”
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PPUBIRD1_1060 phosphogluconate dehydratase from Pseudomonas putida BIRD-1
29% identity, 80% coverage
H16_B2567 phosphogluconate dehydratase from Cupriavidus necator H16
H16_B2567 phosphogluconate dehydratase from Ralstonia eutropha H16
29% identity, 81% coverage
- The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16
Arenas-López, Biotechnology for biofuels 2019 - “...which were statistically significant. These included the genes for 6-phosphogluconolactonase (H16_B2565, no change), 6-phosphogluconate dehydratase (H16_B2567, no change) and 2-keto-3-deoxy-6-phosphogluconate aldolase (B16_B1213, 3.4-fold downregulated; p adj >0.05) (Additional file 3 : Table S1). A second 6-phosphogluconate dehydratase gene, H16_A1178, was strongly downregulated (38-fold), but this change...”
YagF / b0269 CP4-6 prophage; D-xylonate dehydratase (EC 4.2.1.82) from Escherichia coli K-12 substr. MG1655 (see 5 papers)
yagF / P77596 CP4-6 prophage; D-xylonate dehydratase (EC 4.2.1.82) from Escherichia coli (strain K12) (see 4 papers)
YAGF_ECOLI / P77596 D-xylonate dehydratase YagF; EC 4.2.1.82 from Escherichia coli (strain K12) (see 2 papers)
b0269 CP4-6 prophage; predicted dehydratase from Escherichia coli str. K-12 substr. MG1655
32% identity, 64% coverage
- function: Catalyzes the dehydration of D-xylonic acid to form 2- dehydro-3-deoxy-D-pentonate.
catalytic activity: D-xylonate = 2-dehydro-3-deoxy-D-arabinonate + H2O (RHEA:19157)
disruption phenotype: Disruption mutant has reduced ability to catabolize D-xylonic acid. YjhG-yagF double mutant cannot use D- xylonate as the sole source of carbon. - NfiS, a species-specific regulatory noncoding RNA of Pseudomonas stutzeri, enhances oxidative stress tolerance in Escherichia coli
Hu, AMB Express 2019 - “...fsaB 1.74 Fructose-6-phosphate aldolase 2 3.38E03 27.16 b3413 gntX 1.73 DNA catabolic protein 3.60E03 27.03 b0269 yagF 17.39 CP4-6 prophage dehydratase family protein 3.89E03 26.86 b0875 aqpZ 3.05 Aquaporin Z 4.12E03 26.74 b3115 tdcD 1.58 Propionate kinase/acetate kinase C anaerobic 4.52E03 26.55 b0089 ftsW 1.48 Putative...”
- Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
Orth, BMC systems biology 2012 - “...(b0928)* R03530 (F) ndk (bb2518)* R00012 (F) global orphan R01232 (R) yjhG (b4297) 0.028 yagF (b0269) 0.057 R00838 (F) chbF (b1734) 9.00E-42 melA (b4119) 2.00E-21 R00655 (R) global orphan R07300 (F) global orphan R00683 (F) global orphan R00367 (F) global orphan R02559 (F) global orphan R02560...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...b0259 yi52_1 1 IS5 transposase 0.61* 0.50* 1.04 b0268 b0269 yagE yagF 2 2 Putative lyase/synthase Putative dehydratase 0.25* 0.33* 0.85 b0306 b0307 b0308 ykgE...”
- High-density microarray-mediated gene expression profiling of Escherichia coli
Wei, Journal of bacteriology 2001 - “...rhlB, rhoL, sdhC, selB, tdcA, tnaL, b0177, b0250, b0269, b0271, b0291, b0322, b0574, b1437, b1595, b1824, b1978, b2067, b2086, b2088, b2097, b2270, b2292,...”
IYO_006345 phosphogluconate dehydratase from Pseudomonas syringae pv. actinidiae ICMP 18884
29% identity, 80% coverage
CC2055 phosphogluconate dehydratase from Caulobacter crescentus CB15
CCNA_02134 phosphogluconate dehydratase from Caulobacter crescentus NA1000
28% identity, 86% coverage
- Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media
Hottes, Journal of bacteriology 2004 - “...Carbohydrate metabolism CC2054, glucokinase, glk CC2055, phosphogluconate dehydratase, edd CC2056, 6-phosphogluconolactonase, pgl CC2057, glucose-6-phosphate...”
- “...10, 2017 by University of California, Berkeley to CC2055, a homolog of the E. coli edd gene encoding phosphogluconate dehydratase, which catalyzes the...”
- Enzymatic Synthesis of 2-Keto-3-Deoxy-6-Phosphogluconate by the 6-Phosphogluconate-Dehydratase From Caulobacter crescentus
Krevet, Frontiers in bioengineering and biotechnology 2020 - “...From C . crescentus and Functional Overexpression in E . coli The EDD encoding gene CCNA_02134 comprising 1809 bp was amplified from C . crescentus genomic DNA using the primer set 5-GTAGATC CATATG AGCCTGAATCCCGTCATC-3 and 5-CTA AAGCTT CCTCAAGCAAAGACGGAGGCG3 ( Nde I/ Hin dIII, restriction sites underlined)...”
- “...Successful cloning was confirmed by sequencing (LGC genomics, Germany). For expression the resulting construct pET15b- CCNA_02134 was transformed into E . coli BL21 (DE3) and cells were grown in 400 ml Luria-Bertani medium supplemented with 100 g/ml ampicillin and 5 mM manganese chloride. After growth to...”
SO2487 6-phosphogluconate dehydratase from Shewanella oneidensis MR-1
SO_2487, WP_011072452 phosphogluconate dehydratase from Shewanella oneidensis MR-1
29% identity, 81% coverage
- Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor
Rosenbaum, PloS one 2012 - “...oxidase, CcoN 0.0020 cbb3 -type cytochrome c oxidase 2.29432 SO2417 iron-sulfur cluster-binding protein 0.0303 1.316717 SO2487 6-phosphogluconate dehydratase 0.0147 1.328647 SO2489 glucose-6-phosphate 1-dehydrogenase 0.0230 1.653075 SO2491 pyruvate kinase II 0.0057 Glycolysis/Gluconeogenesis 1.594663 SO2638 leucine dehydrogenase 0.0127 2.578122 SO2727 STC small tetraheme cytochrome c 0.0000 Periplasmic cytochrome...”
