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

Gene: ynfE Accession Numbers: G6845 (EcoCyc), b1587, ECK1582

Regulation Summary Diagram

Regulation summary diagram for ynfE

Component of: putative selenate reductase (summary available)

YnfE 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].

YnfE 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. In a plasmid expression system, expression of YnfE appears to inhibit expression of YnfFGH [Lubitz03].

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

Locations: periplasmic space, inner membrane

Map Position: [1,656,093 -> 1,658,519] (35.69 centisomes, 128°)
Length: 2427 bp / 808 aa

Molecular Weight of Polypeptide: 89.78 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005302, DIP:DIP-12765N, EchoBASE:EB3604, EcoGene:EG13843, EcoliWiki:b1587, ModBase:P77374, OU-Microarray:b1587, PortEco:ynfE, Pride:P77374, Protein Model Portal:P77374, RefSeq:NP_416104, RegulonDB:G6845, SMR:P77374, String:511145.b1587, UniProt:P77374

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, Pfam:IN-FAMILY:PF00384, Pfam:IN-FAMILY:PF01568, Pfam:IN-FAMILY:PF04879, 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 ynfE

GO Terms:
Biological Process:
Inferred by computational analysisGO:0009061 - anaerobic respiration [Gaudet10]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11, GOA01]
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 [GOA01, Gaudet10]
Inferred by computational analysisGO:0009389 - dimethyl sulfoxide reductase activity [GOA01]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11, GOA01]
Inferred by computational analysisGO:0030151 - molybdenum ion binding [GOA01, Gaudet10]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11, Gaudet10]
Inferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11, GOA01]
Cellular Component:
Inferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11a, UniProtGOA11]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11]
Inferred by computational analysisGO:0030288 - outer membrane-bounded periplasmic space [Gaudet10, DiazMejia09]

MultiFun Terms: metabolismmetabolism of other compounds

Essentiality data for ynfE 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]

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 Citations Comment
Signal-Sequence 1 -> 43
Inferred by computational analysis[UniProt15]
UniProt: Tat-type signal.
Chain 44 -> 808
Author statement[UniProt15]
UniProt: Putative dimethyl sulfoxide reductase chain YnfE.
Conserved-Region 49 -> 110
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S Mo/W bis-MGD-type.
Metal-Binding-Site 56
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 60
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 64
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 96
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 196
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 49 -> 108
Inferred by computational analysis[Finn14]
Molybdop_Fe4S4 : Molybdopterin oxidoreductase Fe4S4 domain
Pfam PF00384 111 -> 566
Inferred by computational analysis[Finn14]
Molybdopterin : Molybdopterin oxidoreductase
Pfam PF01568 687 -> 800
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


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

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

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

GOA01: 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."

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 Pathway Tools version 19.5 (software by SRI International) on Thu Nov 26, 2015, biocyc14.