Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: predicted oxidoreductase



Gene: ydhV Accession Numbers: G6901 (EcoCyc), b1673, ECK1669

Regulation Summary Diagram: ?

Summary:
YdhV is a putative member of the aldehyde ferredoxin oxidoreductase family of molybdoenzymes [Kozmin07]. Based on sequence similarity, the ydhYVWXUT operon may encode an oxidoreductase system [Partridge08].

A ydhY-T mutant does not show a growth defect under anaerobic conditions, although utilization of certain sources of sulphur is impaired [Partridge08].

In a ΔtusA strain, expression of ydhV is decreased in mid-exponential phase and under aerobic conditions [Dahl13a].

Map Position: [1,749,752 <- 1,751,854] (37.71 centisomes)
Length: 2103 bp / 700 aa

Molecular Weight of Polypeptide: 77.876 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005587 , DIP:DIP-11741N , EchoBASE:EB3714 , EcoGene:EG13956 , EcoliWiki:b1673 , ModBase:P76192 , OU-Microarray:b1673 , PortEco:ydhV , Protein Model Portal:P76192 , RefSeq:NP_416188 , RegulonDB:G6901 , SMR:P76192 , String:511145.b1673 , UniProt:P76192

Relationship Links: InterPro:IN-FAMILY:IPR001203 , InterPro:IN-FAMILY:IPR013983 , InterPro:IN-FAMILY:IPR013984 , InterPro:IN-FAMILY:IPR013985 , Pfam:IN-FAMILY:PF01314 , Pfam:IN-FAMILY:PF02730 , Smart:IN-FAMILY:SM00790

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016625 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11]

Gene Class: ORFs

Essentiality data for ydhV 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]

Credits:
Last-Curated ? 08-Jan-2013 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 307
[UniProt11]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 310
[UniProt11]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 314
[UniProt11]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 558
[UniProt11]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Dahl13a: Dahl JU, Radon C, Buhning M, Nimtz M, Leichert LI, Denis Y, Jourlin-Castelli C, Iobbi-Nivol C, Mejean V, Leimkuhler S (2013). "The sulfur carrier protein TusA has a pleiotropic role in Escherichia coli that also affects molybdenum cofactor biosynthesis." J Biol Chem 288(8);5426-42. PMID: 23281480

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

Kozmin07: Kozmin SG, Schaaper RM (2007). "Molybdenum cofactor-dependent resistance to N-hydroxylated base analogs in Escherichia coli is independent of MobA function." Mutat Res 619(1-2);9-15. PMID: 17349664

Partridge08: Partridge JD, Browning DF, Xu M, Newnham LJ, Scott C, Roberts RE, Poole RK, Green J (2008). "Characterization of the Escherichia coli K-12 ydhYVWXUT operon: regulation by FNR, NarL and NarP." Microbiology 154(Pt 2);608-18. PMID: 18227264

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Kang05: Kang Y, Weber KD, Qiu Y, Kiley PJ, Blattner FR (2005). "Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function." J Bacteriol 187(3);1135-60. PMID: 15659690


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 18.5 on Fri Dec 19, 2014, BIOCYC14B.