Escherichia coli K-12 substr. MG1655 Polypeptide: oxidoreductase, predicted membrane anchor subunit

Gene: ynfH Accession Numbers: G6848 (EcoCyc), b1590, ECK1585

Regulation Summary Diagram

Regulation summary diagram for ynfH

Component of: putative selenate reductase (summary available)

YnfH contains eight potential transmembrane helices and is similar to DmsC, the membrane anchor subunit of the dimethyl sulfoxide reductase heterotrimer. When expressed together with DmsA and either DmsB or YnfG in a plasmid expression system, YnfH can form a complex with DmsA and DmsB/YnfG and support growth on DMSO [Lubitz03].

A ynfH mutant reaches slightly higher cell density in stationary phase than wild type when growing in media with sublethal levels of streptomycin, an aminoglycoside antibiotic [Vlasblom14].

Locations: inner membrane

Map Position: [1,661,633 -> 1,662,487] (35.81 centisomes, 129°)
Length: 855 bp / 284 aa

Molecular Weight of Polypeptide: 30.524 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005311, EchoBASE:EB3607, EcoGene:EG13846, EcoliWiki:b1590, OU-Microarray:b1590, PortEco:ynfH, Protein Model Portal:P76173, RefSeq:NP_416107, RegulonDB:G6848, String:511145.b1590, UniProt:P76173

Relationship Links: InterPro:IN-FAMILY:IPR007059, Pfam:IN-FAMILY:PF04976

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for ynfH

GO Terms:
Biological Process:
Inferred by computational analysisGO:0019645 - anaerobic electron transport chain [GOA01a]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11]
Molecular Function:
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11]
Inferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11, GOA01a]

MultiFun Terms: metabolismmetabolism of other compounds

Essentiality data for ynfH knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

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)

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]

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

Enzymatic reaction of: selenate reductase

Inferred from experiment

EC Number:

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 membrane anchor subunit with features indicated

Feature Class Location Citations Comment
Pfam PF04976 1 -> 274
Inferred by computational analysis[Finn14]
DmsC : DMSO reductase anchor subunit (DmsC)
Transmembrane-Region 10 -> 30
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 46 -> 66
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 87 -> 107
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 116 -> 136
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 149 -> 169
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 181 -> 201
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 223 -> 243
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 251 -> 271
Inferred by computational analysis[UniProt15]
UniProt: Helical.

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

Gene local context diagram

Transcription Unit

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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

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

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

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

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

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

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

Vlasblom14: Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A, Deineko V, Kumar A, Leung E, Rizzolo K, Samanfar B, Chang L, Phanse S, Golshani A, Greenblatt JF, Houry WA, Emili A, Morris Q, Bader G, Babu M (2014). "Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli." Bioinformatics. PMID: 25316676

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
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