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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

Regulation summary diagram for ynfG

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].

Locations: membrane

Map Position: [1,661,014 -> 1,661,631] (35.8 centisomes, 129°)
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:PF12800, Pfam:IN-FAMILY:PF13247, Prosite:IN-FAMILY:PS00198, Prosite:IN-FAMILY:PS51379

In Paralogous Gene Group: 223 (21 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for ynfG


GO Terms:
Biological Process:
Inferred by computational analysisGO:0009061 - anaerobic respiration [Gaudet10]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a]
Molecular Function:
Inferred by computational analysisGO:0009055 - electron carrier activity [Gaudet10]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [Gaudet10]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a]
Inferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0016020 - membrane [Gaudet10]

MultiFun Terms: metabolismmetabolism of other compounds

Essentiality data for ynfG knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucoseYes 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:
Inferred from experimentGO:0055114 - oxidation-reduction process [Lubitz03, Guymer09]
Molecular Function:
Inferred from experimentGO:0033797 - selenate reductase activity [Guymer09]

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


Enzymatic reaction of: selenate reductase

Inferred from experiment

EC Number: 1.97.1.9

selenate + an reduced unknown electron acceptor → selenite + an oxidized unknown electron acceptor + H2O

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.


Sequence Features

Protein sequence of oxidoreductase, predicted Fe-S subunit with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Inferred by computational analysis[UniProt15]
UniProt: Removed.
Chain 2 -> 205
Author statement[UniProt15]
UniProt: Probable anaerobic dimethyl sulfoxide reductase chain YnfG.
Conserved-Region 5 -> 33
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 1.
Metal-Binding-Site 14
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Metal-Binding-Site 17
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Metal-Binding-Site 20
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Metal-Binding-Site 24
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Conserved-Region 59 -> 89
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 2.
Metal-Binding-Site 67
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Metal-Binding-Site 70
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Metal-Binding-Site 75
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Metal-Binding-Site 79
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 4 (4Fe-4S).
Conserved-Region 90 -> 119
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 3.
Metal-Binding-Site 99
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 4 (4Fe-4S).
Metal-Binding-Site 102
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 4 (4Fe-4S).
Metal-Binding-Site 105
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 4 (4Fe-4S).
Metal-Binding-Site 109
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Metal-Binding-Site 126
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 129
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 141
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 145
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).


Sequence Pfam Features

Protein sequence of oxidoreductase, predicted Fe-S subunit with features indicated

Feature Class Location Citations Comment
Pfam PF12800 11 -> 25
Inferred by computational analysis[Finn14]
Fer4_4 : 4Fe-4S binding domain
Pfam PF13247 60 -> 153
Inferred by computational analysis[Finn14]
Fer4_11 : 4Fe-4S dicluster domain


Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram

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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." 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


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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