|Gene:||ydbK||Accession Numbers: G6701 (EcoCyc), b1378, ECK1374|
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)
|Biological Process:||GO:0006979 - response to oxidative stress
GO:0008152 - metabolic process [GOA01]
GO:0022900 - electron transport chain [GOA01]
GO:0055114 - oxidation-reduction process [UniProtGOA11, GOA01]
|Molecular Function:||GO:0043873 - pyruvate-flavodoxin oxidoreductase activity
GO:0003824 - catalytic activity [GOA01]
GO:0005506 - iron ion binding [GOA01]
GO:0016491 - oxidoreductase activity [UniProtGOA11, GOA01]
GO:0016903 - oxidoreductase activity, acting on the aldehyde or oxo group of donors [GOA01]
GO:0030976 - thiamine pyrophosphate binding [GOA01]
GO:0046872 - metal ion binding [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding [UniProtGOA11, GOA01]
GO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11]
|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]|
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.-
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].
|Conserved-Region||680 -> 709|
|Conserved-Region||736 -> 765|
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
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
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
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
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
©2015 SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493