- An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences
Turse, PloS one 2010 - “...the environmental Shewanella isolates, only one enzyme in the pentose phosphate pathway, phosphogluconate dehydratase (Edd, SO2487 and CN32_1868) was observed. When the S. oneidensis MR-1 genome sequence was used to identify proteins expressed by the isolates, phosphogluconate dehydratase was observed in those strains that were more...”
- “...4 SO1200 tpiA 3 SO2345 gapA-2 7 3 SO2347 gapA-3 4 SO2486 eda 3 2 SO2487 edd 5 SO2488 pgl 2 SO2489 zwf 4 SO2491 pykA 10 4 SO2644 ppsA 15 6 3 SO3440 eno 8 3 2 2 SO3547 pgi 3 SO3991 fbp 4 3...”
- Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins
Gao, Journal of bacteriology 2006 - “...aldolase/4-hydroxy-2-oxoglutarate aldolase; 2.7-fold induction), so2487 (edd, 6-phosphogluconate dehydratase; 2.6-fold), so2488 (pgl, 6-phosphogluconolactonase;...”
- The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family
Rahman, Scientific reports 2018 - “...6PGDHT and So 6PGDHT are 6-phosphogluconate dehydratasesfrom Zymomonas mobilis (GeneBank: WP_013934127) and Shewanella oneidensis (GeneBank: WP_011072452). The N- and C-terminal domain are shown in red and blue, connecting loop in green. The [2Fe-2S] cluster coordinating residues are shown in yellow, Mg 2+ ion coordinating residues are...”
- Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions
Deutschbauer, PLoS genetics 2011 - “...minimal media with DL-lactate and N-acetyl-glucosamine (NAG) as carbon sources. Gene codes correspond to edd (SO_2487; phosphogluconate dehydratase), zwf (SO_2489; glucose-6-phosphate 1-dehydrogenase), and nag ( nagP (SO_3503), nagA (SO_3505), nagB-II (SO_3506), nagK-I (SO_3507), and nagR (SO_3516)). The NAG genes were annotated by Osterman and colleagues [80]...”
SF5M90T_1806 phosphogluconate dehydratase from Shigella flexneri 5a str. M90T
29% identity, 81% coverage
- RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
Vergara-Irigaray, BMC genomics 2014 - “...gamma-glutamate kinase 1.26 -0.58 SF5M90T_2533 glyA serine hydroxymethyltransferase 1.16 SF5M90T_2967 gsp glutathionylspermidine synthetase/amidase 1.16 0.70 SF5M90T_1806 edd 6-phosphogluconate dehydratase 1.15 -0.72 SF5M90T_807 glutathione transporter ATP-binding protein 1.08 SF5M90T_2317 hisJ histidine-binding periplasmic protein of high-affinity histidine transport system 1.05 SF5M90T_806 ybiK putative asparaginase 1.02 SF5M90T_1122 potC spermidine/putrescine...”
Edd / b1851 phosphogluconate dehydratase (EC 4.2.1.12) from Escherichia coli K-12 substr. MG1655 (see 30 papers)
edd / P0ADF6 phosphogluconate dehydratase (EC 4.2.1.12) from Escherichia coli (strain K12) (see 29 papers)
EDD_ECOLI / P0ADF6 Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; Entner-Doudoroff dehydrase; EC 4.2.1.12 from Escherichia coli (strain K12) (see 4 papers)
edd / RF|NP_416365 phosphogluconate dehydratase from Escherichia coli K12 (see 2 papers)
b1851 phosphogluconate dehydratase from Escherichia coli str. K-12 substr. MG1655
29% identity, 81% coverage
- function: Catalyzes the dehydration of 6-phospho-D-gluconate to 2- dehydro-3-deoxy-6-phospho-D-gluconate.
catalytic activity: 6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D- gluconate + H2O (RHEA:17277)
cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster.)
disruption phenotype: The mutant grows at normal rates on glucose and fructose, whereas on gluconate it grows about one-third as fast as the wild-type. - Plastid ancestors lacked a complete Entner-Doudoroff pathway, limiting plants to glycolysis and the pentose phosphate pathway
Evans, Nature communications 2024 - “...and an AlphaFold model 26 generated from the E. coli K12 EDD sequence (Uniprot ID P0ADF6) were used in substrate docking simulations. The predicted N-terminal transit peptide from the DHAD structure was removed before docking analysis. The dimeric dehydratase structures were generated using crystallographic symmetry from...”
- Functional Prediction of Biological Profile During Eutrophication in Marine Environment
Sbaoui, Bioinformatics and biology insights 2022 - “...proteins (oxidoreductase) with quinone as electron acceptor, reoxidizes DsbA DsrB P0AEG8 Dissimilatory sulfate reductase Edd P0ADF6 Phosphogluconate dehydratase Eno P0A6P9 Enolase EutC P19636 Ethanolamine ammonia-lyase subunit EutG P76553 Polypeptide putative alcohol dehydrogenase FAZ83_23975 A0A6D2XMK9 Branched-chain amino acid ABC transporter permease FbaA P0AB71 Fructose-1,6-bisphosphate aldolase Fbp P0A993...”
- Awakening a latent carbon fixation cycle in Escherichia coli
Satanowski, Nature communications 2020 - “...P00350), KHG/KDPG aldolase ( eda , Uniprot: P0A955), and phosphogluconate dehydratase ( edd , UniProt: P0ADF6) were amplified from E. coli MG1655genomic DNA with high-fidelity Phusion Polymerase (ThermoScientific, Dreieich, Germany) using primers listed in Supplementary Table 2 . Silent mutations were introduced to remove relevant restriction...”
- A Sinorhizobium meliloti RpoH-Regulated Gene Is Involved in Iron-Sulfur Protein Metabolism and Effective Plant Symbiosis under Intrinsic Iron Limitation
Sasaki, Journal of bacteriology 2016 - “...conserved: edd (6-PGDH; 59% identity; RefSeq accession numbers P0ADF6 and CAC45274 for the sequences in E. coli and S. meliloti, respectively), acnA (aconitase;...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Identification of genome-scale metabolic network models using experimentally measured flux profiles
Herrgård, PLoS computational biology 2006 - “...sucA (b0726), sucB (b0727), pgl (b0767), galU (b1236), fdnG (b1474), fdnH (b1475), fdnI (b1476), edd (b1851), nuoN (b2276), nuoM (b2277), nuoL (b2278), nuoK (b2279), nuoJ (b2280), nuoI (b2281), nuoH (b2282), nuoG (b2283), nuoF (b2284), nuoE (b2285), nuoC (b2286), nuoB (b2287), nuoA (b2288), fdoI (b3892), fdoH (b3893),...”
