PaperBLAST
PaperBLAST Hits for ABIE51_RS17405 (63 a.a., MSETAATTTF...)
Show query sequence
>ABIE51_RS17405
MSETAATTTFRTWMCVVCGFIYDEALGLPEEGIAPGTRWEDVPDTWTCPDCGVTKDDFEM
MPL
Running BLASTp...
Found 136 similar proteins in the literature:
PP_5371 rubredoxin/rubredoxin reductase from Pseudomonas putida KT2440
66% identity, 11% coverage
RUBR2_PSEAE / Q9HTK8 Rubredoxin-2; Rdxs from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 3 papers)
PA5350 rubredoxin 2 from Pseudomonas aeruginosa PAO1
BWR11_30365 rubredoxin from Pseudomonas aeruginosa
74% identity, 86% coverage
- function: Involved in the hydrocarbon hydroxylating system, which transfers electrons from NADH to rubredoxin reductase and then through rubredoxin to alkane 1 monooxygenase.
cofactor: Fe(3+) (Binds 1 Fe(3+) ion per subunit.) - Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean
Vázquez, mSystems 2023 - “...UniProt Consortium) the sequences from well-characterized AlkB proteins: Q0VTH3, Q0VKZ3, O31250, and P12691; AlkG: Q9HTK7, Q9HTK8, P00272, Q9WWW4, and Q0VKZ2; AlkT: P17052, P42454, Q0VTB0, Q9HTK9, and Q9L4M8; AlkJ: Q00593, and Q9WWW2; AlkH: P12693. Identified alkane degradation coding genes and publicly available references were concatenated and aligned...”
- “...UniProt Consortium) and NCBI well-characterized AlkG proteins: P00271, Q9WWW4, Q0VKZ2, WP_138436252.1, WP_161463810.1, WP_089423380.1, WP_084394766.1, WP_015486580.1, Q9HTK8, and Q9HTK7. The reference and COG1651 sequences were aligned using MAFFT v7.487 ( 46 ) (globalpair maxiterate 16 reorder). RESULTS Microbial diversity and abundance of clone libraries To determine the...”
- Pseudomonas aeruginosa two-component system CprRS regulates HigBA expression and bacterial cytotoxicity in response to LL-37 stress
Song, PLoS pathogens 2024 - “...0.000102 PA0144 CIA_04931 nucleoside deoxyribosyltransferase -1.81691 0.033387 PA5518 CIA_05132 Probable potassium efflux transporter -1.89154 0.033531 PA5350 CIA_05306 Rubredoxin-2 AlkG2 -1.47695 0.031127 PA4784 CIA_05893 transcriptional regulator -1.16402 0.006777 10.1371/journal.ppat.1011946.g003 Fig 3 CprRS system senses LL-37 and regulates the expression of genes associated with virulence factors and drug...”
- A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes
Grady, BMC genomics 2017 - “...require the alkane hydroxylases alkB1 (PA2574) and alkB2 (PA1525), the rubredoxins rubA1 (PA5351) and rubA2 (PA5350) and the rubredoxin reductase rubB (PA5349) [ 8 , 11 , 12 ]. PAO1 and ATCC 33988 encode identical versions of alkB1/2 and rubA1/2 , and highly similar versions of...”
- Characterization of Pseudomonas aeruginosa with discrepant carbapenem susceptibility profile
Pragasam, Annals of clinical microbiology and antimicrobials 2016 - “...P. aeruginosa (MRIS) PA4381 6 4 3 Negative Negative Negative Not done Not done 3.37 PA5350 4 32 4 Negative Negative Negative Not done Not done 2.54 PA26815 3 8 12 Negative Negative Negative Not done Not done 1.09 Genes tested: blaIMP,blaVIM, blaNDM, blaKPC, blaOXA -...”
- “...isolates, phenotypic characterization of efflux pumps with carbenicillin with PAN showed>fourfold difference for PA4381 and PA5350, which was also correlated well with the relative quantification of mexAB pump which showed>1 for mexB expression in comparison to the control ATCC 27853 P. aeruginosa. This confirms that the...”
- Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa
Hagelueken, Proceedings of the National Academy of Sciences of the United States of America 2007 - “...by the gene cluster rubB (PA5349), rubA2 (PA5350), and rubA1 (PA5351). Whereas alkB1 and alkB2 expression is strictly n-alkane-dependent, RubB/RubA1/RubA2 are...”
- “...(16). For simplicity, the gene products of PA5349, PA5350, and PA5351 are henceforth referred to as RdxR and Rdx, respectively. Several RdxR-like enzymes and...”
- Pseudomonas aeruginosa L10: A Hydrocarbon-Degrading, Biosurfactant-Producing, and Plant-Growth-Promoting Endophytic Bacterium Isolated From a Reed (Phragmites australis)
Wu, Frontiers in microbiology 2018 - “...( BWR11_30 < 360 ), genes coding for Rubredoxin-1 ( BWR11_30370 ) and Rubredoxin-2 ( BWR11_30365 ), 7 genes encoding methyl-accepting chemotaxis protein, and 7 genes coding for alcohol dehydrogenases (ADH). We also used AromaDeg 1 (last accessed in May 2017) to detect genes putatively associated...”
Pnuc_0238 rubredoxin-type Fe(Cys)4 protein from Polynucleobacter sp. QLW-P1DMWA-1
69% identity, 86% coverage
2v3bB / Q9HTK8 Crystal structure of the electron transfer complex rubredoxin - rubredoxin reductase from pseudomonas aeruginosa. (see paper)
77% identity, 83% coverage
- Ligand: fe (iii) ion (2v3bB)
Pnuc_1377 rubredoxin-type Fe(Cys)4 protein from Polynucleobacter sp. QLW-P1DMWA-1
67% identity, 86% coverage
RSc0667 PROBABLE RUBREDOXIN PROTEIN from Ralstonia solanacearum GMI1000
63% identity, 86% coverage
E3H47_10395 rubredoxin RubA from Acinetobacter radioresistens
65% identity, 86% coverage
- Complete Genome Sequence of Hydrocarbon-Degrading Halotolerant Acinetobacter radioresistens DD78, Isolated from the Aconcagua River Mouth in Central Chile
Macaya, Microbiology resource announcements 2019 - “...Catabolic genes encoding an alkane monooxygenase ( alkM , E3H47_10210), a rubredoxin NAD(H) reductase/rubredoxin system (E3H47_10395 and E3H47_10400), and the catechol ( catBCA : E3H47_07710, E3H47_07715, and E3H47_07720) and benzoate catabolic pathways ( benABCDE : E3H47_07725, E3H47_07730, E3H47_07735, E3H47_07740, and E3H47_07745) are chromosomal. Comparative complete 16S...”
ABO_0163 rubredoxin from Alcanivorax borkumensis SK2
69% identity, 86% coverage
- Differential protein expression during growth on linear versus branched alkanes in the obligate marine hydrocarbon-degrading bacterium Alcanivorax borkumensis SK2T
Gregson, Environmental microbiology 2019 - “...the FMO (flavinbinding monooxygenase)like family (PF00743), which specializes in the oxidation of xenobiotics. The rubA (ABO_0163) and rubB (ABO_0162) genes code rubredoxin and rubredoxin reductase, respectively, and are arranged in a putative operon. RubA (ABO_0163), which transfers electrons to the alkane monooxygenase from the rubredoxin reductase,...”
- “...AlkB active site via a rubredoxin. There are two rubredoxin genes, alkG (ABO_2708) and rubA (ABO_0163) in the A. borkumensis genome (Schneiker et al., 2006 ). Both rubredoxins were however not detected in this data set. Rubredoxin reductases oxidizes NAD(P)H to transfer electrons to rubredoxin reducing...”
- Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis
Schneiker, Nature biotechnology 2006 - “...alkF gene encoding rubredoxin 1 in P. putida GPo1. However, two genes, rubA and rubB (ABO_0163 and ABO_0162) encode a rubredoxin and a rubredoxin reductase, respectively, and are likely to be involved in alkane catabolism. Rubredoxin reductase genes map in many alkane-degrading bacteria separately from the...”
PP_5315 rubredoxin from Pseudomonas putida KT2440
67% identity, 86% coverage
ACP86_07290 rubredoxin from Marinobacter sp. CP1
67% identity, 86% coverage
RUBR_ACIAD / P42453 Rubredoxin; Rdxs from Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1) (see paper)
rubA / RF|YP_045776.1 rubredoxin from Acinetobacter sp. ADP1 (see 3 papers)
rubA / CAA86925.1 rubredoxin from Acinetobacter baylyi (see 3 papers)
65% identity, 86% coverage
- function: Involved in the hydrocarbon hydroxylating system, which transfers electrons from NADH to rubredoxin reductase and then through rubredoxin to alkane 1 monooxygenase.
cofactor: Fe(3+) (Binds 1 Fe(3+) ion per subunit.)
HWW27_RS03965 rubredoxin from Burkholderia ambifaria
62% identity, 100% coverage
RUBR1_PSEAE / Q9HTK7 Rubredoxin-1; Rdxs from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 2 papers)
PA5351 Rubredoxin 1 from Pseudomonas aeruginosa PAO1
PA14_70640 Rubredoxin 1 from Pseudomonas aeruginosa UCBPP-PA14
BWR11_30370, CIA_05306 rubredoxin from Pseudomonas aeruginosa
69% identity, 86% coverage
- function: Involved in the hydrocarbon hydroxylating system, which transfers electrons from NADH to rubredoxin reductase and then through rubredoxin to alkane 1 monooxygenase.
cofactor: Fe(3+) (Binds 1 Fe(3+) ion per subunit.) - BatR: A novel regulator of antibiotic tolerance inPseudomonas aeruginosabiofilms
Piazza, 2024 - Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...PA4124 hpcB 4.0 Homoprotocatechuate 2,3-dioxygenase PA4125 hpcD 4.0 5-Carboxymethyl-2-hydroxymuconate isomerase PA4127 hpcG 3.8 2-Oxo-hept3ene-1,7-dioate hydratase PA5351 rubA1 1.4 Rubredoxin 1 PA4670 prs 1.6 2.0 Ribose-phosphate pyrophosphokinase PA2862 lipA 1.8 2.7 Lactonizing lipase precursor PA3363 amiR 1.5 1.0 Aliphatic amidase regulator Central intermediary metabolism PA0654 speD 1.5...”
- The Pseudomonas aeruginosa Orphan Quorum Sensing Signal Receptor QscR Regulates Global Quorum Sensing Gene Expression by Activating a Single Linked Operon
Ding, mBio 2018 - “...to and transcribed divergently from qscR (PA1898) ( Fig.1 ), and a rubredoxin reductase gene, PA5351 ( 10 ). In QS transcriptome studies, PA1897 and PA5351 have been reported to be 3OC12-HSL-regulated genes ( 12 , 13 ), but they are not regulated by LasR (...”
- “...defined at 54 to 29bp from the PA1897 transcription start site. We did not identify PA5351 in this ChIP-seq experiment, possibly reflecting the previous finding that the level of PA5351 promoter binding was substantially lower than that of PA1897 ( 10 ). Our finding of only...”
- A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes
Grady, BMC genomics 2017 - “...]. These reactions require the alkane hydroxylases alkB1 (PA2574) and alkB2 (PA1525), the rubredoxins rubA1 (PA5351) and rubA2 (PA5350) and the rubredoxin reductase rubB (PA5349) [ 8 , 11 , 12 ]. PAO1 and ATCC 33988 encode identical versions of alkB1/2 and rubA1/2 , and highly...”
- GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation
Han, Nature microbiology 2016 - “...162 PA4880 bacterioferritin 22,422 1.82e-53 82 21 PA5300 cycB cytochrome C5 154,313 5.38e-236 1,348 238 PA5351 rubA1 rubredoxin 158,050 3.48e-116 1,121 241 PA4812 fdnG formate dehydrogenase-O, major subunit 13,169 4.16e-80 61 17 PA5490 cc4 cytochrome c4 precursor 14,265 1.38e-64 659 198...”
- An evolving perspective on the Pseudomonas aeruginosa orphan quorum sensing regulator QscR
Chugani, Frontiers in cellular and infection microbiology 2014 - “...activated by QscR-3OC12-HSL. An in silico search of the PAO1 genome identified a second gene, PA5351 that encodes rubredoxin 1, that had a putative QscR binding site in its promoter. Although QscR-3OC12-HSL can bind to this site, the binding was not cooperative and the apparent binding...”
- Acyl-homoserine lactone binding to and stability of the orphan Pseudomonas aeruginosa quorum-sensing signal receptor QscR
Oinuma, Journal of bacteriology 2011 - “...to rapid aggregation or proteolysis. known function, and PA5351 codes for rubredoxin 1, an electron carrier protein that functions in an alkane hydroxylase...”
