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Escherichia coli K-12 substr. MG1655 Polypeptide: trimethylamine N-oxide reductase, c-type cytochrome subunit



Gene: torY Accession Numbers: G7023 (EcoCyc), b1873, ECK1874

Synonyms: yecK

Regulation Summary Diagram: ?

Regulation summary diagram for torY

Component of: trimethylamine N-oxide reductase TorYZ (summary available)

Summary:
TorY is a c-type cytochrome that is anchored to the inner membrane; 5 predicted heme binding sites (CXXCH) have been identified. TorY has 36% identity with "TorC" [Gon00].

Locations: cell wall, inner membrane

Map Position: [1,955,056 <- 1,956,156] (42.14 centisomes, 152°)
Length: 1101 bp / 366 aa

Molecular Weight of Polypeptide: 40.286 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006246 , DIP:DIP-11829N , EchoBASE:EB3062 , EcoGene:EG13277 , EcoliWiki:b1873 , ModBase:P52005 , OU-Microarray:b1873 , PortEco:torY , PR:PRO_000024092 , Protein Model Portal:P52005 , RefSeq:NP_416387 , RegulonDB:G7023 , SMR:P52005 , String:511145.b1873 , UniProt:P52005

Relationship Links: InterPro:IN-FAMILY:IPR005126 , InterPro:IN-FAMILY:IPR009154 , InterPro:IN-FAMILY:IPR011031 , Pfam:IN-FAMILY:PF03264 , Prosite:IN-FAMILY:PS51008

In Paralogous Gene Group: 237 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0005506 - iron ion binding Inferred by computational analysis [GOA01a]
GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01a]
GO:0020037 - heme binding Inferred by computational analysis [GOA01a, Gon00]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005887 - integral component of plasma membrane Inferred from experiment [Gon00]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09]
GO:0009276 - Gram-negative-bacterium-type cell wall Inferred by computational analysis [GOA01a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

MultiFun Terms: metabolism energy metabolism, carbon anaerobic respiration
metabolism energy production/transport electron carriers

Essentiality data for torY knockouts: ?

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

Subunit of: trimethylamine N-oxide reductase TorYZ

Subunit composition of trimethylamine N-oxide reductase TorYZ = [TorZ][TorY]
         trimethylamine N-oxide reductase, TorZ subunit = TorZ (summary available)
         trimethylamine N-oxide reductase, c-type cytochrome subunit = TorY (summary available)

Summary:
torYZ encodes a trimethylamine N-oxide (TMAO) reductase complex in E. coli K-12. TorZ is the catalytic subunit and TorY the pentahemic c-type cytochrome subunit. The enzyme has broad substrate specificity; it is able to reduce N- and S-oxide compounds. TMAO is the best substrate for the enzyme; dimethyl sulfoxide (DMSO) is a weak substrate in vitro; DMSO is a competitive inhibitor [Gon00]

Expression of torYZ is very low and not inducible by TMAO or dimethyl sulfoxide [Gon00].

GO Terms:

Molecular Function: GO:0050626 - trimethylamine-N-oxide reductase (cytochrome c) activity Inferred from experiment [Gon00]

Credits:
Last-Curated ? 27-Nov-2014 by Mackie A , Macquarie University


Enzymatic reaction of: trimethylamine N-oxide reductase

Synonyms: TMAO reductase, biotin sulfoxide reductase

Transport reaction diagram for trimethylamine N-oxide reductase

Alternative Substrates for trimethylamine N-oxide: methionine S-oxide [Gon00 ] , tetrahydrothiophene 1-oxide [Gon00 ] , 4-methylmorpholine N-Oxide [Gon00 ] , d-biotin d-sulfoxide [Gon00 ]

Summary:

Inhibitors (Competitive): dimethyl sulfoxide [Gon00]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
trimethylamine N-oxide
670.0, 950.0
[Yamamoto86, BRENDA14]
trimethylamine N-oxide
1440.0
[Gon00, BRENDA14]
trimethylamine N-oxide
70.0
151.0
2.16
[IobbiNivol96, BRENDA14]
trimethylamine N-oxide
7.65, 27.8, 31.6
58.0, 114.0, 258.0
7.58, 14.9, 33.73, 2.09, 4.1, 9.28, 1.84, 3.61, 8.16
[Buc99, BRENDA14]
4-methylmorpholine N-Oxide
1400.0
[Gon00]
tetrahydrothiophene 1-oxide
3370.0
[Gon00]
methionine S-oxide
800.0
[Gon00]
d-biotin d-sulfoxide
360.0
[Gon00]

T(opt): 80 °C [BRENDA14, Buc99]

pH(opt): 6.9 [BRENDA14, Yamamoto86]


Sequence Features

Protein sequence of trimethylamine N-oxide reductase, c-type cytochrome subunit with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 7 -> 27
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 39
[UniProt10a]
UniProt: Heme 1 (covalent); Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 42
[UniProt10a]
UniProt: Heme 1 (covalent); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 43
[UniProt10a]
UniProt: Iron (heme 1 axial ligand); Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 68
[UniProt10a]
UniProt: Heme 2 (covalent); Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 71
[UniProt10a]
UniProt: Heme 2 (covalent); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 72
[UniProt10a]
UniProt: Iron (heme 2 axial ligand); Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 129
[UniProt10a]
UniProt: Heme 3 (covalent); Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 132
[UniProt10a]
UniProt: Heme 3 (covalent); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 133
[UniProt10a]
UniProt: Iron (heme 3 axial ligand); Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 161
[UniProt10a]
UniProt: Heme 4 (covalent); Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 164
[UniProt10a]
UniProt: Heme 4 (covalent); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 165
[UniProt10a]
UniProt: Iron (heme 4 axial ligand); Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 313
[UniProt10a]
UniProt: Heme 5 (covalent); Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 316
[UniProt10a]
UniProt: Heme 5 (covalent); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 317
[UniProt10a]
UniProt: Iron (heme 5 axial ligand); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to 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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Buc99: Buc J, Santini CL, Giordani R, Czjzek M, Wu LF, Giordano G (1999). "Enzymatic and physiological properties of the tungsten-substituted molybdenum TMAO reductase from Escherichia coli." Mol Microbiol 32(1);159-68. PMID: 10216869

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

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."

Gon00: Gon S, Patte JC, Mejean V, Iobbi-Nivol C (2000). "The torYZ (yecK bisZ) operon encodes a third respiratory trimethylamine N-oxide reductase in Escherichia coli." J Bacteriol 2000;182(20);5779-86. PMID: 11004177

IobbiNivol96: Iobbi-Nivol C, Pommier J, Simala-Grant J, Mejean V, Giordano G (1996). "High substrate specificity and induction characteristics of trimethylamine-N-oxide reductase of Escherichia coli." Biochim Biophys Acta 1996;1294(1);77-82. PMID: 8639717

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." 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."

Yamamoto86: Yamamoto I, Okubo N, Ishimoto M (1986). "Further characterization of trimethylamine N-oxide reductase from Escherichia coli, a molybdoprotein." J Biochem (Tokyo) 1986;99(6);1773-9. PMID: 3528139


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 19.0 on Fri May 29, 2015, BIOCYC13A.