KVU_PB0156 phosphogluconate dehydratase from Ketogulonicigenium vulgare WSH-001
32% identity, 82% coverage
ABBFA_003050 phosphogluconate dehydratase from Acinetobacter baumannii AB307-0294
29% identity, 79% coverage
edd / AAA23722.1 6-phosphogluconate dehydratase from Escherichia coli (see paper)
29% identity, 81% coverage
A1S_0483 phosphogluconate dehydratase from Acinetobacter baumannii ATCC 17978
29% identity, 85% coverage
Snov_3400 phosphogluconate dehydratase from Ancylobacter novellus DSM 506
30% identity, 77% coverage
SACE_1740 phosphogluconate dehydratase from Saccharopolyspora erythraea NRRL 2338
28% identity, 79% coverage
- Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraea
Karničar, Microbial cell factories 2016 - “...proteins of the carbohydrate metabolism (e.g. succinyl-CoA synthetase subunit, SACE_6668; dihydrolipoamide succinyltransferase, SACE_1638; phosphogluconate dehydratase, SACE_1740; 6-phosphofructokinase, SACE_1704; ribose-phosphate pyrophosphokinase, SACE_0816) and nucleotide metabolism (inosine-5-monophosphate dehydrogenase, SACE_6708; phospho-2-dehydro-3-deoxyheptonate aldolase, SACE_1708; phosphoribosylaminoimidazolecarboxamide formyltransferase, SACE_6664) were observed in the WT strain, but not in the HP strain. Additionally,...”
JHW33_RS05140 phosphogluconate dehydratase from Rahnella aceris
28% identity, 81% coverage
- Comparative Genomics Assisted Functional Characterization of Rahnella aceris ZF458 as a Novel Plant Growth Promoting Rhizobacterium
Xu, Frontiers in microbiology 2022 - “...gntk gluconokinase JHW33_RS05130 WP_200225227.1 WP_015689980.1 99 WP_015689980.1 99 WP_015689980.1 98 WP_013573544.1 52 edd phosphogluconate dehydratase JHW33_RS05140 WP_200225228.1 WP_119261688.1 99 WP_015689978.1 99 WP_013575660.1 99 WP_015697147.1 95 eda bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase JHW33_RS05145 WP_037035690.1 WP_013575316.1 99 WP_013575316.1 99 WP_013575316.1 99 WP_015697180.1 91 eda bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase JHW33_RS06765...”
BCAL3367 phosphogluconate dehydratase from Burkholderia cenocepacia J2315
28% identity, 79% coverage
- Low iron-induced small RNA BrrF regulates central metabolism and oxidative stress responses in Burkholderia cenocepacia
Sass, PloS one 2020 - “...] BCAL2198 iscS Cysteine desulfurase n.d. n.d. [ 10 , 35 , 36 ] Other BCAL3367 edd [Fe-S]-dependent phosphogluconate dehydratase -3.60 -1.54 *Log2-fold change after addition of 200 M dipyridyl to a culture at mid-log phase, harvest after 30 min of further incubation, compared to untreated...”
- “...iron depletion ( Table 1 ), while cyoB did not change expression. The edd gene (BCAL3367; encoding a [Fe-S]-cluster containing phosphogluconate dehydratase) was downregulated in response to iron depletion in a BrrF-dependent manner ( Table 1 , S4 Table ). edd is the first gene of...”
ACIAD0542 phosphogluconate dehydratase (6-phosphogluconate dehydratase) from Acinetobacter sp. ADP1
29% identity, 78% coverage
EIO_3349 phosphogluconate dehydratase from Ketogulonicigenium vulgare Y25
31% identity, 81% coverage
jhp1026 PHOSPHOGLUCONATE DEHYDRATASE from Helicobacter pylori J99
28% identity, 80% coverage
MSMEG_0313 phosphogluconate dehydratase from Mycobacterium smegmatis str. MC2 155
29% identity, 82% coverage
CtCNB1_3428 6-phosphogluconate dehydratase from Comamonas testosteroni CNB-2
27% identity, 79% coverage
lpp0485 hypothetical protein from Legionella pneumophila str. Paris
29% identity, 79% coverage
- The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system
Sahr, PLoS genetics 2017 - “.../ lpp1461 Pdh, Pyruvate dehydrogenase complex 46.09 / 0.65 lpp0483 Glucose-6-phosphate 1-dehydrogenase 12.91 0.55 / lpp0485 6-phosphogluconate dehydratase 23.40 0.47 / lpp0728 Acetoacetate decarboxylase 113.00 3.84 2.60 lpp0108 Ribose-5-phosphate isomerase A 18.08 / 0.62 lpp1516 Pyruvate/2-oxoglutarate dehydrogenase complex 18.92 0.62 / lpp2838 Tpi, Triosephosphate isomerase 9.46...”
- “...(Lpp1369), glycerol kinase, Tpi (Lpp2838), Triosephosphate isomerase, Zwf (Lpp0483), Glucose-6-phosphate 1-dehydrogenase, Pgl (Lpp0484), 6-Phosphogluconolactonase, Edd (Lpp0485), 6-Phosphogluconate dehydratase, Gap (Lpp0153), Glyceraldehyde 3-phosphate dehydrogenase, Pgk (Lpp0152), 3-Phosphoglycerate kinase, Eno (Lpp2020), Enolase, Pyk (Lpp0151), Pyruvate kinase, PpsA (Lpp0567), Phosphoenolpyruvate synthase, Pdh (Lpp1461), Pyruvate dehydrogenase complex, Pyc (Lpp0531), Pyruvate...”
- Isotopologue profiling of Legionella pneumophila: role of serine and glucose as carbon substrates
Eylert, The Journal of biological chemistry 2010 - “...determined via RT-PCR. lpp0483, zwf, lpp0484, pgl; lpp0485, edd; lpp0486, glk; lpp0487, eda; lpp0488 (putative sugar transport protein); lpp0150, sdhB...”
BPSL2932 phosphogluconate dehydratase from Burkholderia pseudomallei K96243
28% identity, 79% coverage
- Transcriptional profiles of Burkholderia pseudomallei reveal the direct and indirect roles of Sigma E under oxidative stress conditions
Jitprasutwit, BMC genomics 2014 - “...bpsl2729 , and bpsl2736 ), and two genes of the Entner-Doudoroff pathway ( bpsl2931 and bpsl2932 ). In addition, many genes related to amino acid utilization ( bpsl1076, bpsl2305 and bpsl2497 ) and amino acid biosynthesis ( bpsl3419 ) were up-regulated when B. pseudomallei was exposed...”
