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

Gene: ynfF Accession Numbers: G6846 (EcoCyc), b1588, ECK1583

Regulation Summary Diagram

Regulation summary diagram for ynfF

Component of: putative selenate reductase (summary available)

YnfF has been implicated as a Tat-dependent selenate reductase enzyme in E.coli. A ynfEF double null mutant is unable to reduce selenate to elemental selenium [Guymer09]. The disruption is specific to the initial selenate reduction process since selenium production is restored when selenite is added to the growth medium [Guymer09]. Production of either YnfE or YnfF from a plasmid restored the ability of the E. coli ynfEF double mutant to reduce selenate to selenium in vivo [Guymer09].

YnfF is highly similar to DmsA, the catalytic subunit of the dimethyl sulfoxide reductase heterotrimer, and cross-reacts with an anti-DmsA antibody. The protein is poorly expressed. When expressed together with DmsB and DmsC in a plasmid expression system, YnfF can form a complex with DmsB and DmsC, but the chimeric enzyme does not support growth on DMSO [Lubitz03].

The YnfF signal peptide can direct export through the twin arginine translocation (Tat) pathway and the general secretory pathway (Sec) pathway [TullmanErcek07].

YnfF is a predicted molybdoenzyme; deletion of ynfF does not confer a 6-N-hydroxylaminopurine (HAP)-sensitive phenotype [Kozmin07].

Locations: periplasmic space, inner membrane

Map Position: [1,658,580 -> 1,661,003] (35.75 centisomes, 129°)
Length: 2424 bp / 807 aa

Molecular Weight of Polypeptide: 89.987 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005307, DIP:DIP-12766N, EchoBASE:EB3605, EcoGene:EG13844, EcoliWiki:b1588, ModBase:P77783, OU-Microarray:b1588, PortEco:ynfF, Pride:P77783, Protein Model Portal:P77783, RefSeq:NP_416105, RegulonDB:G6846, SMR:P77783, String:511145.b1588, UniProt:P77783

Relationship Links: InterPro:IN-FAMILY:IPR006311, InterPro:IN-FAMILY:IPR006655, InterPro:IN-FAMILY:IPR006656, InterPro:IN-FAMILY:IPR006657, InterPro:IN-FAMILY:IPR006963, InterPro:IN-FAMILY:IPR009010, InterPro:IN-FAMILY:IPR011888, InterPro:IN-FAMILY:IPR027467, Pfam:IN-FAMILY:PF00384, Pfam:IN-FAMILY:PF01568, Pfam:IN-FAMILY:PF04879, Prosite:IN-FAMILY:PS00551, Prosite:IN-FAMILY:PS00932, Prosite:IN-FAMILY:PS51318, Prosite:IN-FAMILY:PS51669, Smart:IN-FAMILY:SM00926

In Paralogous Gene Group: 222 (14 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for ynfF

GO Terms:
Biological Process:
Inferred by computational analysisGO:0009061 - anaerobic respiration [Gaudet10]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Chan09]
Inferred from experimentGO:0033797 - selenate reductase activity [Guymer09]
Inferred by computational analysisGO:0003954 - NADH dehydrogenase activity [Gaudet10]
Inferred by computational analysisGO:0009055 - electron carrier activity [GOA01a, Gaudet10]
Inferred by computational analysisGO:0009389 - dimethyl sulfoxide reductase activity [GOA01a]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0030151 - molybdenum ion binding [GOA01a, Gaudet10]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a, Gaudet10]
Inferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a, GOA01a]
Cellular Component:
Inferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a]
Inferred by computational analysisGO:0030288 - outer membrane-bounded periplasmic space [Gaudet10, DiazMejia09]

MultiFun Terms: metabolismmetabolism of other compounds

Essentiality data for ynfF 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]

Curated 14-May-2007 by Keseler I, SRI International
Last-Curated 07-Jul-2009 by Mackie A, Macquarie University

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 subunit with features indicated

Feature Class Location Common Name Citations Comment
Signal-Sequence 1 -> 45 signal peptide
Chain 46 -> 807  
Author statement[UniProt15]
UniProt: Probable dimethyl sulfoxide reductase chain YnfF.
Conserved-Region 52 -> 113  
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S Mo/W bis-MGD-type.
Metal-Binding-Site 59  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 63  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 67  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 99  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 195  
Inferred by computational analysis[UniProt15]
UniProt: Molybdenum.

Sequence Pfam Features

Protein sequence of oxidoreductase subunit with features indicated

Feature Class Location Citations Comment
Pfam PF04879 52 -> 111
Inferred by computational analysis[Finn14]
Molybdop_Fe4S4 : Molybdopterin oxidoreductase Fe4S4 domain
Pfam PF00384 114 -> 565
Inferred by computational analysis[Finn14]
Molybdopterin : Molybdopterin oxidoreductase
Pfam PF01568 686 -> 799
Inferred by computational analysis[Finn14]
Molydop_binding : Molydopterin dinucleotide binding domain

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

Gene local context diagram

Transcription Unit

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06].
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

Chan09: Chan CS, Chang L, Rommens KL, Turner RJ (2009). "Differential interactions between Tat-specific redox enzyme peptides and their chaperones." J Bacteriol 191(7):2091-101. PMID: 19151138

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

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

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

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

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

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

TullmanErcek07: Tullman-Ercek D, DeLisa MP, Kawarasaki Y, Iranpour P, Ribnicky B, Palmer T, Georgiou G (2007). "Export pathway selectivity of Escherichia coli twin arginine translocation signal peptides." J Biol Chem 282(11);8309-16. PMID: 17218314

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

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

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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