- “...32, 33, 38). Direct binding to PA1897 and PA5351 was established by electrophoretic mobility shift assays (EMSAs) with purified His-tagged QscR (15)....”
- Host and invader impact of transfer of the clc genomic island into Pseudomonas aeruginosa PAO1
Gaillard, Proceedings of the National Academy of Sciences of the United States of America 2008 - “...to PA4153, or aco genes) and in glycolate catabolism (PA5351 to PA5355, or glcDEF) (Table S1). None of these operons has known links to the 3-chlorocatechol or...”
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- Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean
Vázquez, mSystems 2023 - “...(The UniProt Consortium) the sequences from well-characterized AlkB proteins: Q0VTH3, Q0VKZ3, O31250, and P12691; AlkG: Q9HTK7, Q9HTK8, P00272, Q9WWW4, and Q0VKZ2; AlkT: P17052, P42454, Q0VTB0, Q9HTK9, and Q9L4M8; AlkJ: Q00593, and Q9WWW2; AlkH: P12693. Identified alkane degradation coding genes and publicly available references were concatenated and...”
- “...and NCBI well-characterized AlkG proteins: P00271, Q9WWW4, Q0VKZ2, WP_138436252.1, WP_161463810.1, WP_089423380.1, WP_084394766.1, WP_015486580.1, Q9HTK8, and Q9HTK7. The reference and COG1651 sequences were aligned using MAFFT v7.487 ( 46 ) (globalpair maxiterate 16 reorder). RESULTS Microbial diversity and abundance of clone libraries To determine the taxonomic diversity...”
- Loss of the Two-Component System TctD-TctE in Pseudomonas aeruginosa Affects Biofilm Formation and Aminoglycoside Susceptibility in Response to Citric Acid
Taylor, mSphere 2019 - “...LPS alpha 1,3-glucosyltransferase 2.15 PA14_17675 dgkA Diacylglycerol kinase 2.16 PA14_09050 secY Secretion protein SecY 2.18 PA14_70640 rubA1 Rubredoxin 1 2.20 PA14_73420 rnpA Ribonuclease P protein component 2.20 PA14_25760 holB DNA polymerase III, delta prime subunit 2.21 PA14_57580 rpsI 30S ribosomal protein S9 2.22 PA14_09020 rpsE 30S...”
- Pseudomonas aeruginosa two-component system CprRS regulates HigBA expression and bacterial cytotoxicity in response to LL-37 stress
Song, PLoS pathogens 2024 - “...PA0144 CIA_04931 nucleoside deoxyribosyltransferase -1.81691 0.033387 PA5518 CIA_05132 Probable potassium efflux transporter -1.89154 0.033531 PA5350 CIA_05306 Rubredoxin-2 AlkG2 -1.47695 0.031127 PA4784 CIA_05893 transcriptional regulator -1.16402 0.006777 10.1371/journal.ppat.1011946.g003 Fig 3 CprRS system senses LL-37 and regulates the expression of genes associated with virulence factors and drug resistance....”
- Pseudomonas aeruginosa L10: A Hydrocarbon-Degrading, Biosurfactant-Producing, and Plant-Growth-Promoting Endophytic Bacterium Isolated From a Reed (Phragmites australis)
Wu, Frontiers in microbiology 2018 - “...) and rubredoxin-NAD + reductase ( BWR11_30 < 360 ), genes coding for Rubredoxin-1 ( BWR11_30370 ) and Rubredoxin-2 ( BWR11_30365 ), 7 genes encoding methyl-accepting chemotaxis protein, and 7 genes coding for alcohol dehydrogenases (ADH). We also used AromaDeg 1 (last accessed in May 2017)...”
MSMEG_1841 rubredoxin from Mycolicibacterium smegmatis MC2 155
MSMEG_1841 rubredoxin from Mycobacterium smegmatis str. MC2 155
61% identity, 89% coverage
A1S_0995 rubredoxin from Acinetobacter baumannii ATCC 17978
BUM88_04810 rubredoxin RubA from Acinetobacter nosocomialis
63% identity, 86% coverage
- Genome-wide identification of Acinetobacter baumannii genes necessary for persistence in the lung
Wang, mBio 2014 - “...replicated. We chose mutants with disruptions in genes associated with a modest increase in recovery (A1S_0995, +2-fold), unchanged recovery ( dotB ), a modest decrease in recovery ( znuB , 2-fold), and large decreases in recovery ( lpsB , decreased 15.0-fold, and A1S_0065, 18.6-fold) in the...”
- “...versus individual competition assays. Data show the competitive indices of mutants containing transposon insertions in A1S_0995, dotB , znuB , lpsB , or A1S_0065 in the context of the INSeq screen () compared to those of the corresponding targeted deletion mutants in individual 1:1 competition assays...”
- Complete Genome Sequence of Acinetobacter calcoaceticus CA16, a Bacterium Capable of Degrading Diesel and Lignin
Ho, Genome announcements 2017 - “...involved in hydrocarbon degradation are located on the chromosome, including alkane monooxygenase (BUM88_05740, BUM88_08900), rubredoxin (BUM88_04810), esterase (BUM88_04820, BUM88_05375, BUM88_06405, BUM88_11675, BUM88_14825, BUM88_15860, BUM88_18905, BUM88_18980, BUM88_19775), and WeeF (BUM88_00230), a protein involved in biosurfactant production ( 12 , 17 19 ). The assembled genome sequence presented...”
rubA rubredoxin from Acinetobacter sp. M-1 (see paper)
63% identity, 86% coverage
2kn9A / O05893 Solution structure of zinc-substituted rubredoxin b (rv3250c) from mycobacterium tuberculosis. Seattle structural genomics center for infectious disease target mytud.01635.A (see paper)
56% identity, 73% coverage
CFU_RS05585 rubredoxin from Collimonas fungivorans Ter331
60% identity, 95% coverage
rubB / I6YFL7 rubredoxin 1 (EC 1.14.15.3) from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
MT3348 rubredoxin from Mycobacterium tuberculosis CDC1551
NP_217767 rubredoxin RubB from Mycobacterium tuberculosis H37Rv
BCG_3279c putative rubredoxin rubB from Mycobacterium bovis BCG str. Pasteur 1173P2
Rv3250c PROBABLE RUBREDOXIN RUBB from Mycobacterium tuberculosis H37Rv
59% identity, 89% coverage
- Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress
Lin, Infection and immunity 2016 - “...MT0038 MT0175 MT0258 MT1702 MT2559 MT2667 MT3216** MT3326 MT3348 MT3349 MT3350 MT3591 MT3933 Rv0033 Rv0166 Rv1467c Rv1662 Rv2485c Rv2590 Rv3130c Rv3229c Rv3250c...”
- The Mycobacterium tuberculosis Rv2745c plays an important role in responding to redox stress
McGillivray, PloS one 2014 - “...Rv3854c 3.630 2.818 3.209 3.219 9.310 MT3349 rubA rubredoxin Rv3251c 2.793 2.330 2.688 2.604 6.078 MT3348 rubB rubredoxin Rv3250c 2.064 1.773 2.262 2.033 4.093 Cell wall associated MT3169 lipR acetylhydrolase Rv3084 2.807 1.934 1.114 1.951 3.867 MT2912 efpA efflux protein Rv2846c 1.691 1.269 1.243 1.401 2.641...”
- Solution-state NMR structure and biophysical characterization of zinc-substituted rubredoxin B (Rv3250c) from Mycobacterium tuberculosis.
Buchko, Acta crystallographica. Section F, Structural biology and crystallization communications 2011 - GeneRIF: indicated that Mt-RubB was a monomer in solution
- Antimycobacterial Activities of Hydroxamic Acids and Their Iron(II/III), Nickel(II), Copper(II) and Zinc(II) Complexes
Yang, Microorganisms 2023 - “...protein encoded by the gene pstC2 with an FC of 2.19 and rubredoxin encoded by BCG_3279c with an FC of 2.19 were also up-regulated. The proteins encoded by the genes crgA , BCG_3932 , BCG_1708 , BCG_1384c , BCG_0352 , BCG_2826 , BCG_3492c , gltD ,...”
- M. tuberculosis AlkX Encoded by rv3249c Regulates a Conserved Alkane Hydroxylase System That Is Important for Replication in Macrophages and Biofilm Formation
Stokas, Microbiology spectrum 2022 - “...of mmpL3 and mmpL11 between the mutant and wild-type strains. (C) qRT-PCR analysis showed that rv3250c ( rubB ) and rv3252c ( alkB ) were highly upregulated in the alkX mutant relative to wild-type M. tuberculosis . The difference between rubB and alkB expression in the...”
- “...AlkX. (A) PCR was used to amplify regions overlapping rv3249c - 3252c (primer set 1), rv3250c - rv3252c (primer set 2), and rv3253c-alkB (primer set 3) in genomic DNA (gDNA), RNA (RT, minus reverse transcription reaction), and cDNA (+RT) samples. cDNA template produced only a product...”
- A Persistent Tuberculosis Outbreak in the UK Is Characterized by Hydrophobic fadB4-Deficient Mycobacterium tuberculosis That Replicates Rapidly in Macrophages
Farzand, mBio 2022 - “...A R54H Toxin antitoxin system 3265893 rv2934 ppsD 3646G > A A1216T PDIM biosynthesis 3630522 rv3250c rubB 45G > C E15D Rubredoxin 3646060 rv3265c wbbL1 825G > A Synonymous Glycosyltransferase (cell wall) 4316405 rv3843c rv3843c 192C > T Synonymous Membrane protein Each of the fadB4 ,...”
- Multiple genetic paths including massive gene amplification allow Mycobacterium tuberculosis to overcome loss of ESX-3 secretion system substrates
Wang, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...with the double mutant at day 3 were rubA ( rv3251c ) and rubB ( rv3250c ) ( Dataset S3 ), genes encoding rubredoxins, small iron-sulfur proteins that act as electron carriers and play roles in oxidative stress responses ( 44 ); the rubredoxins are induced...”
- Solution NMR Studies of Mycobacterium tuberculosis Proteins for Antibiotic Target Discovery
Kim, Molecules (Basel, Switzerland) 2017 - “...as demonstrated by decreased { 1 H} 15 N HetNOE values and solvent exchange/accessibility data. Rv3250c, also known as rubredoxinB, is a small nonheme iron-binding protein involved in the electron-transfer process [ 13 ]. Because of their roles in electron-transfer processes, rubredoxin proteins are considered potential...”
- “...Van Voorhis W.C. Myler P.J. Solution-state NMR structure and biophysical characterization of zinc-substituted rubredoxin B (Rv3250c) from Mycobacterium tuberculosis Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 2011 67 1148 1153 10.1107/S1744309111008189 21904065 14. Blake P.R. Park J.B. Zhou Z.H. Hare D.R. Adams M.W. Summers M.F....”
- Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress
Lin, Infection and immunity 2016 - “...Rv0033 Rv0166 Rv1467c Rv1662 Rv2485c Rv2590 Rv3130c Rv3229c Rv3250c Rv3251c Rv3252c Rv3847c Rv3825c acpA (acpP) fadD5 fadE15 pks8 lipQ fadD9 tgs1 desA3 rubB...”
- The Mycobacterium tuberculosis Rv2745c plays an important role in responding to redox stress
McGillivray, PloS one 2014 - “...3.209 3.219 9.310 MT3349 rubA rubredoxin Rv3251c 2.793 2.330 2.688 2.604 6.078 MT3348 rubB rubredoxin Rv3250c 2.064 1.773 2.262 2.033 4.093 Cell wall associated MT3169 lipR acetylhydrolase Rv3084 2.807 1.934 1.114 1.951 3.867 MT2912 efpA efflux protein Rv2846c 1.691 1.269 1.243 1.401 2.641 MT0870 lpqS hypothetical...”
- Rapid restriction enzyme-free cloning of PCR products: a high-throughput method applicable for library construction
Chaudhary, PloS one 2014 - “...in(bp) Mol.wt.(kDa) Recombinants/Totalamplified (%) a ExpressionResults b 1. Rv0666 174 9.8 8/8 (100) N 2. Rv3250c 183 10.7 6/6 (100) Y 3. Rv2803c 216 11.5 8/8 (100) Y 4. Rv1211 228 11.8 7/7 (100) Y 5. Rv1134 237 12.2 8/8 (100) Y 6. Rv1298 243 12.7...”
- Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-β-D-arabinose biosynthetic and utilization pathway genes
Safi, Nature genetics 2013 - “...Rv3213c-gpm2 Intergenic T>G 46 bp upstream of Rv3213c ; 108 bp upstream of gpm2 + Rv3250c rubB p.Glu53Gly + Rv3795 embB p.Met306Val + p.Gln445Arg + + + Rv3806c ubiA p.Gly165Cys + + a Method used to test MIC. b Gene sequence is wild type except where...”