- “...stress related rubrerythrin protein 3.36 1.68 bpss1838 Ferredoxin 3.31 1.79 bpsl2931 Eda (KHG/KDPG_aldolase) 3.26 2.59 bpsl2932 Phosphogluconate dehydratase 3.17 2.13 bpsl2605 TrxB 2.75 1.18 bpsl1799 Putative fimbrial chaperone 2.70 1.71 bpsl1800 Putative outer membrane usher protein precursor 2.59 1.86 bpss1437 Lipoprotein 2.42 2.27 bpss1251 N-carbamoyl-L-amino N-acid...”
G4234_18415 phosphogluconate dehydratase from Serratia marcescens
29% identity, 82% coverage
- Whole genome sequence of Serratia marcescens 39_H1, a potential hydrolytic and acidogenic strain
Obi, Biotechnology reports (Amsterdam, Netherlands) 2020 - “...further oxidation to 6-phosphogluconate was catalysed by gluconokinase (G4234_10115) and to 2-keto-3-deoxy-6-phosphogluconate by 6-phosphogluconate dehydratase (G4234_18415). 2-keto-3-deoxy-6-phosphogluconate was then oxidised to pyruvate and glyceraldehyde-3-phosphate by 2-keto-3-deoxy-6-phosphogluconate aldolase (G4234_10110). In the course of the phosphate solubilising assay, the strain possibly secreted an organic acid that initiated the...”
P56111 Phosphogluconate dehydratase from Helicobacter pylori (strain ATCC 700392 / 26695)
HP1100 6-phosphogluconate dehydratase from Helicobacter pylori 26695
28% identity, 80% coverage
- Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
Wei, ACS omega 2022 - “...O25925 mreB 139 P56431 trxB 140 O25327 MtrC 141 P25177 glmM 142 O25147 HP_0385 143 P56111 edd 144 P56146 pheS 145 O25731 glk 146 O25820 Dld 147 O25372 gatB 148 P56034 rplF 149 P42445 recA 150 P56460 metK 151 P56071 thrS 152 O25088 tatA 153 P56154...”
- “...P56030 rplB 109 O25088 tatA 110 P56060 kdsA 111 P56047 rplV 112 P55980 cagA 113 P56111 edd 114 O25313 HP_0591 115 O25045 pyrC 116 P56420 tig 117 O25776 fldA 118 O25257 Cag1 119 P56088 guaB 120 O25771 Omp25 121 O25936 fbp 122 O25176 HP_0422 123 P56007...”
- Targeted identification of glycosylated proteins in the gastric pathogen Helicobacter pylori (Hp)
Champasa, Molecular & cellular proteomics : MCP 2013 - “...unknown 3 2 7.9 HP0859 AAD07905 rfaD 39.4 mannoheptose epimerase cytoplasm 5 2 7.8 HP1100 P56111 70.2 6-phophogluconate dehydratase cytoplasm 55 2 6.4 HP0210 P56116 htpG 74.8 chaperone and heat shock protein cytoplasm 2 2 7.2 HP0056 AAD07126 141.6 pyrroline-5-carboxylate dehydrogenase cytoplasm 14 5 7.1 HP0728...”
- Identification of anti-Helicobacter pylori antibody signatures in gastric intestinal metaplasia
Song, Journal of gastroenterology 2023 - “...18 35 0.41 0.006 0.57 HP0153 RecA Recombinase 10 22 17 30 0.48 0.030 0.55 HP1100 Edd Phosphogluconate dehydratase 10 22 5 11 0.43 0.118 0.55 HP1118 Ggt Gamma-glutamyltranspeptidase 10 34 25 33 0.68 0.213 0.58 HP1110 PorA Pyruvate flavodoxin oxidoreductase subunit alpha 10 30 24...”
- “...12 1.81 0.178 0.52 HP0175 PpiC Peptidylprolyl isomerase 22 9 17 11 1.76 0.228 0.56 HP1100 Edd Phosphogluconate dehydratase 24 12 9 5 2.10 0.264 0.51 HP0875 KatA Catalase 22 12 25 18 1.46 0.325 0.53 HP0606 MtrC Membrane fusion protein 22 12 16 15 1.10...”
- Genomic Distribution of Pro-Virulent cpdB-like Genes in Eubacteria and Comparison of the Enzyme Specificity of CpdB-like Proteins from Salmonella enterica, Escherichia coli and Streptococcus suis
Ribeiro, International journal of molecular sciences 2023 - “...mm 4 mm) of the same material (octadecylsilica; Teknokroma, San Cugat del Valls, Barcelona). An HP1100 system was used with a diode array detector adjusted to measure A 260 . Samples of 20 L were injected and the elution was performed at 1 mL/min with four...”
- Structure-based inhibitor design for reshaping bacterial morphology
Choi, Communications biology 2022 - “...ThermoFinnigan LCQ Classic, Quadrupole Ion-Trap Mass Spectrometer. HPLC analyses were carried out on an Agilent HP1100 system (Santa Clara, CA, USA), comprised of an auto sampler, quaternary pump, photodiode array detector (DAD), and HP Chemstation software. The separation was carried out on a poroshell 120 EC-C18...”
- Antimicrobial and Immunomodulating Activities of Two Endemic Nepeta Species and Their Major Iridoids Isolated from Natural Sources
Aničić, Pharmaceuticals (Basel, Switzerland) 2021 - “...EOs, diluted in 99.6% methanol (w:v = 1:50), was performed on an HPLC system, model HP1100 with DAD (Hewlett Packard, Santa Clara, CA, USA), connected to a Fraction collector 1200 Series (Agilent Technologies, Waldbronn, Germany). Chromatographic separation was performed using a ZORBAX SB-C18 (9.4 100 mm,...”
- Bacillus subtilis Strain DSM 29784 Modulates the Cecal Microbiome, Concentration of Short-Chain Fatty Acids, and Apparent Retention of Dietary Components in Shaver White Chickens during Grower, Developer, and Laying Phases
Neijat, Applied and environmental microbiology 2019 - “...was assayed for SCFA and simple sugars using an HP1100 series HPLC (Woldbronn, Germany) equipped with an ROA LC column (300 by 7.8 mm; Phenomenex, Torrance, CA)...”
