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Escherichia coli K-12 substr. MG1655 Polypeptide: oxidoreductase, predicted Fe-S subunit



Gene: ynfG Accession Numbers: G6847 (EcoCyc), b1589, ECK1584

Regulation Summary Diagram: ?

Component of: putative selenate reductase (summary available)

Summary:
YnfG is highly similar to DmsB, the iron-sulfur cluster-containing subunit of the dimethyl sulfoxide reductase heterotrimer, and cross-reacts with an anti-DmsB antibody. It contains iron-sulfur clusters which are indistinguishable from DmsB by EPR spectroscopy. When expressed together with DmsA and YnfH in a plasmid expression system, YnfG can form a complex with DmsA and YnfH and support growth on DMSO [Lubitz03].

Map Position: [1,661,014 -> 1,661,631] (35.8 centisomes)
Length: 618 bp / 205 aa

Molecular Weight of Polypeptide: 22.752 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005309 , DIP:DIP-48224N , EchoBASE:EB3606 , EcoGene:EG13845 , EcoliWiki:b1589 , ModBase:P0AAJ1 , OU-Microarray:b1589 , PortEco:ynfG , Protein Model Portal:P0AAJ1 , RefSeq:NP_416106 , RegulonDB:G6847 , SMR:P0AAJ1 , String:511145.b1589 , UniProt:P0AAJ1

Relationship Links: InterPro:IN-FAMILY:IPR001450 , InterPro:IN-FAMILY:IPR014297 , InterPro:IN-FAMILY:IPR017896 , InterPro:IN-FAMILY:IPR017900 , Pfam:IN-FAMILY:PF00037 , Pfam:IN-FAMILY:PF12797 , Pfam:IN-FAMILY:PF12798 , Prosite:IN-FAMILY:PS00198 , Prosite:IN-FAMILY:PS51379

In Paralogous Gene Group: 223 (21 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: metabolism metabolism of other compounds

Essentiality data for ynfG knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]
Yes [Feist07, Comment 3]

Subunit of: putative selenate reductase

Synonyms: YnfFGH, YnfEFGH

Subunit composition of putative selenate reductase = [YnfE][YnfF][YnfG][YnfH]
         oxidoreductase subunit = YnfE (summary available)
         oxidoreductase subunit = YnfF (extended summary available)
         oxidoreductase, predicted Fe-S subunit = YnfG (summary available)
         oxidoreductase, predicted membrane anchor subunit = YnfH (summary available)

Summary:
On the basis of sequence similarity the ynfEFGH operon was predicted to encode an oxidoreductase complex closely related to DMSO reductase. A strain carrying a deletion of dmsABC and containing ynfFGH on a multicopy plasmid is able to grow poorly under anaerobic conditions utilizing dimethyl sulfoxide as a terminal oxidant [Lubitz03]. More recently, genetic analysis of E.coli ynfE and ynfF null mutants suggests these proteins are Tat-targeted selenate reductases [Guymer09]. E.coli ubiE and menA null mutants are unable to reduce selenate to elemental red selenium in vivo thus implicating menaquinone in the reductase activity [Guymer09].

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred from experiment [Lubitz03, Guymer09]
Molecular Function: GO:0033797 - selenate reductase activity Inferred from experiment [Guymer09]

Credits:
Last-Curated ? 07-Jul-2009 by Mackie A , Macquarie University


Enzymatic reaction of: selenate reductase

EC Number: 1.97.1.9

selenate + a reduced electron acceptor <=> selenite + an oxidized electron acceptor + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[UniProt10a]
UniProt: Removed; Non-Experimental Qualifier: by similarity;
Chain 2 -> 205
[UniProt09]
UniProt: Probable anaerobic dimethyl sulfoxide reductase chain ynfG;
Conserved-Region 5 -> 33
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 1;
Metal-Binding-Site 14
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 17
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 20
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 24
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 59 -> 89
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 2;
Metal-Binding-Site 67
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 70
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 75
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 79
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 90 -> 119
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 3;
Metal-Binding-Site 99
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 102
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 105
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 109
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 126
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 129
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 141
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 145
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Guymer09: Guymer D, Maillard J, Sargent F (2009). "A genetic analysis of in vivo selenate reduction by Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12." Arch Microbiol 191(6);519-28. PMID: 19415239

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

Lubitz03: Lubitz SP, Weiner JH (2003). "The Escherichia coli ynfEFGHI operon encodes polypeptides which are paralogues of dimethyl sulfoxide reductase (DmsABC)." Arch Biochem Biophys 418(2);205-16. PMID: 14522592

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

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

Xu09: Xu M, Busby SJ, Browning DF (2009). "Activation and repression at the Escherichia coli ynfEFGHI operon promoter." J Bacteriol 191(9);3172-6. PMID: 19251855


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 Wed Dec 17, 2014, biocyc13.