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Q0VKZ2 Rubredoxin-2 from Alcanivorax borkumensis (strain ATCC 700651 / DSM 11573 / NCIMB 13689 / SK2)
ABO_2708 rubredoxin from Alcanivorax borkumensis SK2
60% identity, 33% coverage
- Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean
Vázquez, mSystems 2023 - “...from well-characterized AlkB proteins: Q0VTH3, Q0VKZ3, O31250, and P12691; AlkG: Q9HTK7, Q9HTK8, P00272, Q9WWW4, and Q0VKZ2; AlkT: P17052, P42454, Q0VTB0, Q9HTK9, and Q9L4M8; AlkJ: Q00593, and Q9WWW2; AlkH: P12693. Identified alkane degradation coding genes and publicly available references were concatenated and aligned using MAFFT v7.487 (...”
- “...We also downloaded from UniProt (The UniProt Consortium) and NCBI well-characterized AlkG proteins: P00271, Q9WWW4, Q0VKZ2, WP_138436252.1, WP_161463810.1, WP_089423380.1, WP_084394766.1, WP_015486580.1, Q9HTK8, and Q9HTK7. The reference and COG1651 sequences were aligned using MAFFT v7.487 ( 46 ) (globalpair maxiterate 16 reorder). RESULTS Microbial diversity and abundance...”
- Differential protein expression during growth on linear versus branched alkanes in the obligate marine hydrocarbon-degrading bacterium Alcanivorax borkumensis SK2T
Gregson, Environmental microbiology 2019 - “...transferred to the AlkB active site via a rubredoxin. There are two rubredoxin genes, alkG (ABO_2708) and rubA (ABO_0163) in the A. borkumensis genome (Schneiker et al., 2006 ). Both rubredoxins were however not detected in this data set. Rubredoxin reductases oxidizes NAD(P)H to transfer electrons...”
- Adaptation of the hydrocarbonoclastic bacterium Alcanivorax borkumensis SK2 to alkanes and toxic organic compounds: a physiological and transcriptomic approach
Naether, Applied and environmental microbiology 2013 - “...was increased. Also, the genes for rubredoxin (ABO_2708), two aldehyde dehydrogenases (ABO_2414 and ABO_2709 [alkH]), and the alcohol dehydrogenase alkJ2...”
- Proteomic insights into metabolic adaptations in Alcanivorax borkumensis induced by alkane utilization
Sabirova, Journal of bacteriology 2006 - “...(AlkJ-2) Cytochrome P450-1 Cytochrome P450-2 ABO_2706 ABO_2707 ABO_2708 ABO_2709 ABO_2710 ABO_0190 ABO_0202 ABO_0201 ABO_2288 Fatty acid oxidation 23M 15C 17M,...”
- “...of ABO_2707 encoding the AlkB1 alkane monooxygenase, ABO_2708 encoding the AlkG rubredoxin, ABO_2709 encoding the AlkH aldehyde dehydrogenase, and ABO_2710...”
alkG / CAC38028.1 rubredoxin from Alcanivorax borkumensis (see 2 papers)
60% identity, 33% coverage
NE1426 Rubredoxin:Rubredoxin-type Fe(Cys)4 protein from Nitrosomonas europaea ATCC 19718
57% identity, 95% coverage
Mvan_1744 Rubredoxin-type Fe(Cys)4 protein from Mycobacterium vanbaalenii PYR-1
59% identity, 89% coverage
- Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil
Kim, Applied and environmental microbiology 2015 - “...other genes, including two rubredoxins (Mvan_1743 and Mvan_1744) and a TetR-type transcriptional regulator, AlkU (Mvan_1745), which is known to activate...”
- “...acids (48). Interestingly, two rubredoxin genes (Mvan_1743 and Mvan_1744) in a row are located immediately downstream of the alkane hydroxylase gene in the alkB...”
mdpB / A2SP77 MTBE monooxygenase rubredoxin component from Methylibium petroleiphilum (strain ATCC BAA-1232 / LMG 22953 / PM1) (see 4 papers)
Mpe_B0602 rubredoxin from Methylibium petroleiphilum PM1
60% identity, 87% coverage
FXO12_18785 rubredoxin from Pseudomonas sp. J380
61% identity, 86% coverage
AC1659_RS17120 rubredoxin from Rhodococcus erythropolis
56% identity, 100% coverage
alkG / CAB51049.1 rubredoxin 2 from Pseudomonas putida (see 2 papers)
Q9WWW4 Rubredoxin-1 from Pseudomonas putida
53% identity, 33% coverage
- Polystyrene-colonizing bacteria are enriched for long-chain alkane degradation pathways
Hsueh, PloS one 2023 - “...query sequences for identifying AlkG and AlkT homologs were also taken from P . putida (Q9WWW4 and Q9L4M8, respectively). The query sequence for identifying CYP153 homologs was from Mycobacterium marinum (B2HGN5). For AlmA, the homolog from Acinetobacter baylyi (Q6F7T9) was used as the query. Hits that...”
- Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean
Vázquez, mSystems 2023 - “...the sequences from well-characterized AlkB proteins: Q0VTH3, Q0VKZ3, O31250, and P12691; AlkG: Q9HTK7, Q9HTK8, P00272, Q9WWW4, and Q0VKZ2; AlkT: P17052, P42454, Q0VTB0, Q9HTK9, and Q9L4M8; AlkJ: Q00593, and Q9WWW2; AlkH: P12693. Identified alkane degradation coding genes and publicly available references were concatenated and aligned using MAFFT...”
- “...MAGs. We also downloaded from UniProt (The UniProt Consortium) and NCBI well-characterized AlkG proteins: P00271, Q9WWW4, Q0VKZ2, WP_138436252.1, WP_161463810.1, WP_089423380.1, WP_084394766.1, WP_015486580.1, Q9HTK8, and Q9HTK7. The reference and COG1651 sequences were aligned using MAFFT v7.487 ( 46 ) (globalpair maxiterate 16 reorder). RESULTS Microbial diversity and...”
rubA4 / CAC37040.1 rubredoxin 4 from Rhodococcus erythropolis (see 2 papers)
AC1659_RS04740 rubredoxin from Rhodococcus erythropolis
54% identity, 89% coverage
alkG / P00272 rubredoxin 2 (EC 1.14.15.3) from Pseudomonas oleovorans (see 2 papers)
RUBR2_ECTOL / P00272 Rubredoxin-2; Rdxs; Two-iron rubredoxin from Ectopseudomonas oleovorans (Pseudomonas oleovorans) (see 4 papers)
alkG / CAB54052.1 rubredoxin 2 from Pseudomonas putida (see 6 papers)
54% identity, 33% coverage
- function: Involved in the hydrocarbon hydroxylating system, which transfers electrons from NADH to rubredoxin reductase and then through rubredoxin to alkane 1 monooxygenase.
cofactor: Fe(3+) (Binds 2 Fe(3+) ions per subunit.) - Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean.
Vázquez, mSystems 2023 - “...Consortium) the sequences from well-characterized AlkB proteins: Q0VTH3, Q0VKZ3, O31250, and P12691; AlkG: Q9HTK7, Q9HTK8, P00272, Q9WWW4, and Q0VKZ2; AlkT: P17052, P42454, Q0VTB0, Q9HTK9, and Q9L4M8; AlkJ: Q00593, and Q9WWW2; AlkH: P12693. Identified alkane degradation coding genes and publicly available references were concatenated and aligned using...”
CLJU_RS09545 flavin reductase from Clostridium ljungdahlii DSM 13528
57% identity, 21% coverage
OLMES_3726 rubredoxin from Oleiphilus messinensis
57% identity, 84% coverage
1s24A / P00272 Rubredoxin domain ii from pseudomonas oleovorans (see paper)
57% identity, 84% coverage
- Ligand: cadmium ion (1s24A)
WP_010878381 rubredoxin from Archaeoglobus fulgidus DSM 4304
AF0880 rubredoxin (rd-1) from Archaeoglobus fulgidus DSM 4304
56% identity, 79% coverage
Cbei_0465 rubredoxin-type Fe(Cys)4 protein from Clostridium beijerincki NCIMB 8052
59% identity, 78% coverage
2pvxB / P24297 Nmr and x-ray analysis of structural additivity in metal binding site- swapped hybrids of rubredoxin (see paper)
56% identity, 83% coverage
8f6tA / A0A1I2I8Z9 Cryo-em structure of alkane 1-monooxygenase alkb-alkg complex from fontimonas thermophila (see paper)
55% identity, 12% coverage
- Ligands: fe (iii) ion; dodecane (8f6tA)
NMB0993 rubredoxin from Neisseria meningitidis MC58
60% identity, 79% coverage
PAP_03330 rubredoxin from Palaeococcus pacificus DY20341
58% identity, 79% coverage
Tsac_1153 rubredoxin from Thermoanaerobacterium saccharolyticum JW/SL-YS485
56% identity, 83% coverage
RUBR_CLOAB / Q9AL94 Rubredoxin; Rd; EC 1.-.-.- from Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W) (see 5 papers)
CA_C2778 rubredoxin from Clostridium acetobutylicum ATCC 824
CAC2778 Rubredoxin from Clostridium acetobutylicum ATCC 824
59% identity, 78% coverage
- function: Rubredoxin is a small nonheme, iron protein lacking acid- labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Functions as an intermediate component in the electron transfer chain: NADH->NROR->Rd->FprA1/2 in which Rd serves as the proximal electron donor to the FDPs that exhibit H(2)O-forming NADH oxidase activity. Also functions as the proximal electron donor to the Dfx and revRbr proteins that display superoxide reductase (SOR) and NADH peroxidase activity, respectively. Therefore, is a key electron carrier in an efficient multienzyme complex that can scavenge O(2) and reactive oxygen species (ROS), and thus plays an important role in the oxidative stress defense system in C.acetobutylicum, an obligate anaerobic bacterium.
cofactor: Fe(3+) (Binds 1 Fe(3+) ion per subunit.) - Cap0037, a Novel Global Regulator of Clostridium acetobutylicum Metabolism
Nguyen, mBio 2016 - “...( rbr3A-rbr3B ), desulfoferrodoxin ( dfx ), glutaredoxin ( CA_C2777 ), rubredoxin ( rd and CA_C2778 ), NADH-dependent rubredoxin oxidoreductase ( nror ), the oxygen-reducing flavoproteins ( fprA1 and fprA2 ), and a flavodoxin ( CA_C2452 ), were upregulated ( 5 ). The CA_P0037 :: int...”
- Metabolic response of Clostridium ljungdahlii to oxygen exposure
Whitham, Applied and environmental microbiology 2015 - “...CODH), and C. acetobutylicum NROR (CA_C2448) and rubredoxin (CA_C2778) showed less than 40% identity for all combinations (see Table S4). A putative...”
- Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum
Venkataramanan, Biotechnology for biofuels 2015 - “...gene (CAC3597 and CAC3598) and three other proteins, with an identity of 50%, namely, CAC2575, CAC2778, and CAC3018, which are also annotated as rubrerythrins. Expression from our proteomic data mapped with the two copies of CAC3597CAC3598, forming an operon in an arrangement viewed as a gene...”
- O2 and reactive oxygen species detoxification complex, composed of O2-responsive NADH:rubredoxin oxidoreductase-flavoprotein A2-desulfoferrodoxin operon enzymes, rubperoxin, and rubredoxin, in Clostridium acetobutylicum
Kawasaki, Applied and environmental microbiology 2009 - “...(encoding NROR), CAC2449 (encoding FprA2), CAC2450 (encoding Dsr), and CAC2778 (encoding Rd) were amplified from the initial codon to the end codon by PCR using...”
- “...no. CAC2777) or rubredoxin (Rd gene; GenBank accession no. CAC2778). The Gd and Rd genes were amplified by PCR using chromosomal DNA from C. acetobutylicum as a...”
- The role of PerR in O2-affected gene expression of Clostridium acetobutylicum
Hillmann, Journal of bacteriology 2009 - “...CAC1570 CAC1571 CAC2448 CAC2449 CAC2450 CAC2567 CAC2575 CAC2777 CAC2778 CAC3018 CAC3306 CAC3597 Gene VOL. 191, 2009 O2 STIMULON OF C. ACETOBUTYLICUM 6087 TABLE...”
- “...CAC1570 and CAC1571, CAC2448 to CAC2450, CAC2777 and CAC2778, CAC0447 and CAC0448, CAC0788 to CAC0791, CAC1029 to CAC1032, CAC1988 to CAC1990, CAC1991 to...”