- High-Salt Conditions Alter Transcription of Helicobacter pylori Genes Encoding Outer Membrane Proteins
Loh, Infection and immunity 2018 - “...HP1317 HP1309 HP1286 HP1254 HP1246 HP1245 HP1244 HP1192 HP1163 HP1100 HP0389 HP0549 HP0565 HP0588 0.59 0.60 0.56 0.67 0.68 0.53 0.63 0.68 0.67 0.65 0.54 0.66...”
- “...J99 genome HP1435 HP1317 HP1426 HP1286 HP1246 HP1245 HP1100 HP0389 HP1412 jhp1408 HP0565 HP0601 HP0630 HP0642 HP0696 HP0731 HP0751 HP0802 HP0809 HP0318 HP0291...”
- Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
Marcus, Helicobacter 2018 - “...0.18 0.05 1.47 0.15 0.10 1.90 0.09 0.00 glucose-6-phosphate 1-dehydrogenase ( zwf, g6pD ) HPG27_RS05450 HP1100 1.44 0.04 0.00 1.66 0.04 0.00 2.04 0.08 0.00 phosphogluconate dehydratase ( edd ) HPG27_RS05445 HP1099 1.98 0.11 0.00 2.44 0.10 0.00 2.64 0.12 0.00 2-keto-3-deoxy-6-phosphogluconate aldolase ( eda )...”
- IpdAB, a virulence factor in Mycobacterium tuberculosis, is a cholesterol ring-cleaving hydrolase
Crowe, Proceedings of the National Academy of Sciences of the United States of America 2018 - “...COCHEA-CoA (tR = 6.1 min) was purified using an HP1100 series HPLC (Agilent Technologies) equipped with a Luna 3u PFP (2) 50- x 4.6-mm column (Phenomenex)...”
- “...succinate, and MOODA. Reaction products were analyzed using a HP1100 Series HPLC attached to a 4.6- x 50-mm Luna 3u PFP (2) column operated at 1 mL*min-1....”
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HPG27_RS05450 phosphogluconate dehydratase from Helicobacter pylori G27
28% identity, 80% coverage
Mal48_25960 YjhG/YagF family D-xylonate dehydratase from Thalassoglobus polymorphus
33% identity, 64% coverage
EDD_ZYMMO / P21909 Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 from Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (see paper)
ZZ6_0880 phosphogluconate dehydratase from Zymomonas mobilis subsp. mobilis ATCC 29191
ZMO0368 phosphogluconate dehydratase from Zymomonas mobilis subsp. mobilis ZM4
27% identity, 82% coverage
- function: Catalyzes the dehydration of 6-phospho-D-gluconate to 2- dehydro-3-deoxy-6-phospho-D-gluconate.
catalytic activity: 6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D- gluconate + H2O (RHEA:17277)
cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster.) - Neutral red-mediated microbial electrosynthesis by Escherichia coli, Klebsiella pneumoniae, and Zymomonas mobilis
Harrington, Bioresource technology 2015 - “...difference. However, there were several proteins involved in central metabolism that were over-expressed (glk, pgi, ZZ6_0880, ZZ6_1055, ZZ6_1712), suggesting that these enzymes were not rate-limiting. For instance, pyruvate decarboxylase was slightly overexpressed during electrosynthesis (Log 2 = 0.78), but this did not manifest as an increase...”
- Characterization and Application of the Sugar Transporter Zmo0293 from Zymomonas mobilis
Zhang, International journal of molecular sciences 2023 - “...for glucose metabolism. Four genes, glf ( ZMO0366 ), zwf ( ZMO0367 ), edd ( ZMO0368 ), and glk ( ZMO0369 ), constitute an operon that enables efficient glucose utilization [ 31 ]. glf is the main sugar transporter for glucose uptake in ZM4. To examine...”
- “...2 1.64 0.98 0.8 0.78 ZMO0367 zwf glucose-6-phosphate dehydrogenase 0.98 0.04 0.11 1 0.13 0.63 ZMO0368 edd phosphogluconate dehydratase 1.02 1.85 0.27 1 3.29 5.13 ZMO0369 glk glucokinase 1 0.22 0.09 1.01 0.45 1.68 ZMO1236 adhA alcohol dehydrogenase 1 0.96 0.59 1 0.23 1.32 ZMO1237 ldhA...”
- Genome Wide Phosphoproteome Analysis of Zymomonas mobilis Under Anaerobic, Aerobic, and N2-Fixing Conditions
Tatli, Frontiers in microbiology 2019 - “...sites in most enzymes in glycolysis ( Figure 3B ). For example, 6-phosphogluconate dehydratase (EDD, ZMO0368) had two phosphorylation sites (Thr 2 , Tyr 339 ), glyceraldehyde phosphate dehydrogenase (GAPDH, ZMO0177) had three phosphorylation sites (Thr 212 , Ser 211 and Ser 195 ), and pyruvate...”
- Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment
Yi, Biotechnology for biofuels 2015 - “...selected genes included ZMO0152 (pyruvate kinase), ZMO0177 (16S rRNA), ZMO0179 (fructose-bisphosphate aldolase), ZMO0367 (glucose-6-phosphate 1-dehydrogenase), ZMO0368 (6-phosphogluconate dehydrogenase), ZMO0369 (glucokinase), ZMO0387 (hpcH/hpaI aldolase), ZMO0543 (aconitate hydratase), ZMO0544 (isocitrate dehydrogenase), ZMO0567 (succinyl-CoA synthetase), ZMO0569 (succinate dehydrogenase), ZMO0997 (KDPG aldolase), ZMO1237 ( d -isomer specific 2-hydroxyacid dehydrogenase), ZMO1307...”
- Transcriptome profiling of Zymomonas mobilis under ethanol stress
He, Biotechnology for biofuels 2012 - “...glk (glucokinase) 0.86 ZMO0367 zwf 0.79 ZMO1649 gnl 0.34 ZMO1757 gntK 0.48 ZMO1478 pgl 0.67 ZMO0368 edd 0.89 ZMO0997 eda 0.88 ZMO0177 gap 0.97 ZMO0178 pgk 0.8 ZMO1240 gpm 0.91 ZMO1608 eno 0.87 ZMO0152 pyk 0.87 ZMO1496 Ppc 0.64 ZMO1237 ldhA 0.54 ZMO1360 pdc 0.76 ZMO1596...”
