Escherichia coli K-12 substr. MG1655 Enzyme: pyruvate:flavodoxin oxidoreductase

Gene: ydbK Accession Numbers: G6701 (EcoCyc), b1378, ECK1374

Synonyms: pfo

Regulation Summary Diagram: ?

Regulation summary diagram for ydbK

Based on sequence similarity, YdbK is predicted to function as a pyruvate:flavodoxin oxidoreductase and/or pyruvate synthase [Serres01, Reed03]. The activity has been assayed in crude extracts with methyl viologen as the electron acceptor [Nakayama13]. Coexpression of YdbK with a heterologous hydrogenase enzyme enhances the production of hydrogen; the effect depends on the coexpression of an E. coli flavodoxin or a heterologous ferredoxin [Kalim09]. Overexpression of YdbK in an engineered strain that utilizes ethanol aerobically as the sole source of carbon and secretes valine enables better growth and higher valine production, suggesting enhanced availability of pyruvate [Eremina10].

The authors of [Kalim09] suggest that YdbK is most likely the enzyme characterized by [Blaschkowski82], pyruvate:ferredoxin oxidoreductase. Under the conditions employed by [Eremina10], the enzyme may function in the direction of pyruvate synthesis.

A ydbK mutant is unable to grow on glucose under oxidative stress conditions [Eremina10]. ydbK is needed for superoxide resistance during growth on minimal medium [Fabrega12], and a ydbK fpr double mutant is sensitive to methyl viologen [Nakayama13].

Expression of ydbK is induced by superoxide and is SoxS-dependent [Nakayama13].

Map Position: [1,435,284 <- 1,438,808] (30.94 centisomes, 111°)
Length: 3525 bp / 1174 aa

Molecular Weight of Polypeptide: 128.82 kD (from nucleotide sequence), 128.0 kD (experimental) [Eremina10 ]

Unification Links: ASAP:ABE-0004613 , DIP:DIP-11636N , EchoBASE:EB2975 , EcoGene:EG13183 , EcoliWiki:b1378 , Mint:MINT-1299276 , ModBase:P52647 , OU-Microarray:b1378 , PortEco:ydbK , Pride:P52647 , Protein Model Portal:P52647 , RefSeq:NP_415896 , RegulonDB:G6701 , SMR:P52647 , String:511145.b1378 , Swiss-Model:P52647 , UniProt:P52647

Relationship Links: InterPro:IN-FAMILY:IPR001450 , InterPro:IN-FAMILY:IPR002869 , InterPro:IN-FAMILY:IPR002880 , InterPro:IN-FAMILY:IPR009014 , InterPro:IN-FAMILY:IPR011766 , InterPro:IN-FAMILY:IPR011895 , InterPro:IN-FAMILY:IPR017896 , InterPro:IN-FAMILY:IPR017900 , InterPro:IN-FAMILY:IPR019456 , InterPro:IN-FAMILY:IPR019752 , InterPro:IN-FAMILY:IPR029061 , Pfam:IN-FAMILY:PF00037 , Pfam:IN-FAMILY:PF01558 , Pfam:IN-FAMILY:PF01855 , Pfam:IN-FAMILY:PF02775 , Pfam:IN-FAMILY:PF10371 , Prosite:IN-FAMILY:PS00198 , Prosite:IN-FAMILY:PS51379 , Smart:IN-FAMILY:SM00890

In Paralogous Gene Group: 223 (21 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for ydbK

GO Terms:

Biological Process: GO:0006979 - response to oxidative stress Inferred from experiment [Fabrega12, Eremina10]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
GO:0022900 - electron transport chain Inferred by computational analysis [GOA01]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01]
Molecular Function: GO:0043873 - pyruvate-flavodoxin oxidoreductase activity Inferred from experiment [Nakayama13]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0016903 - oxidoreductase activity, acting on the aldehyde or oxo group of donors Inferred by computational analysis [GOA01]
GO:0030976 - thiamine pyrophosphate binding Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: metabolism

Essentiality data for ydbK knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Last-Curated ? 27-Sep-2013 by Keseler I , SRI International

Enzymatic reaction of: pyruvate:flavodoxin oxidoreductase

Synonyms: pyruvate synthase, pyruvate oxidoreductase, pyruvic-ferredoxin oxidoreductase, pyruvate:ferredoxin oxidoreductase, pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)

EC Number: 1.2.99.-

pyruvate + an oxidized flavodoxin + coenzyme A + H+ <=> acetyl-CoA + CO2 + a reduced flavodoxin

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

The activity was measured in crude extracts, substituting methyl viologen as the electron acceptor in place of flavodoxin/ferredoxin [Nakayama13].

Cofactors or Prosthetic Groups: thiamin diphosphate [Kalim09]

Sequence Features

Protein sequence of pyruvate:flavodoxin oxidoreductase with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 40
[Bunch97, UniProt10a]
UniProt: (in Ref. 4);
Sequence-Conflict 51
[Bunch97, UniProt10a]
UniProt: (in Ref. 4);
Conserved-Region 680 -> 709
UniProt: 4Fe-4S ferredoxin-type 1;
Metal-Binding-Site 689
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 692
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 695
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 699
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: potential;
Conserved-Region 736 -> 765
UniProt: 4Fe-4S ferredoxin-type 2;
Metal-Binding-Site 745
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 748
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 751
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 755
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Blaschkowski82: Blaschkowski HP, Neuer G, Ludwig-Festl M, Knappe J (1982). "Routes of flavodoxin and ferredoxin reduction in Escherichia coli. CoA-acylating pyruvate: flavodoxin and NADPH: flavodoxin oxidoreductases participating in the activation of pyruvate formate-lyase." Eur J Biochem 1982;123(3);563-9. PMID: 7042345

Bunch97: Bunch PK, Mat-Jan F, Lee N, Clark DP (1997). "The ldhA gene encoding the fermentative lactate dehydrogenase of Escherichia coli." Microbiology 143 ( Pt 1);187-95. PMID: 9025293

Eremina10: Eremina NS, Yampolskaya TA, Altman IB, Mashko SV, Stoynova NV (2010). "Overexpression of ydbK-encoding Putative Pyruvate Synthase Improves L-valine Production and Aerobic Growth on Ethanol Media by an Escherichia coli Strain Carrying an Oxygen-Resistant Alcohol Dehydrogenase." J Microbial Biochem Technol 2: 077-083.

Fabrega12: Fabrega A, Rosner JL, Martin RG, Sole M, Vila J (2012). "SoxS-dependent coregulation of ompN and ydbK in a multidrug-resistant Escherichia coli strain." FEMS Microbiol Lett 332(1);61-7. PMID: 22515487

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kalim09: Kalim Akhtar M, Jones PR (2009). "Construction of a synthetic YdbK-dependent pyruvate:H(2) pathway in Escherichia coli BL21(DE3)." Metab Eng 11(3);139-47. PMID: 19558967

Nakayama13: Nakayama T, Yonekura S, Yonei S, Zhang-Akiyama QM (2013). "Escherichia coli pyruvate:flavodoxin oxidoreductase, YdbK - regulation of expression and biological roles in protection against oxidative stress." Genes Genet Syst 88(3);175-88. PMID: 24025246

Reed03: Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)." Genome Biol 4(9);R54. PMID: 12952533

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Raghavan11: Raghavan R, Sage A, Ochman H (2011). "Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli." J Bacteriol 193(11);2871-4. PMID: 21460078

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Tue Oct 13, 2015, biocyc13.