- Desulfoferrodoxin of Clostridium acetobutylicum functions as a superoxide reductase
Riebe, FEBS letters 2007 (PubMed)- “...enzyme exhibited superoxide reductase activity with rubredoxin (cac2778) of C. acetobutylicum as the proximal electron donor. Rubredoxin was reduced by...”
- “...Dfx NROR Normal Rbr Reverse Rbr C. acetobutylicum cac2778 cac2450 cac2448 cac2575 cac3597 ATCC 824 cac3018 cac3598 C. difficile cd0828 cd0827 cd1623 cd2845...”
- Adaptive responses to oxygen stress in obligatory anaerobes Clostridium acetobutylicum and Clostridium aminovalericum
Kawasaki, Applied and environmental microbiology 2005 - “...been elucidated because the rd gene (accession no. CAC2778), which encodes rubredoxin, the expected electron acceptor from NROR, is located 340 kb apart from...”
TK0524 rubredoxin from Thermococcus kodakaraensis KOD1
60% identity, 79% coverage
BT_2539 rubredoxin from Bacteroides thetaiotaomicron VPI-5482
61% identity, 78% coverage
alr1174 rubrerythrin from Nostoc sp. PCC 7120
51% identity, 22% coverage
- Metalloproteins in the Biology of Heterocysts
Pernil, Life (Basel, Switzerland) 2019 - “...2 e + 2H + 2H 2 O. Heterocysts harbor a specific rubrerythrin enzyme (RbrA, Alr1174 in Anabaena sp. PCC 7120; Table 6 ) that is poorly expressed in vegetative cells in the diazotrophic filament [ 356 ]. RbrA exhibits only a moderate similarity to rubrerythrins...”
- “...1 Mn FeSOD SodB Non-heme Fe center 1 Fe Non-heme peroxidases (ferritin-like superfamily) Rubrerythrin RbrA (Alr1174 ) Non-heme FeFe center 3 Fe [Fe4S] cluster Dps proteins Dps1 (All0458 ) Non-heme FeFe center 2 Fe Dps2 (All4145 ) Non-heme FeFe center 2 Fe Dps3 (All1173 ) Non-heme...”
- Functional Overlap of hetP and hetZ in Regulation of Heterocyst Differentiation in Anabaena sp. Strain PCC 7120
Zhang, Journal of bacteriology 2018 - “...alr0663 alr0668 alr0669 alr0671 alr0672 alr0691 alr0874 alr1174 alr1404 alr1407 alr1555 alr1810 alr2463 alr2464 alr2514 alr2515 alr2516 alr2517 alr2518 alr2520...”
RUBR_HELMO / P56263 Rubredoxin; Rd from Heliobacterium mobile (Heliobacillus mobilis) (see paper)
55% identity, 81% coverage
- function: Rubredoxin is a small nonheme, iron protein lacking acid- labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule
cofactor: Fe(3+) (Binds 1 Fe(3+) ion per subunit.)
4xnwC / P00268,P47900 The human p2y1 receptor in complex with mrs2500 (see paper)
51% identity, 14% coverage
- Ligands: [(1r,2s,4s,5s)-4-[2-iodo-6-(methylamino)-9h-purin-9-yl]-2-(phosphonooxy)bicyclo[3.1.0]hex-1-yl]methyl dihydrogen phosphate; zinc ion (4xnwC)
6gpsA / P00268,P41597 Crystal structure of ccr2a in complex with mk-0812 (see paper)
51% identity, 15% coverage
- Ligand: [(3~{s},4~{s})-3-methoxyoxan-4-yl]-[(1~{r},3~{s})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{h}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium (6gpsA)
5xpdA / Q9FGQ2 Sugar transporter of atsweet13 in inward-facing state with a substrate analog (see paper)
51% identity, 18% coverage
- Ligand: 2'-deoxycytidine-5'-monophosphate (5xpdA)
BCAL2458 rubredoxin from Burkholderia cenocepacia J2315
50% identity, 86% coverage
6me8A / P00268,P0ABE7,P49286 Xfel crystal structure of human melatonin receptor mt2 (n86d) in complex with 2-phenylmelatonin (see paper)
51% identity, 11% coverage
- Ligands: n-[2-(5-methoxy-2-phenyl-1h-indol-3-yl)ethyl]acetamide; zinc ion (6me8A)
HRB_MOOTA / Q9FDN6 High molecular weight rubredoxin; Nitric oxide reductase NADH:FprA oxidoreductase from Moorella thermoacetica (strain ATCC 39073 / JCM 9320) (see paper)
51% identity, 21% coverage
- function: Has nitric oxide reductase activity in combination with FprA; probably involved in nitrosative stress protection. Acts as an NADH:FprA oxidoreductase
cofactor: Fe cation (Binds 2 iron ions per homodimer.)
cofactor: FMN (Binds 2 FMN per homodimer. The occupancy is 1.3-1.9.)
subunit: Homodimer
TepiRe1_0396 rubredoxin from Tepidanaerobacter acetatoxydans Re1
54% identity, 79% coverage
5ai2A / P24297 Anomalous neutron phased crystal structure of 113cd-substituted perdeuterated pyrococcus furiosus rubredoxin to 1.75a resolution at 295k (see paper)
PF1282 rubredoxin from Pyrococcus furiosus DSM 3638
P24297 Rubredoxin from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
WP_011012426 rubredoxin from Pyrococcus furiosus DSM 3638
52% identity, 79% coverage
- Ligands: cadmium ion; deuterium(1+) (5ai2A)
- Cluster-Dependent Charge-Transfer Dynamics in Iron-Sulfur Proteins
Mao, Biochemistry 2018 - “...(pETPfRd1). Plasmid pET24d was digested with Nco I and Bam HI. The rubredoxin encoding gene (PF1282) was amplified by PCR from Pyrococcus furiosus genomic DNA with Nco I and Bam HI sites added at the N and C terminii, respectively, and was cloned in frame with...”
- Impact of growth mode, phase, and rate on the metabolic state of the extremely thermophilic archaeon Pyrococcus furiosus
Khatibi, Biotechnology and bioengineering 2017 - “...the same comparison. An antioxidative response, consisting of superoxide reductase (PF1281), its electron donor rubredoxin (PF1282) ( Thorgersen et al. 2012 ) and peroxiredoxins (PF0722 and PF1033) ( Burton et al. 1995 ), was up-regulated with increasing dilution rate ( Table SIII ). In particular, PF1033...”
- Reconstruction of SAXS Profiles from Protein Structures
Putnam, Computational and structural biotechnology journal 2013 - “...3 ]. This figure depicts the experimental SAXS curves and parameters measured for Pyrococcus furiosis PF1282 rubredoxin (magenta), a designed scaffoldin protein S4 (red), a designed minicellulosome containing three catalytic subunits (green), and the DNA-dependent protein kinase (blue). (a) D max of the scattering particle is...”
- Mechanism of oxygen detoxification by the surprisingly oxygen-tolerant hyperthermophilic archaeon, Pyrococcus furiosus
Thorgersen, Proceedings of the National Academy of Sciences of the United States of America 2012 - “...shI shII PF1114 None, restored PF1114, PF1281 PF1282 PF0751 PF1281, PF0751 PF1114, PF0891-PF0894, PF1329-PF1332 PF0891-PF0894, PF1329-PF1332 (41) This work This...”
- Improving protein template recognition by using small-angle x-ray scattering profiles
dos, Biophysical journal 2011 - “...) and real ( right ) spaces. ( A and A ) PF1282 P.furiosus , with SAXS data and structural model taken from the BIOISIS databank (BIOISIS ID: 1RBDGP). ( B and B...”
- Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
Hura, Nature methods 2009 - “...biochemical characterizations. For example, a fusion protein created to aid PF1205 purification by adding rubredoxin (PF1282), was purified and soluble, but as indicated by SAXS analyses PF1282/1205 lacked structure and would be unlikely to crystallize. Comparison of SAXS data to those calculated from known structures may...”
- “...8.0, 300 mM NaCl and 2 mM DTT for SAXS analysis. Recombinant, native (untagged) rubredoxin (PF1282, Rd), superoxide reductase (PF1281, SOR) and ferredoxin (PF1909, Fd) were expressed and purified as described previously 39 41 . Analytical procedures Protein concentrations were estimated using the Biuret protein assay...”
- Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain
Proudfoot, Journal of molecular biology 2008 - “...TFIIS ( 1tfi ). (e) Structure of the P. furiosus Rd PF1282 ( 1brf ). (f) Structure of KTI11 ( 1yop and 1yws ). Metals are shown as dark gray spheres (zinc;...”
- “..., 1rb9 , and 1yk4 ). The best-studied Rd, PF1282 from P. furiosus , has been characterized using several forms of this protein containing different metals:...”
- Transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium Thermotoga maritima
Pysz, Applied and environmental microbiology 2004 - “...(76, 120) 68% identity, 51 aa with P. furiosis rubredoxin PF1282 (9, 21), 2 conserved CXXC motifs 57% identity, 128 aa with P. furiosis SOR (PF1281) (38, 125)...”
- Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus
Iwasaki, Archaea (Vancouver, B.C.) 2010 - “...Rieske protein fragment, P13272; S. solfataricus ARF (hypothetical ORF c06009), CAA669492, AB047031; P. furiosus rubredoxin, P24297; C. pasteurianum rubredoxin, P00268. The metal-binding motifs are underlined (left), and the structure of the cluster ligand residues of a bovine mitochondrial Rieske protein domain fragment (PDB code, 1rie.pdb) [...”
- Crystallization and preliminary X-ray diffraction studies of a hyperthermophilic Rieske protein variant (SDX-triple) with an engineered rubredoxin-like mononuclear iron site
Iwasaki, Acta crystallographica. Section F, Structural biology and crystallization communications 2006 - “...ORF c06009), CAA669492, AB047031; P. furiosus Rd, P24297; C. pasteurianum Rd, P00268. The metal-binding motifs are underlined. doi:10.1107/S1744309106034476 993...”
- Hyperthermophile protein behavior: partially-structured conformations of Pyrococcus furiosus rubredoxin monomers generated through forced cold-denaturation and refolding.
Chandrayan, PloS one 2014 - GeneRIF: Data indicate that differential cold-denaturation treatments allow rubredoxin (PfRd) to access multiple partially-unfolded states.
- The key to the extraordinary thermal stability of P. furiosus holo-rubredoxin: iron binding-guided packing of a core aromatic cluster responsible for high kinetic stability of the native structure.
Prakash, PloS one 2014 - GeneRIF: Data indicate that the extraordinary thermal stability of holo-rubredoxin (PfRd) was caused by iron binding-guided packing of a core aromatic cluster.
- The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography.
Meilleur, Acta crystallographica. Section D, Biological crystallography 2013 (PubMed)- GeneRIF: The first high-resolution neutron protein structure of perdeuterated rubredoxin from Pyrococcus furiosus has been determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory.
- A billion-fold range in acidity for the solvent-exposed amides of Pyrococcus furiosus rubredoxin.
Anderson, Biochemistry 2008 (PubMed)- GeneRIF: electrostatic calculations are analyzed to characterize structural elements that appear to be responsible for the range of peptide acidities observed for solvent-exposed amides.
- Effects of environment on the structure of Pyrococcus furiosus rubredoxin: a molecular dynamics study.
Ergenekan, Proteins 2005 (PubMed)- GeneRIF: Temperature has a greater impact on the protein structure than the close molecular contacts of the crystal matrix in rubredoxin.
1yk5A / Q9V099 Pyrococcus abyssi rubredoxin (see paper)
54% identity, 79% coverage
- Ligand: fe (iii) ion (1yk5A)
6li2A / P00268,Q9Y2T5 Crystal structure of gpr52 ligand free form with rubredoxin fusion (see paper)
50% identity, 15% coverage
WP_048064374 rubredoxin from Archaeoglobus fulgidus DSM 4304
54% identity, 79% coverage
G3EIL7 alkane 1-monooxygenase (EC 1.14.15.3) from Dietzia sp. DQ12-45-1b (see paper)
47% identity, 12% coverage
AF1349 rubredoxin (rd-2) from Archaeoglobus fulgidus DSM 4304
57% identity, 64% coverage
Fisuc_2091 Rubredoxin-type Fe(Cys)4 protein from Fibrobacter succinogenes subsp. succinogenes S85
62% identity, 75% coverage
- Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85
Wu, Scientific reports 2017 - “...NADH/NADPH, small subunit Fisuc_1820 1.5 0.02261 ammonium transporter Fisuc_1821 3.0 1.36E-09 nitrogen regulatory protein P-II Fisuc_2091 2.5 0.001303 Rubredoxin-type Fe(Cys)4 protein Fisuc_2123 2.3 0.002766 4Fe-4S ferredoxin iron-sulfur binding domain protein Fisuc_2558 1.9 2.99E-15 Chorismate mutase Fisuc_2559 2.0 1.03E-16 Prephenate dehydrogenase Fisuc_2908 2.1 0.000191 (Sulfur transfer protein...”