- The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4
Seo, Nature biotechnology 2005 - “...dehydrated to 6-phosphogluconate by lactonase (ZMO1478). 6-phosphogluconate is dehydrated by 6-phosphogluconate dehydratase ( edd , ZMO0368) to yield 2-keto-3-deoxy-6-phosphogluconate (KDPG). KDPG aldolase ( eda , ZMO0997) cleaves KDPG to form pyruvate and glyceraldehyde-3-phosphate ( Fig. 2 ). Glyceraldehyde-3-phosphate is then metabolized via the triose phosphate common...”
PA3194 phosphogluconate dehydratase from Pseudomonas aeruginosa PAO1
PA14_22910 6-phosphogluconate dehydratase from Pseudomonas aeruginosa UCBPP-PA14
27% identity, 80% coverage
- Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
Rubio-Gómez, Frontiers in microbiology 2020 - “...PA3183 zwf Glucose-6-phosphate 1-dehydrogenase 1.7 0.000 2.0 0.000 PA3193 glk Glucokinase 0.6 0.004 0.7 0.002 PA3194 edd Phosphogluconate dehydratase 1.5 0.000 1.9 0.000 PA3195 gapA Glyceraldehyde-3-phosphate dehydrogenase 1.0 0.001 1.1 0.000 PA3219 Uncharacterized protein 1.2 0.000 1.3 0.000 PA3280 oprO Pyrophosphate-specific outer membrane porin 1.1 0.000...”
- “...transporter 0.8 0.004 PA3192 gltR Two-component response regulator 1.6 0.000 PA3193 glk Glucokinase 0.7 0.002 PA3194 edd Phosphogluconate dehydratase 1.9 0.000 PA3195 gapA Glyceraldehyde-3-phosphate dehydrogenase 1.1 0.000 PA3219 Uncharacterized protein 1.3 0.000 PA3262 Peptidyl-prolyl cis-trans isomerase 0.8 0.001 PA3280 oprO Pyrophosphate-specific outer membrane porin 1.1 0.000...”
- Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...PA2516 xylZ 4.1 1.7 Toluate 1,2-dioxygenase electron transfer component PA3183 zwf 2.1 + Glucose-6-phosphate 1-dehydrogenase PA3194 edd 1.5 + Phosphogluconate dehydratase PA3195 gapA 2.5 + Glyceraldehyde 3-phosphate dehydrogenase PA3394 nosF 1.6 + NosF protein a PA numbers are from http://www.pseudomonas.com ; ORF, open reading frame. b...”
- 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 - “...ABC sugar transporter 0,2 2,92 8,1 CCM/catabolism glk PA3193 Glucokinase 0,02 1,11 3,15 CCM/catabolism edd PA3194 Phosphogluconate dehydratase 1,07 1,11 4,22 CCM gapA PA3195 Glyceraldehyde 3-phosphate dehydrogenase 0,1 2,08 6,02 Transport PA3271 Probable two-component sensor 2,75 0,32 1,85 Catabolism pauA5 PA3356 Glutamylpolyamine synthetase 0,85 0,13 1,21...”
- Creation of stable Pseudomonas aeruginosa promoter-reporter fusion mutants using linear plasmid DNA transformation
Chen, BMC research notes 2016 - “...containing the promoter of a hypothetical protein (PA45) gene, the promoter of a phosphogluconate dehydratase (PA3194) gene, and the promoter of pyochelin (PA4228) gene using different versions of gfp reporter genes. For each transformation, although there are variations in transformation efficiencies, we were able to obtain...”
- Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa
San, Nature communications 2015 - “...the kinase mutant, including the two putative kinases (PA4673.15-16), a molybdenum cofactor biosynthetic protein A1 (PA3194) and a nitrite extrusion protein (PA3887). These last two genes were underexpressed in both the plasmid-bearing helicase mutant and the plasmid-free kinase mutant (Wald Test BenjaminiHochberg corrected, PA3887 P =0.044...”
- “...with each other, since mutations in both helicase and kinase lead to the underexpression of PA3194 and PA3887 genes. In addition, helicases are known to interact with plasmid replication proteins 36 37 . Taken together, these lines of evidence suggest that the kinases may be responsible...”
- MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
Tsuyuzaki, BMC bioinformatics 2015 - “...Hypothetical Translational termination - - PA0502 - 878654 Biotin biosynthesis Biotin biosynthetic process - - PA3194 edd 882909 Carbohydrate metabolism Generation of precursor metabolites and energy (+3) Phosphoenolpyruvate carboxylase activity - PA1775 cmpX 877590 Cytoplasmic membrane protein - - - PA0427 oprM 877851 Multidrug efflux transport...”
- “...Microbial Sensitivity Test (+4) Drug Resistance, Multiple (+10) PA0502 - - - - - - PA3194 Cell-Free System (+2) Salmonella typhimurium (+3) Chromosome Aberrations DNA, Bacterial (+45) Spectrophotometry (+8) Sequence Homology, Nucleic Acid (+28) PA1775 - - - - - - PA0427 Brain (+6) Animals, Newborn...”
- Inhibition of Pseudomonas aeruginosa swarming motility by 1-naphthol and other bicyclic compounds bearing hydroxyl groups
Oura, Applied and environmental microbiology 2015 - “...PA2247 PA2248 PA2249 PA2250 PA2321 PA2554 PA2555 PA3183 PA3194 PA3195 PA3559 PA3584 PA3723 PA3924 PA4022 PA5056 PA5435 PA5436 Cell motility and secretion PA0176...”
- Comparative genome analysis of ciprofloxacin-resistant Pseudomonas aeruginosa reveals genes within newly identified high variability regions associated with drug resistance development
Su, Microbial drug resistance (Larchmont, N.Y.) 2013 - “...high variability regions (PA5199 and PA5200 in Zone C and PA3194 in Zone B). In light of our observations and these published data, we also suspected that an...”
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- Glycerol metabolism impacts biofilm phenotypes and virulence in Pseudomonas aeruginosa via the Entner-Doudoroff pathway
Pan, mSphere 2024 - “...and anabolism. We deleted fda ( PA14_07230 ), tpiA ( PA14_62830 ), or edd ( PA14_22910 ), each of which encodes a key enzyme in glycerol metabolism: anabolic production of fructose/glucose, direct breakdown of DHAP and use in the TCA cycle, and the derivation of energy...”
- “...MTC2686 tpiA ( PA14_62830 ) PA14 with markerless tpiA deletion This study MTC2687 edd ( PA14_22910 ) PA14 with markerless edd deletion This study MTC2783 edd attB :: edd PA14 with markerless edd deletion and complementation of edd under its native promoter in CTX-1 at attB...”
- Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation
Dahal, Communications biology 2023 - “...that only the mutant of one of the indirect targets of RpoN, 6-phosphogluconate dehydratase (6PGDH, PA14_22910) could replicate the gluconate overproduction phenotype of the rpoN mutant 32 . We used i SD1509 to recapitulate the results of the study 32 on the glucose minimal (M9) medium....”
- “...FBA simulations accurately predicted that only the deletion of 6PGDH ( edd gene, locus tag: (PA14_22910)) leads to a significant increase in the gluconate production compared to the wildtype (Fig. 4 a). The model also correctly predicted that the growth of the edd mutant is considerably...”
- Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence
Panayidou, Scientific reports 2020 - “...37 PA14_26890 ( pyrF ) 38* PA14_62930 ( carA ) 39 Pentose phosphate pathway (pau00030) PA14_22910 ( edd ) 40 PA14_23090 ( edaA ) 41 Arginine biosynthesis (pau00220) PA14_70280 ( argB ) 42 PA14_69500 ( argH ) 43 Glycine, serine and threonine metabolism (pau00260) PA14_65560 (...”
- Genomewide identification of genetic determinants of antimicrobial drug resistance in Pseudomonas aeruginosa
Dötsch, Antimicrobial agents and chemotherapy 2009 - “...PA14_24150 PA14_23670 PA14_23470 PA14_23240 PA14_23210 PA14_22910 PA14_22910 PA14_22480 PA14_22330 PA14_21990 PA14_21860 PA14_21410 PA14_21050 PA14_20730...”
Atu0598 phosphogluconate dehydratase from Agrobacterium tumefaciens str. C58 (Cereon)
27% identity, 81% coverage
GOX0431 Phosphogluconate dehydratase from Gluconobacter oxydans 621H
28% identity, 76% coverage
- Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
Kranz, BMC genomics 2018 - “...(GOX1335); ald , aldehyde dehydrogenase (GOX2018); eda , KDPG aldolase (GOX0430); edd , phosphogluconate dehydratase (GOX0431); eno , enolase (GOX2279); fba , fructose-bisphosphate aldolase (GOX0780); fbp , fructose 1,6-bisphosphatase (GOX1516); frk , fructokinase (GOX0284); fumC , fumarate hydratase (GOX1643); gap , glyceraldehyde 3-phosphate dehydrogenase (GOX0508); gdhM...”
- (13)C Tracers for Glucose Degrading Pathway Discrimination in Gluconobacter oxydans 621H
Ostermann, Metabolites 2015 - “...]. One strain was lacking the genes edd (6-phosphogluconate dehydratase, GOX0430) and eda (2-keto-3-deoxy-6-phosphogluconate aldolase, GOX0431), thus disabling the EDP. The other two mutant strains were lacking the gnd gene (6-phosphogluconate dehydrogenase, GOX1705), thus disabling the PPP, and one of these had in addition an inactive...”
- “...Ehrenreich, Technical University of Munich, Germany [ 25 ]. In-frame deletion of the genes edd (GOX0431), eda (GOX0430), and gnd (GOX1705) was performed as described recently [ 9 ]. Precultures of G. oxydans strains were cultivated in a complex medium containing 5 gL 1 yeast extract,...”
- 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 - “...GOX2222 GOX1540 GOX1703 GOX1704 GOX1705 GOX0145 GOX1381 GOX1643 GOX0431 GOX1335 GOX1336 mRNA ratio of 45 genes, 2.0; 66 genes, 0.5 Triosephosphate isomerase...”
- “...level at sample point II was phosphogluconate dehydratase (edd, GOX0431, mRNA ratio of 0.4), the first of the two key enzymes of the EDP. Furthermore, three...”
- 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 - “...derivative with a deletion of the edd (GOX0431) and eda (GOX0430) genes coding for 6-phosphogluconate dehydratase and 2-keto-3desoxy-6-phosphogluconate aldolase...”
- “...Strains carrying in-frame deletion mutations of the edd (GOX0431) and eda (GOX0430) genes and of gnd (GOX1705) were constructed via a twostep homologous...”
Mal4_05000 YjhG/YagF family D-xylonate dehydratase from Maioricimonas rarisocia
32% identity, 67% coverage
Dshi_1769 6-phosphogluconate dehydratase from Dinoroseobacter shibae DFL 12
29% identity, 78% coverage
- Adaptation of Dinoroseobacter shibae to oxidative stress and the specific role of RirA
Beier, PloS one 2021 - “...small heat shock protein Hsp20 (Dshi_2892), three enzymes belonging to the 2-Keto-3-desoxy-6-phosphogluconate (KDPG) pathway (Dshi_1768, Dshi_1769, Dshi_1684) and one hypothetical protein (Dshi_2778) ( S2 Table ). In contrast, amounts of the processing peptidase Dshi_1147 and the 5-aminolevulinic acid synthase Dshi_1182 were decreased in response to the...”
VIBHAR_00512 phosphogluconate dehydratase from Vibrio harveyi ATCC BAA-1116
31% identity, 70% coverage
WP_013934127 phosphogluconate dehydratase from Zymomonas mobilis subsp. pomaceae
27% identity, 82% coverage
RD1_2879 phosphogluconate dehydratase from Roseobacter denitrificans OCh 114
27% identity, 78% coverage
- Peroxidase activity and involvement in the oxidative stress response of roseobacter denitrificans truncated hemoglobin
Wang, PloS one 2015 - “...Forward: tgcagccatttgtgaaacat Phosphoglucomutase Reverse: atgcgttttgtgatgtcgaa RD1_2720 Forward: cagtgacgttacggatgtgg Glucose-6-phosphate (pgi) Reverse: aatggtcgtgaaggtcttgg isomerase Carbohydrate catabolism RD1_2879 Forward: CGCACGGTGCTTTTTTCG 6-phosphogluconate dehydrase (edd) Reverse: GTTCCTGCCAGCGGGTC RD1_2878 Forward: CCAGAAGTGGTAATTCCAGCG 2-dehydro-3-deoxy-phospho- (eda) Reverse: TTCACCCGGCGCGAC gluconate aldolase Carbon assimilation RD1_3376 Forward: CCTTGGGCTTGCGGATC Pyruvate carboxylase (Pyc) Reverse: CATCTGGTTCACCTCGGCA RD1_0421 Forward: ACCCCCGGAAAGTTCGAG Malic...”
- “...12-h dark periods (B): 1 . RD1_2870 (phosphoglucomutase); 2 . RD1_2720 (glucose-6-phosphate isomerase); 3 . RD1_2879 (6-phosphogluconate dehydrase); 4 . RD1_2878 (KDPG aldolase); 5 . RD1_3376 (pyruvate carboxylase); 6 . RD1_0421 (malic enzyme); 7 . RD1_1609 (2-ketoglutarate dehydrogenase); 8 . RD1_2204 (isocitrate dehydrogenase); 9 . RD1_4240...”
- Carbohydrate metabolism and carbon fixation in Roseobacter denitrificans OCh114
Tang, PloS one 2009 - “...found in R. denitrificans : eda (RD1_2878), encoding 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase (EC 4.1.2.14), and edd (RD1_2879), encoding phosphogluconate dehydratase (EC 4.2.1.12). If R. denitrificans uses the ED pathway as one of the alternative carbohydrate utilization pathways, [1- 13 C]glucose is converted into [1- 13 C]-2-keto-3-deoxy-6-phosphogluconate, which...”
- “...consistent with our experimental data. The QRT-PCR results indicate that both eda (RD1_2878) and edd (RD1_2879) genes are expressed and the transcript level of these genes is higher in the minimal medium containing either pyruvate or glucose than in the rich medium, similar to the gene...”
HELO_3628 phosphogluconate dehydratase from Halomonas elongata DSM 2581
28% identity, 77% coverage
- Adaptation to Varying Salinity in Halomonas elongata: Much More Than Ectoine Accumulation
Hobmeier, Frontiers in microbiology 2022 - “...version of the Entner-Doudoroff pathway are preferentially expressed on glucose: zwf (HELO_3637), pgl (HELO_3636), edd (HELO_3628), and eda (HELO_3635). Genes encoding glucose-6-phosphate isomerases pgi1 (HELO_4245) and pgi2 (HELO_1718), pyruvate kinase pykA1 (HELO_4243) and alcohol dehydrogenase adh2 (HELO_2818) are upregulated on glucose as well. Cells growing on...”
C7W88_RS12360 phosphogluconate dehydratase from Novosphingobium sp. THN1
29% identity, 81% coverage
XOC_2610 phosphogluconate dehydratase from Xanthomonas oryzae pv. oryzicola BLS256
28% identity, 77% coverage
- VmsR, a LuxR-Type Regulator, Contributes to Virulence, Cell Motility, Extracellular Polysaccharide Production and Biofilm Formation in Xanthomonas oryzae pv. oryzicola
Zhang, International journal of molecular sciences 2024 - “..., XOC_2478 , XOC_2590 , XOC_2602 , XOC_2603 , XOC_2604 , XOC_2605 , XOC_2606 , XOC_2610 , XOC_2612 , XOC_2614 , XOC_2615 , XOC_2617 , and XOC_2861 . The expression levels of the mRNA for these genes corresponded closely with the RNA-Seq data ( Figure 3...”
RL0751 putative phosphogluconate dehydratase from Rhizobium leguminosarum bv. viciae 3841
28% identity, 76% coverage
H16_A1178 phosphogluconate dehydratase from Ralstonia eutropha H16
H16_A1178 phosphogluconate dehydratase from Cupriavidus necator H16
28% identity, 78% coverage
- Engineering Cupriavidus necator H16 for enhanced lithoautotrophic poly(3-hydroxybutyrate) production from CO2
Kim, Microbial cell factories 2022 - “...the conversion of phosphoenolpyruvate and ADP to pyruvate and ATP 18.0 glk (H16_B2564) Glucokinase 3.4 H16_A1178 Phosphogluconate dehydratase 2.7 H16_B1213 2-Keto-3-deoxy-6-phosphogluconate aldolase 1.8 zwf1 (H16_A0316) Glucose-6-phosphate 1-dehydrogenase, NADPH generation 2.2 pgl (H16_B2565) 6-Phosphogluconolactonase 2.6 edd1 phosphogluconate dehydratase 2.7 Fold changes>1.5, p value<0.05 *p value<0.1 Fig. 4...”
- The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16
Arenas-López, Biotechnology for biofuels 2019 - “...downregulated; p adj >0.05) (Additional file 3 : Table S1). A second 6-phosphogluconate dehydratase gene, H16_A1178, was strongly downregulated (38-fold), but this change was also not significant under the stringent criteria applied here ( p adj of 0.0526). Taken together, the obtained data were consistent with...”
- Proteomic and transcriptomic elucidation of the mutant ralstonia eutropha G+1 with regard to glucose utilization
Raberg, Applied and environmental microbiology 2011 - “...H16_A0372 H16_A0394 H16_A0472 H16_A0850 H16_A0935 H16_A1178 H16_A1264 H16_A1381 H16_A1438 H16_A2038 H16_A2055 H16_A2394 H16_A2621 H16_A2626 H16_A2634 H16_A3030...”
- “...transcriptomic and proteomic analyses: 6-phosphogluconate dehydratase (Edd1, H16_A1178) was apparent in significantly larger amounts in mutant G1 when glucose...”
HWN72_12855 phosphogluconate dehydratase from Novosphingobium sp. HR1a
28% identity, 78% coverage
- LuxR402 of Novosphingobium sp. HR1a regulates the correct configuration of cell envelopes
Segura, Frontiers in microbiology 2023 - “...Cell envelope BES08_27855 HWN72_28660 7. 7 0 Catalase (EC 1.11.1.6) Oxidative stress 0 Cytosol edd HWN72_12855 14 0 Phosphogluconate dehydratase (EC 4.2.1.12) Carbohydrate metabolism; Entner-Doudoroff pathway. 0 Cytosol sdhA HWN72_10715 15.3 0.9 4.1 Succinate dehydrogenase flavoprotein subunit (EC 1.3.99.1) Carbohydrate metabolism/TCA cycle 0 Cell envelop/inner membrane...”
BMEII0511 PHOSPHOGLUCONATE DEHYDRATASE from Brucella melitensis 16M
26% identity, 81% coverage
BAB2_0458 Dihydroxy-acid and 6-phosphogluconate dehydratase:6-phosphogluconate dehydratase from Brucella melitensis biovar Abortus 2308
26% identity, 81% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 784,739 different protein sequences to 1,253,012 scientific articles. Searches against EuropePMC were last performed on November 25 2024.
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