Csac_1990 Rubredoxin-type Fe(Cys)4 protein from Caldicellulosiruptor saccharolyticus DSM 8903
60% identity, 75% coverage
5vblB / P00268,P35414 Structure of apelin receptor in complex with agonist peptide (see paper)
49% identity, 16% coverage
- Ligands: peptide; zinc ion (5vblB)
2dsxA / P00270 Crystal structure of rubredoxin from desulfovibrio gigas to ultra-high 0.68 a resolution (see paper)
55% identity, 78% coverage
- Ligand: fe (iii) ion (2dsxA)
Deba_2049 rubredoxin from Desulfarculus baarsii DSM 2075
51% identity, 81% coverage
- Complete genome sequence of Desulfarculus baarsii type strain (2st14)
Sun, Standards in genomic sciences 2010 - “...dismutase [ 28 ]. The cloned genes were identified in the whole genome sequence as Deba_2049 ( rub ) and Deba_2050 ( rbo ) and found in close proximity to a gene encoding rubrerythrin (Deba_2051), which is supposed to play an important role in the oxygen...”
6ln2A / P00268,P43220 Crystal structure of full length human glp1 receptor in complex with fab fragment (fab7f38) (see paper)
51% identity, 11% coverage
- Ligand: n-{4-[(r)-(3,3-dimethylcyclobutyl)({6-[4-(trifluoromethyl)-1h-imidazol-1-yl]pyridin-3-yl}amino)methyl]benzene-1-carbonyl}-beta-alanine (6ln2A)
alkB / CAB51024.2 alkane 1-monooxygenase from Prauserella rugosa (see 3 papers)
59% identity, 9% coverage
TDE1052 rubredoxin from Treponema denticola ATCC 35405
57% identity, 75% coverage
TM_0659 rubredoxin from Thermotoga maritima MSB8
TM0659 rubredoxin from Thermotoga maritima MSB8
53% identity, 78% coverage
- An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales
Le, Environmental microbiology 2011 (PubMed)- “...an NADH oxidoreductase (NRO), a rubredoxin (Rd) and a flavo-diiron protein (FprA) (locus tags: TM_0754, TM_0659 and TM_0755, respectively). In vitro experiments showed that the NADH-dependent O(2) consumption rate was 881.9 ( 106.7) mol O(2) consumed min(-1) per mol of FprA at 37 C and that water...”
- The genus Thermotoga: recent developments
Frock, Environmental technology 2010 - “...44 , 45 ]. Homologs of these proteins have been identified in T. maritima (TM0754, TM0659, and TM0658, respectively), and the putative superoxide reductase is upregulated in response to oxidative stress [ 42 ]. Other genes upregulated by oxygen exposure include TM1368, which encodes a protein...”
- Reductive dioxygen scavenging by flavo-diiron proteins of Clostridium acetobutylicum
Hillmann, FEBS letters 2009 - “...FDP homolog (TM0755)). E. coli expression strains for N-terminal His-tagged NROR tma (TM0754) and Rd (TM0659) from T. maritima were obtained from the Joint Center for Structural Genomics ( http://www.jcsg.org/ ) and are described on the Harvard Institute of Proteomics Plasmid ID website ( http://plasmid.med.harvard.edu/PLASMID/GetCloneDetail.do?cloneid=85043&species= )....”
- Responses of wild-type and resistant strains of the hyperthermophilic bacterium Thermotoga maritima to chloramphenicol challenge
Montero, Applied and environmental microbiology 2007 - “...comprised of TM0657 (rubrerythrin), TM0658 (neelaredoxin), and TM0659 (rubredoxin). TM0657 to TM0659 were up-regulated upon exposure to CAM, especially in...”
- “...role of the P. furiosus homologs to TM0657 to TM0659 has been recently demonstrated in vivo in E. coli (24); in addition to NAD(P)H rubredoxin oxidoreductase,...”
- Transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium Thermotoga maritima
Pysz, Applied and environmental microbiology 2004 - “...reductase (SOR, TM0658, 3.4-fold), and rubredoxin (TM0659, 3.1-fold) in biofilm cells, along with an ahpC-related alkylhydroperoxide reductase (TM0807,...”
- “...acetivorans strain CZA (MA2882) TM0392 TM1241 TM0786 TM0457 TM0456 TM1874 TM0659 2.2 2.4 2.4 2.5 2.6 2.8 3.1 7.3 7.4 6.0 9.3 9.0 9.6 9.9 TM0658 3.5 11.4 TM0657...”
6iivA / P00268,P0ABE7,P21731 Crystal structure of the human thromboxane a2 receptor bound to daltroban (see paper)
51% identity, 11% coverage
- Ligands: 2-[4-[2-[(4-chlorophenyl)sulfonylamino]ethyl]phenyl]ethanoic acid; zinc ion; cholesterol (6iivA)
Cthe_2164 rubredoxin from Acetivibrio thermocellus ATCC 27405
Cthe_2164 Rubredoxin-type Fe(Cys)4 protein from Clostridium thermocellum ATCC 27405
57% identity, 78% coverage
AOP6_0414 rubredoxin from Desulfuromonas sp. AOP6
53% identity, 75% coverage
- Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains
Guo, BMC genomics 2021 - “...DTF_RS22095 cydB cytochrome bd ubiquinol oxidase subunit II AOP6_2874 BQ4888_RS11720 DSOUD_0335 DBW_0565 DTF_RS0105770 rub Rubredoxin AOP6_0414, AOP6_0415 BQ4888_RS07685 DSOUD_3135 DBW_3237 DTF_RS25905 Desulfoferredoxin (superoxide reductase) AOP6_2966 DSOUD_0362 DBW_3006 rbr Rubrerythrin AOP6_0339 BQ4888_RS13615 DSOUD_0365 DBW_3641 DTF_RS0115795 sodA Superoxide dismutase BQ4888_RS04500 macA Cytochrome c peroxidase AOP6_0104, AOP6_0558 BQ4888_RS09810, BQ4888_RS15550...”
Dde_3194 rubredoxin from Oleidesulfovibrio alaskensis G20
Dde_3194 rubredoxin from Desulfovibrio desulfuricans G20
52% identity, 79% coverage
rubR2 / OMNI|NTL03CP0780 rubredoxin 2 from Clostridium perfringens (see 2 papers)
CPE0780 rubredoxin from Clostridium perfringens str. 13
P14072 Rubredoxin-2 from Clostridium perfringens (strain 13 / Type A)
52% identity, 76% coverage
6bd4A / P00268,Q9ULV1 Crystal structure of human apo-frizzled4 receptor (see paper)
48% identity, 14% coverage
MCP_2757 rubredoxin from Methanocella paludicola SANAE
50% identity, 79% coverage
DBW_3237 rubredoxin from Desulfuromonas sp. DDH964
50% identity, 79% coverage
- Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains
Guo, BMC genomics 2021 - “...ubiquinol oxidase subunit II AOP6_2874 BQ4888_RS11720 DSOUD_0335 DBW_0565 DTF_RS0105770 rub Rubredoxin AOP6_0414, AOP6_0415 BQ4888_RS07685 DSOUD_3135 DBW_3237 DTF_RS25905 Desulfoferredoxin (superoxide reductase) AOP6_2966 DSOUD_0362 DBW_3006 rbr Rubrerythrin AOP6_0339 BQ4888_RS13615 DSOUD_0365 DBW_3641 DTF_RS0115795 sodA Superoxide dismutase BQ4888_RS04500 macA Cytochrome c peroxidase AOP6_0104, AOP6_0558 BQ4888_RS09810, BQ4888_RS15550 DSOUD_0544, DSOUD_1166, DSOUD_2534 DBW_1968...”
AC1659_RS04745 rubredoxin from Rhodococcus erythropolis
56% identity, 81% coverage
Tpen_1457 Rubredoxin-type Fe(Cys)4 protein from Thermofilum pendens Hrk 5
46% identity, 83% coverage
AAA23279.1 rubredoxin from Clostridium pasteurianum (see paper)
P00268 Rubredoxin from Clostridium pasteurianum
51% identity, 78% coverage
- Quantum mechanics insights into melatonin and analogs binding to melatonin MT1 and MT2 receptors.
de, Scientific reports 2024 - “...RMSD in residues of MT 2 C-terminal corresponding to another fusion protein, rubredoxin (Rub, UniProt P00268). Notably, these residues are distant from the ligand binding pocket, suggesting that they have insignificant influence on the ligand binding mode. Finally, replicate 1 showed intermediate fluctuations with values near...”
- XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity.
Johansson, Nature 2019 - “...2 with a six-residue linker (amino acid sequence GDGARP). Another fusion protein, rubredoxin (Rub, Uniprot P00268), was fused in the ICL3, replacing receptor residues 232240. For construct optimisation (to increase monodispersity, thermostability, and crystallisability), the following point mutations were added: D86 2.50 N 9 , L108...”
- Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus
Iwasaki, Archaea (Vancouver, B.C.) 2010 - “...S. solfataricus ARF (hypothetical ORF c06009), CAA669492, AB047031; P. furiosus rubredoxin, P24297; C. pasteurianum rubredoxin, P00268. The metal-binding motifs are underlined (left), and the structure of the cluster ligand residues of a bovine mitochondrial Rieske protein domain fragment (PDB code, 1rie.pdb) [ 145 ] is shown,...”
- Crystallization and preliminary X-ray diffraction studies of a hyperthermophilic Rieske protein variant (SDX-triple) with an engineered rubredoxin-like mononuclear iron site
Iwasaki, Acta crystallographica. Section F, Structural biology and crystallization communications 2006 - “...Rd, P24297; C. pasteurianum Rd, P00268. The metal-binding motifs are underlined. doi:10.1107/S1744309106034476 993 crystallization communications promote...”
7f1tA / P00268,P10147,P51681 Crystal structure of the human chemokine receptor ccr5 in complex with mip-1a (see paper)
49% identity, 12% coverage
SSCH_180038 flavin reductase from Syntrophaceticus schinkii
51% identity, 21% coverage
KSMBR1_2919 rubredoxin from Candidatus Kuenenia stuttgartiensis
46% identity, 83% coverage
BQ4888_RS07685 rubredoxin from Desulfuromonas acetexigens
50% identity, 76% coverage
- Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains
Guo, BMC genomics 2021 - “...cytochrome bd ubiquinol oxidase subunit II AOP6_2874 BQ4888_RS11720 DSOUD_0335 DBW_0565 DTF_RS0105770 rub Rubredoxin AOP6_0414, AOP6_0415 BQ4888_RS07685 DSOUD_3135 DBW_3237 DTF_RS25905 Desulfoferredoxin (superoxide reductase) AOP6_2966 DSOUD_0362 DBW_3006 rbr Rubrerythrin AOP6_0339 BQ4888_RS13615 DSOUD_0365 DBW_3641 DTF_RS0115795 sodA Superoxide dismutase BQ4888_RS04500 macA Cytochrome c peroxidase AOP6_0104, AOP6_0558 BQ4888_RS09810, BQ4888_RS15550 DSOUD_0544, DSOUD_1166,...”
HMPREF0389_00337 rubredoxin from Filifactor alocis ATCC 35896
50% identity, 79% coverage
DEFDS_0573 rubredoxin from Deferribacter desulfuricans SSM1
48% identity, 76% coverage
- Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1
Takaki, DNA research : an international journal for rapid publication of reports on genes and genomes 2010 - “...anaerobe: its genome possesses many genes potentially associated with resistance to oxidative stress. DEFDS_1019 and DEFDS_0573 encode a superoxide reductase (SOR) and a rubredoxin (Rd), respectively. The SORRd proteins can catalyse the reduction of superoxide to hydrogen peroxide. Putative rubrerythrins (Rbr) encoded by DEFDS_0019, DEFDS_1568, and...”
- “...one is a rubredoxin-oxygen oxidoreductase (Roo), whose gene is located next to the rubredoxin gene (DEFDS_0573). In the sulphate-reducing Desulfovibrio -related species, the latter enzyme is proposed to be the cytoplasmic terminal oxidase for the non-energy-conserving respiratory reduction of O 2 or nitric oxide. 67 Thus,...”
Tlet_1612 rubredoxin from Pseudothermotoga lettingae TMO
50% identity, 76% coverage
SYNW2369 Rubrerythrin from Synechococcus sp. WH 8102
52% identity, 19% coverage
- Proteomic responses of oceanic Synechococcus WH8102 to phosphate and zinc scarcity and cadmium additions
Cox, Frontiers in microbiology 2013 - “...II, chain, (B) SYNW2008 C-phycoerythrin class II, chain, (C) SYNW2017 C-phycoerythrin class I, chain, (D) SYNW2369 rubrerythrin, (E) SYNW2124 PSI P700 (PsaA), (F) SYNW3191 PSII extrinsic precursor (PsuB), (G) SYNW0486 anchor polypeptide L CM (ApcE), (H) SYNW1264 peptidyl-prolyl cis-trans isomerase, (I) SYNW0082 riboflavin synthase subunit b...”
OA04_09050 anaerobic nitric oxide reductase flavorubredoxin from Pectobacterium versatile
54% identity, 9% coverage
Dret_0139 Rubredoxin-type Fe(Cys)4 protein from Desulfohalobium retbaense DSM 5692
50% identity, 79% coverage
- Complete genome sequence of Desulfohalobium retbaense type strain (HR(100))
Spring, Standards in genomic sciences 2010 - “...O 2 . On the other hand, in the cytoplasm multiprotein complexes containing rubredoxins (Dret_0886, Dret_0139), rubrerythrins (Dret_0191, Dret_1205, Dret_1644, Dret_2310) and desulfoferrodoxin (Dret_0140) could establish electron transfer systems for the reduction of superoxide radicals and H 2 O 2 [ 35 , 36 ]. Finally,...”
STM2840 putative flavoprotein from Salmonella typhimurium LT2
52% identity, 10% coverage
AOP6_0415 rubredoxin from Desulfuromonas sp. AOP6
48% identity, 79% coverage
- Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains
Guo, BMC genomics 2021 - “...cydB cytochrome bd ubiquinol oxidase subunit II AOP6_2874 BQ4888_RS11720 DSOUD_0335 DBW_0565 DTF_RS0105770 rub Rubredoxin AOP6_0414, AOP6_0415 BQ4888_RS07685 DSOUD_3135 DBW_3237 DTF_RS25905 Desulfoferredoxin (superoxide reductase) AOP6_2966 DSOUD_0362 DBW_3006 rbr Rubrerythrin AOP6_0339 BQ4888_RS13615 DSOUD_0365 DBW_3641 DTF_RS0115795 sodA Superoxide dismutase BQ4888_RS04500 macA Cytochrome c peroxidase AOP6_0104, AOP6_0558 BQ4888_RS09810, BQ4888_RS15550 DSOUD_0544,...”
YgaK / b2710 anaerobic nitric oxide reductase flavorubredoxin from Escherichia coli K-12 substr. MG1655 (see 6 papers)
norV / Q46877 anaerobic nitric oxide reductase flavorubredoxin from Escherichia coli (strain K12) (see 24 papers)
NORV_ECODH / B1XCN7 Anaerobic nitric oxide reductase flavorubredoxin; FlRd; FlavoRb from Escherichia coli (strain K12 / DH10B) (see paper)
GB|AAC75752.1 anaerobic nitric oxide reductase flavorubredoxin from Escherichia coli K12 (see 10 papers)
NP_417190 anaerobic nitric oxide reductase flavorubredoxin from Escherichia coli str. K-12 substr. MG1655
Q46877 Anaerobic nitric oxide reductase flavorubredoxin from Escherichia coli (strain K12)
b2710 anaerobic nitric oxide reductase flavorubredoxin from Escherichia coli str. K-12 substr. MG1655
48% identity, 12% coverage
- function: Anaerobic nitric oxide reductase; uses NADH to detoxify nitric oxide (NO), protecting several 4Fe-4S NO-sensitive enzymes. Has at least 2 reductase partners, only one of which (NorW, flavorubredoxin reductase) has been identified. NO probably binds to the di-iron center; electrons enter from the reductase at rubredoxin and are transferred sequentially to the FMN center and the di-iron center. Also able to function as an aerobic oxygen reductase (By similarity).
cofactor: Fe cation (Binds 3 Fe cations per monomer.)
cofactor: FMN (Binds 1 FMN per monomer.)
subunit: Homotetramer. - Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase.
Romão, Journal of molecular biology 2016 (PubMed)- GeneRIF: The overall tetrameric structure revealed a highly conserved flavodiiron core domain, with a metallo-beta-lactamase-like domain containing a diiron center, and a flavodoxin domain with a flavin mononucleotide cofactor.
- An Unexpected Duo: Rubredoxin Binds Nine TPR Motifs to Form LapB, an Essential Regulator of Lipopolysaccharide Synthesis.
Prince, Structure (London, England : 1993) 2015 (PubMed)- GeneRIF: Rubredoxin binds nine TPR motifs to form LapB, an essential regulator of lipopolysaccharide synthesis.
- Oxidative stress modulates the nitric oxide defense promoted by Escherichia coli flavorubredoxin.
Baptista, Journal of bacteriology 2012 - GeneRIF: Authors propose that the time-dependent activation of flavorubredoxin contributes to the adaptation of E. coli to the different fluxes of hydrogen peroxide and nitric oxide to which the bacterium is subjected during the course of macrophage infection.
- Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering.
Petoukhov, Structure (London, England : 1993) 2008 (PubMed)- GeneRIF: Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering.
- Zinc- and iron-dependent cytosolic metallo-beta-lactamase domain proteins exhibit similar zinc-binding affinities, independent of an atypical glutamate at the metal-binding site.
Schilling, The Biochemical journal 2005 - GeneRIF: the atypical glutamate does not guide metal selectivity of the FlRd metallo-beta-lactamase domain but suppresses possible hydrolytic cross-activity
- Redox and spectroscopic properties of the Escherichia coli nitric oxide-detoxifying system involving flavorubredoxin and its NADH-oxidizing redox partner.
Vicente, The Journal of biological chemistry 2005 (PubMed)- GeneRIF: biochemical analyis of FlRd and its physiological partner, the NADH:flavorubredoxin oxidoreductase FlRd-Red
- Functional Prediction of Biological Profile During Eutrophication in Marine Environment
Sbaoui, Bioinformatics and biology insights 2022 - “...nitrite reductase NirS P24474 Nitrite reductase NmpC P21420 DLP12 prophage; putative outer membrane porin NorV Q46877 Nitric oxide reductase NosZ P19573 Nitrous oxide reductase NuoH P0AFD4 NADH: quinone oxidoreductase subunit H NuoJ P0AFE0 NADH: quinone oxidoreductase subunit J PaaZ P77455 Crotonyl-CoA hydratase ParC P0AFI2 Dimer of...”
- Flavodiiron proteins in oxygenic photosynthetic organisms: photoprotection of photosystem II by Flv2 and Flv4 in Synechocystis sp. PCC 6803
Zhang, PloS one 2009 - “...Chlamydomonas reinhardtii (FlvA: XP_001692916, FlvB: XP_001699345); Dgi, Desulfovibrio gigas (ROO: AAG34792); Eco, Escherichia coli (FlRd: Q46877); Gvi, Gloeobacter violaceus PCC 7421 (Flv1: Glr1776, Flv3: Glr1775); Mae, Microcystis aeruginosa NIES-843 (Flv1: MAE61610, Flv2: MAE50820, Flv3: MAE01310, Flv4: MAE50840); Mth, Moorella thermoacetica (FDP: AAG00802); Npu, Nostoc punctiforme ATCC...”
- Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
Bonocora, PLoS genetics 2015 - “...b4441 glmY 1 12.388 C OS25 2830446 11 C TGGC ACGCAATC TGC A 2830442 + b2710 norV 37 12.266 C OS26 2836164 11 C TGGC ATGATTTG TG AA 2836173 - b2713 hydN 27 9.175 C OS27 2848494 91 T TGGC ACAAAAAA TGC T 2848502 - b2725...”
- Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis
Zhao, Nucleic acids research 2010 - “...b3800 aslB putative transcriptional activator of acrylsulfatase synthesis Not classified 3.4 2.4 206 189 agctTGGTAGCGCAACTGGTTTggga b2710 b2710 g flavorubredoxin (FIRd) with NO-binding non-heme diiron center Not classified 9.8 2.3 63 46 aaacTGGCACGCAATCTGCAATtagc b3383 yhfZ unknown CDS Unknown 2.6 2.3 91 74 ccgtTGGCCTGACGCAGGCCGCgttg b4067 yjcG putative transport...”
- Prominent roles of the NorR and Fur regulators in the Escherichia coli transcriptional response to reactive nitrogen species
Mukhopadhyay, Proceedings of the National Academy of Sciences of the United States of America 2004 - “...yfiD ybaR asnA deoC ilvC ybiJ ascF ycgT adhE ycfR b2710 b2711 b2552 b4209 b4062 b2597 b0585 b3547 b2673 b2674 b0445 b1205 b3327 b2732 b3117 b1895 b2717 b0795...”
- Domain architectures of sigma54-dependent transcriptional activators
Studholme, Journal of bacteriology 2003 - “...gltlJKL, nac, potFGHI, yeaGH, ygjG, yhdWXYZ pspABCDE yfhKGA b2710 zraP, zraSR prpBCDE hyp and hyc operons, hydNhypF rtcBA atoDAEB hyf operon ygeW Unknown Phage...”
- Flavorubredoxin, an inducible catalyst for nitric oxide reduction and detoxification in Escherichia coli
Gardner, The Journal of biological chemistry 2002 (PubMed)- “...transcribed are ygaK (encoding a flavorubredoxin (flavoRb) (b2710) with a NO-binding non-heme diiron center) and ygbD (encoding a NADH:(flavo)Rb oxidoreductase...”
- “...genes and the corresponding open reading frames (b2709, b2710, and b2711, respectively) was subcloned from 9G10 into pAlter (Promega Corp., Madison, WI) that...”
- Rubredoxins involved in alkane oxidation
van, Journal of bacteriology 2002 - “...60 and 250 amino acids). A 479-amino-acid hypothetical protein, b2710, from E. coli has an Rd-like domain at its C terminus (ECOLI_FLAV in Fig. 2 and 3,)...”
- Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli
Reitzer, Microbiology and molecular biology reviews : MMBR 2001 - “...with a score of 86. BLAST analysis suggests that b2710 codes for a flavodoxin or a rubredoxin, a redox protein, and that YgbD has homology to oxidoreductases,...”
Cspa_c10950 rubredoxin from Clostridium saccharoperbutylacetonicum N1-4(HMT)
47% identity, 81% coverage
- CRISPR-Cas, a highly effective tool for genome editing in Clostridium saccharoperbutylacetonicum N1-4(HMT)
Atmadjaja, FEMS microbiology letters 2019 - “...The integration site is between two transcriptional terminators of the formate acetyltransferase (Cspa_c10940) and rubredoxin (Cspa_c10950) genes. The vector was constructed through sequential cloning into pMTL82154. First the HR1 region (approx. 950 bp) was PCR amplified from gDNA (Table 1 , ref 1718) and cloned into...”
- “...bp promoter sequence from Cspa_c25620. The second transcriptional terminator site (found 76 bp upstream of Cspa_c10950) was synthesised (Life Technologies) with a modification to remove the PAM site and cloned into the NcoI/XhoI sites. Finally the HR2 region (approx. 950 bp) was PCR amplified from gDNA...”
GSU0847 rubredoxin from Geobacter sulfurreducens PCA
48% identity, 76% coverage
2pveA / P00268 Nmr and x-ray analysis of structural additivity in metal binding site- swapped hybrids of rubredoxin (see paper)
45% identity, 78% coverage
tca_00140 rubredoxin from Methanothermobacter sp. EMTCatA1
52% identity, 79% coverage
- Analysis of a Methanogen and an Actinobacterium Dominating the Thermophilic Microbial Community of an Electromethanogenic Biocathode
Kobayashi, Archaea (Vancouver, B.C.) 2021 - “...such as chaperones and proteasomes (tca_00660, tca_00698, and tca_00826), antioxidant enzymes, and alternative redox proteins (tca_00140, tca_00141, tca_00142, tca_00723, and tca_00821) (marked by red arrowheads in Figure 4 ) (Table S8 ). This likely reflected the process of cellular energy depletion due to the lack of...”
2kkdA / P00269 Nmr structure of ni substitued desulfovibrio vulgaris rubredoxin (see paper)
DVU3184 rubredoxin from Desulfovibrio vulgaris Hildenborough
47% identity, 78% coverage
- Ligand: nickel (ii) ion (2kkdA)
- Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough
Chhabra, PloS one 2011 - “...of CooS such that the two proteins could interact. C. Interacting partners of Rubredoxin, Rub (DVU3184), and Rubredoxin-oxygen oxidoreductase, Roo (DVU3185), differ widely from those of Pyridine nucleotide-disulfide oxidoreductase, Nox (DVU3212) In this study we tagged three oxidoreductases from D. vulgaris that have been suggested to...”
- “...three ( Fig. S9 ) was utilized only for tagging of cooH (DVU2291) and rub (DVU3184). This scheme was developed to tag a gene in the middle of an operon (when scheme two was not permissible) and was designed to allow wild-type expression of the downstream...”
- Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough
Mukhopadhyay, Journal of bacteriology 2007 - “...vulgaris. Other oxidative response genes, including the rubredoxin gene (DVU3184), present in the Sor operon and the Sor gene itself were also identified by the...”
- Rubredoxin:oxygen oxidoreductase enhances survival of Desulfovibrio vulgaris hildenborough under microaerophilic conditions
Wildschut, Journal of bacteriology 2006 - “...as rubredoxin oxidoreductase [Rbo]; 3) and rubredoxin (Rub, DVU3184). Roo has been proposed to be the terminal oxidase of a cytoplasmic, non-energy-conserv- ing...”
- Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough
Chhabra, Journal of bacteriology 2006 - “...DVU1867 DVU2108 DVU2310 DVU2735 DVU2776 DVU2825 DVU3183 DVU3184 DVU3185 DVU3212 DVU3290 DVU3379 DVU0848 DVU0883 DVU0884 DVU0951 ORF00713 DVU2103 DVU2271...”
A0A061F296 Rubredoxin-like superfamily protein from Theobroma cacao
41% identity, 29% coverage
L21SP2_2197 rubredoxin from Salinispira pacifica
49% identity, 78% coverage
U876_23285 anaerobic nitric oxide reductase flavorubredoxin from Aeromonas hydrophila NJ-35
50% identity, 9% coverage
DTF_RS25905 rubredoxin from Desulfuromonas sp. TF
50% identity, 79% coverage
- Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains
Guo, BMC genomics 2021 - “...oxidase subunit II AOP6_2874 BQ4888_RS11720 DSOUD_0335 DBW_0565 DTF_RS0105770 rub Rubredoxin AOP6_0414, AOP6_0415 BQ4888_RS07685 DSOUD_3135 DBW_3237 DTF_RS25905 Desulfoferredoxin (superoxide reductase) AOP6_2966 DSOUD_0362 DBW_3006 rbr Rubrerythrin AOP6_0339 BQ4888_RS13615 DSOUD_0365 DBW_3641 DTF_RS0115795 sodA Superoxide dismutase BQ4888_RS04500 macA Cytochrome c peroxidase AOP6_0104, AOP6_0558 BQ4888_RS09810, BQ4888_RS15550 DSOUD_0544, DSOUD_1166, DSOUD_2534 DBW_1968 DTF_RS0118780...”
ECs3566 putative flavodoxin from Escherichia coli O157:H7 str. Sakai
Z4018 putative flavodoxin from Escherichia coli O157:H7 EDL933
47% identity, 14% coverage
- Analysis of the genome of the Escherichia coli O157:H7 2006 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence
Kulasekara, Infection and immunity 2009 - “...Z4947 Z5317 ECs0739 ECs0774 ECs1858 ECs2408 ECs3100 ECs3566 ECs4412 ECs4733 nei tolA yciR ydiD yojI norV bcsB hemX Endonuclease VIII (formamidopyrimidine-DNA...”
- Analysis of the genome of the Escherichia coli O157:H7 2006 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence
Kulasekara, Infection and immunity 2009 - “...Function Mutation type Z0865 Z0907 Z2516 Z2730 Z3469 Z4018 Z4947 Z5317 ECs0739 ECs0774 ECs1858 ECs2408 ECs3100 ECs3566 ECs4412 ECs4733 nei tolA yciR ydiD yojI...”
- Clonal and antigenic analysis of serogroup A Neisseria meningitidis with particular reference to epidemiological features of epidemic meningitis in the People's Republic of China
Wang, Infection and immunity 1992 - “...Z4051, Z4052, Z4053, Z4949 Z4059, Z4077 Z4110 Z4109 Z4018, Z4019, Z4020, Z4021, Z4048, Z4054, Z4058, Z4062, Z4065, Z4066, Z4069, Z4070, Z4071, Z4073, Z4075,...”
RUBR1_ECTOL / P12692 Rubredoxin-1; Rdxs from Ectopseudomonas oleovorans (Pseudomonas oleovorans) (see paper)
51% identity, 35% coverage
- function: Not known. Probably involved in an electron transport pathway, but not required for the hydrocarbon hydroxylating system. Seems to be non-functional
cofactor: Fe(3+) (Binds 1 Fe(3+) ion per subunit.)
7e0lA / D9PYV4 Class iii hybrid cluster protein (hcp) from methanothermobacter marburgensis
48% identity, 10% coverage
- Ligands: fe-s-o hybrid cluster; iron/sulfur cluster; fe (iii) ion (7e0lA)
GM298_06635 anaerobic nitric oxide reductase flavorubredoxin from Enterobacter sp. HSTU-ASh6
52% identity, 10% coverage
GSU3188 rubredoxin from Geobacter sulfurreducens PCA
50% identity, 79% coverage
WP_048196713 rubredoxin from Methanocaldococcus jannaschii DSM 2661
49% identity, 71% coverage
MJ0740 rubredoxin 2 (rd2) from Methanocaldococcus jannaschii DSM 2661
49% identity, 71% coverage
2ms3A / Q46877 The nmr structure of the rubredoxin domain of the no reductase flavorubredoxin from escherichia coli
50% identity, 76% coverage
FN1424 ACYL-COA dehydrogenase, short-chain specific from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
43% identity, 7% coverage
Mvan_1743 Rubredoxin-type Fe(Cys)4 protein from Mycobacterium vanbaalenii PYR-1
53% identity, 86% coverage
- Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil
Kim, Applied and environmental microbiology 2015 - “...cluster with other genes, including two rubredoxins (Mvan_1743 and Mvan_1744) and a TetR-type transcriptional regulator, AlkU (Mvan_1745), which is known to...”
- “...fatty acids (48). Interestingly, two rubredoxin genes (Mvan_1743 and Mvan_1744) in a row are located immediately downstream of the alkane hydroxylase...”
FPV33_RS05380 anaerobic nitric oxide reductase flavorubredoxin from Klebsiella aerogenes
44% identity, 10% coverage
KPK_1081 anaerobic nitric oxide reductase flavorubredoxin from Klebsiella pneumoniae 342
44% identity, 10% coverage
AC1659_RS17115 rubredoxin from Rhodococcus erythropolis
44% identity, 81% coverage
Fisuc_1369 Rubredoxin-type Fe(Cys)4 protein from Fibrobacter succinogenes subsp. succinogenes S85
41% identity, 83% coverage
- Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85
Wu, Scientific reports 2017 - “...7.56E-36 preprotein translocase, SecE subunit Fisuc_1362 1.4 1.18E-05 lipoprotein (TIGR02167 bacterial surface protein 26-residue repeat) Fisuc_1369 1.9 4.00E-11 Rubredoxin-type Fe(Cys)4 protein Fisuc_1491 2.4 1.41E-12 NADH-ubiquinone/plastoquinone oxidoreductase chain 3 Fisuc_1532 2.1 5.22E-09 Chorismate binding-like protein (Anthranilate/para-aminobenzoate synthases component I) Fisuc_1564 2.8 4.71E-07 hypothetical protein (Predicted Na+-dependent transporter)...”
Acfer_1575 acyl-CoA dehydrogenase domain protein from Acidaminococcus fermentans DSM 20731
39% identity, 7% coverage
- Complete genome sequence of Acidaminococcus fermentans type strain (VR4)
Chang, Standards in genomic sciences 2010 - “...(Acfer_1756) is encoded at the beginning of the gene cluster. Three acyl-CoA dehydrogenase genes (Acfer_1477, Acfer_1575 and Acfer_1583) were annotated at various locations, completing the pathway. Nevertheless, genes encoding 2-hydroxyglutarate dehydrogenase and Butyl-CoA:acetate CoA transferase have not yet been identified. Possibly these enzymes have additional functions...”
- “...decarboxylase subunit r Acfer_1836 glutaconyl-CoA decarboxylase sodium pump, subunit r Acfer_1477 acyl-CoA dehydrogenase domain protein Acfer_1575 acyl-CoA dehydrogenase domain protein Acfer_1583 acyl-CoA dehydrogenase domain protein Enzymes of -lactamase and the related Acfer_0250 -lactamase domain-containing protein Acfer_0522 Zn-dependent hydrolase of the -lactamase fold Acfer_0551 RNA-metabolizing metallo--lactamase Acfer_0879...”
G3EIL3 alkane 1-monooxygenase (EC 1.14.15.3) from Dietzia sp. DQ12-45-1b (see paper)
45% identity, 10% coverage
MT3349 rubredoxin from Mycobacterium tuberculosis CDC1551
49% identity, 79% coverage
Rv3251c PROBABLE RUBREDOXIN RUBA from Mycobacterium tuberculosis H37Rv
49% identity, 79% coverage
- Whole genome CRISPRi screening identifies druggable vulnerabilities in an isoniazid resistant strain of Mycobacterium tuberculosis
Wang, Nature communications 2024 - “...( rv2623) , rv2624c , rv2005c , rv2028c , hspX (rv2031) , a putative rubredoxin rv3251c ( rubA ), and the thioredoxin trxb1 being upregulated, none of which were more vulnerable to CRISPRi (Fig. 3d ). Interestingly, the furA-katG-rv1907c operon was the most highly upregulated (Fig....”
- Understanding the Genetic Diversity of Mycobacterium africanum Using Phylogenetics and Population Genomics Approaches
Balamurugan, Frontiers in genetics 2022 - “...(Rv0848), Phe249Phe (Rv0930), Arg302Arg (Rv1188), and Cys34Phe (Rv1317c), upstream SNP -3721 (Rv1749c), Asn372Ser (Rv2874), Gly18Asp (Rv3251c), Asn234Asn (Rv3534c), Ser84Gly (Rv3608c), and Ile150Thr (Rv3842c)] were reported in our study which were found to be absent in L5.3 (#19 of the total 25 L5.3 isolates reported by Coscolla...”
- Dual RNA Sequencing of Mycobacterium tuberculosis-Infected Human Splenic Macrophages Reveals a Strain-Dependent Host-Pathogen Response to Infection
López-Agudelo, International journal of molecular sciences 2022 - “...mycobacterial respiratory chain [ 62 ]. The nuo gene cluster, particularly the nuoG gene ( rv3251c ), has been shown to induce anti-apoptotic activities and persistence in infected macrophages by neutralizing NOX-2 derived ROS and inhibiting apoptosis mediated by TNF- [ 63 , 64 , 65...”
- Multiple genetic paths including massive gene amplification allow Mycobacterium tuberculosis to overcome loss of ESX-3 secretion system substrates
Wang, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...overexpressed in esxG as compared with the double mutant at day 3 were rubA ( rv3251c ) and rubB ( rv3250c ) ( Dataset S3 ), genes encoding rubredoxins, small iron-sulfur proteins that act as electron carriers and play roles in oxidative stress responses ( 44...”
- Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress
Lin, Infection and immunity 2016 - “...Rv0166 Rv1467c Rv1662 Rv2485c Rv2590 Rv3130c Rv3229c Rv3250c Rv3251c Rv3252c Rv3847c Rv3825c acpA (acpP) fadD5 fadE15 pks8 lipQ fadD9 tgs1 desA3 rubB rubA alkB...”
- The Mycobacterium tuberculosis Rv2745c plays an important role in responding to redox stress
McGillivray, PloS one 2014 - “...6.944 MT3969 ethA monooxygenase, flavin-binding family Rv3854c 3.630 2.818 3.209 3.219 9.310 MT3349 rubA rubredoxin Rv3251c 2.793 2.330 2.688 2.604 6.078 MT3348 rubB rubredoxin Rv3250c 2.064 1.773 2.262 2.033 4.093 Cell wall associated MT3169 lipR acetylhydrolase Rv3084 2.807 1.934 1.114 1.951 3.867 MT2912 efpA efflux protein...”
- Solution-state NMR structure and biophysical characterization of zinc-substituted rubredoxin B (Rv3250c) from Mycobacterium tuberculosis
Buchko, Acta crystallographica. Section F, Structural biology and crystallization communications 2011 - “...world. Among the potential new drug targets are two small nonheme iron-binding proteins, rubredoxin A (Rv3251c) and rubredoxin B (Rv3250c), which are believed to play a role in electron-transfer processes. Here, the solution structure and biophysical properties of one of these two proteins, rubredoxin B (...”
- “...1996 ) at the metal-binding site. The M. tuberculosis genome contains two tandem rubrudoxin genes: Rv3251c (encoding the 55-residue rubredoxin A) and Rv3250c (encoding the 60-residue rubredoxin B). The gene for rubredoxin B is repressed in vitro under mildly acidic and hypoxic conditions that mimic the...”
- Mycobacterium tuberculosis septum site determining protein, Ssd encoded by rv3660c, promotes filamentation and elicits an alternative metabolic and dormancy stress response
England, BMC microbiology 2011 - “...appC 1.0 -0.2 Rv1064c lpqV 1.1 -0.1 Rv2007c fdxA 2.6 0.6 Rv1166 lpqW 0.8 0.0 Rv3251c rubA 0.8 -0.1 Rv1372 pks18 1.1 0.1 Rv1661 pks7 1.3 -0.2 ATP synthesis Rv1662 pks8 1.0 0.2 Rv1304 atpB 0.2 -0.6 Rv1663 pks17 1.2 0.2 Rv1305 atpE 0.2 -0.4 Rv1664...”
- More
DSOUD_3135 rubredoxin from Desulfuromonas soudanensis
43% identity, 81% coverage
- Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains
Guo, BMC genomics 2021 - “...bd ubiquinol oxidase subunit II AOP6_2874 BQ4888_RS11720 DSOUD_0335 DBW_0565 DTF_RS0105770 rub Rubredoxin AOP6_0414, AOP6_0415 BQ4888_RS07685 DSOUD_3135 DBW_3237 DTF_RS25905 Desulfoferredoxin (superoxide reductase) AOP6_2966 DSOUD_0362 DBW_3006 rbr Rubrerythrin AOP6_0339 BQ4888_RS13615 DSOUD_0365 DBW_3641 DTF_RS0115795 sodA Superoxide dismutase BQ4888_RS04500 macA Cytochrome c peroxidase AOP6_0104, AOP6_0558 BQ4888_RS09810, BQ4888_RS15550 DSOUD_0544, DSOUD_1166, DSOUD_2534...”
X551_03234 rubredoxin from Methylibium sp. T29
49% identity, 75% coverage
E5GBR8 Rubredoxin from Cucumis melo subsp. melo
41% identity, 30% coverage
Q9SLI4 At1g54500/F20D21_31 from Arabidopsis thaliana
AT1G54500 rubredoxin family protein from Arabidopsis thaliana
37% identity, 30% coverage
- Commonalities and specialties in photosynthetic functions of PROTON GRADIENT REGULATION5 variants in Arabidopsis
Penzler, Plant physiology 2022 - “...f 0.676 7.52 E 03 P56773 petB Cyt b6 0.621 2.90 E 02 PSI biogenesis Q9SLI4 RBD1 Rubredoxin-like superfamily protein 0.523 1.05 E 02 O23403 PPD1 PsbP domain-containing protein 1 0.589 5.35 E 03 Q9LU01 Y3IP1 Ycf3-interacting protein 1 0.665 1.27 E 02 Q6STH5 HCHF101 Fe-S...”
- Defining the heterogeneous composition of Arabidopsis thylakoid membrane
Trotta, The Plant journal : for cell and molecular biology 2025 (no snippet) - Large-scale top-down proteomics of the Arabidopsis thaliana leaf and chloroplast proteomes
Wang, Proteomics 2023 - “...is, in fact, 37A-38L. Likewise, a cTP cleavage site is predicted for Rubredoxin A (RubA; at1g54500) at residue 59. However, proteoform evidence from both total leaf and chloroplast samples suggest the mature protein sequence begins at residue 55. This is supported by the identification of multiple...”
- Rubredoxin 1 Is Required for Formation of the Functional Photosystem II Core Complex in Arabidopsis thaliana
Che, Frontiers in plant science 2022 - “...from the Arabidopsis Information Resource or GenBank/EMBL databases under the following accession numbers: AtRBD1 ( AT1G54500 , Arabidopsis thaliana ), CrRBD1 (Cre07.g315150.t1.2, Chlamydomonas reinhardtii ), and SyRubA (slr2033, Synechocystis sp. PCC 6803). Results The rbd1 Mutant Is Defective in Growth and PSII Function To investigate the...”
- Advances in the Understanding of the Lifecycle of Photosystem II
Johnson, Microorganisms 2022 - “...accumulation [ 34 , 35 , 36 , 37 ] RubA D1/D2 assembly slr2033 RBD1, At1g54500 Reduced PSII level and activity [ 31 , 83 ] Slr0144-Slr0152 PSII assembly associated slr0144-slr0152 ? Slower growth and lower PSII activity [ 47 , 84 , 85 ] Ycf39...”
- Structural and Functional Heat Stress Responses of Chloroplasts of Arabidopsis thaliana
Paul, Genes 2020 - “...type. HHL1 (AT1G67700) is involved in PSII protection from photo-damage [ 73 ], and RBD1 (AT1G54500) is required for establishing PSII function [ 74 ]. Moreover, Lil3.1 (AT4G17600) is described to be involved in the regulation of late events of chlorophyll biosynthesis [ 75 ]. Besides,...”
- A thylakoid membrane-bound and redox-active rubredoxin (RBD1) functions in de novo assembly and repair of photosystem II
García-Cerdán, Proceedings of the National Academy of Sciences of the United States of America 2019 - “...are listed in SI Appendix , Table S1 . The Arabidopsis full-length RBD1 cDNA (gene At1g54500) was obtained from TAIR, clone U12560. Chlamydomonas RNA isolation, reverse transcriptase PCR, and cDNA synthesis were performed as described in published protocols ( 76 ). PCR products amplified for the...”
- Identification and Roles of Photosystem II Assembly, Stability, and Repair Factors in Arabidopsis
Lu, Frontiers in plant science 2016 - “...et al., 2011 ; Karamoko et al., 2011 ; Lu et al., 2013 RBD1 slr2033 At1g54500 22 16 TM Thiol/disulfide-modulating protein PSII assembly and stability Calderon et al., 2013 CYP20-3/ROC4 slr1251 At3g62030 34 23 CS PPIase Repair and reassembly of PSII under high light; redox regulation...”
- A conserved rubredoxin is necessary for photosystem II accumulation in diverse oxygenic photoautotrophs
Calderon, The Journal of biological chemistry 2013 - “...The ortholog of RBD1 in the flowering plant A. thaliana is encoded by the gene At1g54500 . An Arabidopsis mutant heterozygous for a transposon insertion within At1g54500 was obtained, and seeds harvested from the self-fertilized plant were grown on plates containing 0.5% sucrose to support growth...”
- “...< 0.39), suggesting that the PSII deficiency is caused by a single, recessive mutation in At1g54500 . FIGURE 5. Characterization of A. thaliana T-DNA lines homozygous for an insertion within At1g54500, the RBD1 ortholog. A , growth ( upper panels ) and variable fluorescence (F v...”
- More
LI0697 Rubredoxin 2 (Rd-2) from Lawsonia intracellularis PHE/MN1-00
39% identity, 91% coverage
P00271 Rubredoxin from Megasphaera elsdenii
46% identity, 79% coverage
- Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean.
Vázquez, mSystems 2023 - “...17 MAGs. We also downloaded from UniProt (The UniProt Consortium) and NCBI well-characterized AlkG proteins: P00271, Q9WWW4, Q0VKZ2, WP_138436252.1, WP_161463810.1, WP_089423380.1, WP_084394766.1, WP_015486580.1, Q9HTK8, and Q9HTK7. The reference and COG1651 sequences were aligned using MAFFT v7.487 ( 46 ) (globalpair maxiterate 16 reorder). RESULTS Microbial diversity...”
Q8KPP5 Rubredoxin from Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)
38% identity, 43% coverage
- Dynamic Changes in the Thylakoid Proteome of Cyanobacteria during Light-Regulated Thylakoid Membrane Development
Huang, Plants (Basel, Switzerland) 2023 - “...). Other factors involved in PSI stability, including Alb3 (UniProt ID: Q31MS2), Ycf4 (Q31QI3), RubA (Q8KPP5), Hcf101 (Q31P84), and BtpA (Q31K76), were identified in our analysis, but did not pass the thresholds for quantification. Interestingly, the extent of the reduction of assembly factors was less than...”
8itoB / Q726L3 Crystal structure of ferlp from desulfovibrio vulgaris (hildenborough)
45% identity, 66% coverage
- Ligand: fe (iii) ion (8itoB)
DVU3093 rubredoxin-like protein from Desulfovibrio vulgaris Hildenborough
45% identity, 65% coverage
- Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation
He, Applied and environmental microbiology 2010 - “...DVU1729 DVU1730 DVU2441 DVU2442 DVU2986 DVU2987 DVU2988 DVU3093 DVU3094 DVU3095 DVU0198 DVU0199 DVU0200 DVU0201 DVU0202 DVU0203 DVU0204 DVU2568 DVU2569 NA NA...”
- “...also responds to iron concentrations (11, 12). rdl (DVU3093), which encodes a rubredoxin-like protein and is predicted to be regulated by PerR, was...”
- Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough
Mukhopadhyay, Journal of bacteriology 2007 - “...0.71 correlation of the rubredoxin-like protein encoded by DVU3093, the lowestscoring gene from the predicted PerR regulon, was used as an empirical...”
- “...least correlated was a rubredoxin-like pro- tein gene (DVU3093; correlation, 0.71). Using 0.71 as an empirical score significance cutoff, the PerR mean...”
OLMES_3727 rubredoxin from Oleiphilus messinensis
43% identity, 79% coverage
TP0991 rubredoxin from Treponema pallidum subsp. pallidum str. Nichols
TPANIC_0991 rubredoxin from Treponema pallidum subsp. pallidum str. Nichols
47% identity, 75% coverage
- Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen
Radolf, Nature reviews. Microbiology 2016 - “...dismutase, T. pallidum uses two iron-active center proteins, superoxide reductase (TP0823) and its reductant rubredoxin (TP0991), both acquired from hyperthermophilic anaerobes by a free-living ancestor, 127 to protect against O 2 . The presence of these and other iron-containing proteins creates the need to carefully regulate...”
- Biophysical and bioinformatic analyses implicate the Treponema pallidum Tp34 lipoprotein (Tp0971) in transition metal homeostasis
Brautigam, Journal of bacteriology 2012 - “...iron-requiring proteins: tp0152, tp0612, tp0613, tp0615, tp0972, tp0991, and tp1038 (from UniProtKB annotations), as well as tp0053, tp0080, tp0735, tp0823,...”
- Broad specificity AhpC-like peroxiredoxin and its thioredoxin reductant in the sparse antioxidant defense system of Treponema pallidum
Parsonage, Proceedings of the National Academy of Sciences of the United States of America 2010 - “...reductase (SOR, TP0823) and its putative reductant, rubredoxin (TP0991) (19, 20). T. pallidum lacks catalase and contains no homolog for glutathione peroxidase;...”
- “...Se) No TP1038 No No No No No BB0690 BB0153 TP0823 TDE1754 No TP0991 No No TDE1052 No No No No No No No No No No No No No No No No BB0515 No BB0728 BB0061 No...”
- Comparison of transcriptional profiles of Treponema pallidum during experimental infection of rabbits and in vitro culture: Highly similar, yet different
De, PLoS pathogens 2021 - “...binding* 113 340 1.29 .02 TPANIC_RS01765 helix-turn-helix transcriptional regulator Hypothetical protein 1,037 2,541 1.31 2.91E-39 TPANIC_0991 rubredoxin Energy metabolism; Electron transport 176 435 1.31 4.34E-11 TPANIC_1032 NusG domain II-containing protein Hypothetical protein* 1,206 3,387 1.35 7.24E-11 TPANIC_0197 rpmC Ribosomal proteins; Synthesis and modification 26 67 1.38...”
RUBR2_DESDA / Q93PP8 Rubredoxin-2; Rd-2 from Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB) (see paper)
rd2 / GI|14326007 rubredoxin 2 from Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 (see 2 papers)
39% identity, 78% coverage
- function: Rubredoxin is a small nonheme, iron protein lacking acid- labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule
cofactor: Fe(3+) (Binds 1 Fe(3+) ion per subunit.)
subunit: Monomer.
Dret_0886 Rubredoxin-type Fe(Cys)4 protein from Desulfohalobium retbaense DSM 5692
42% identity, 87% coverage
- Complete genome sequence of Desulfohalobium retbaense type strain (HR(100))
Spring, Standards in genomic sciences 2010 - “...2 O 2 . On the other hand, in the cytoplasm multiprotein complexes containing rubredoxins (Dret_0886, Dret_0139), rubrerythrins (Dret_0191, Dret_1205, Dret_1644, Dret_2310) and desulfoferrodoxin (Dret_0140) could establish electron transfer systems for the reduction of superoxide radicals and H 2 O 2 [ 35 , 36 ]....”
A0A1V5A688 Rubredoxin from Methanoregulaceae archaeon PtaU1.Bin222
38% identity, 75% coverage
Mbur_0092 ferredoxin-dependent glutamate synthase from Methanococcoides burtonii DSM 6242
43% identity, 10% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory