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Escherichia coli K-12 substr. MG1655 Enzyme: acetyl-CoA:oxalate CoA-transferase



Gene: yfdE Accession Numbers: G7234 (EcoCyc), b2371, ECK2367

Regulation Summary Diagram: ?

Subunit composition of acetyl-CoA:oxalate CoA-transferase = [YfdE]2
         acetyl-CoA:oxalate CoA-transferase = YfdE

Summary:
YfdE is a class III CoA-transferase with acetyl-CoA:oxalate CoA-transferase activity. The enzyme may be involved in priming the oxalate-induced acid tolerance response with substrates for oxalyl-CoA decarboxylase and formyl-CoA transferase [Mullins13].

A crystal structure of the enzyme has been solved [Mullins13].

Gene Citations: [Masuda02, Masuda03]

Locations: cytosol

Map Position: [2,486,045 <- 2,487,190] (53.58 centisomes)
Length: 1146 bp / 381 aa

Molecular Weight of Polypeptide: 41.671 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007821 , DIP:DIP-11994N , EchoBASE:EB3069 , EcoGene:EG13284 , EcoliWiki:b2371 , Mint:MINT-1289026 , ModBase:P76518 , OU-Microarray:b2371 , PortEco:yfdE , Protein Model Portal:P76518 , RefSeq:NP_416872 , RegulonDB:G7234 , SMR:P76518 , String:511145.b2371 , Swiss-Model:P76518 , UniProt:P76518

Relationship Links: InterPro:IN-FAMILY:IPR003673 , InterPro:IN-FAMILY:IPR023606 , Panther:IN-FAMILY:PTHR11837 , PDB:Structure:4HL6 , Pfam:IN-FAMILY:PF02515

In Paralogous Gene Group: 14 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis Inferred from experiment [Mullins13, UniProtGOA11a, GOA01a]
Molecular Function: GO:0036412 - acetyl-CoA:oxalate CoA-transferase Inferred from experiment [Mullins13]
GO:0042803 - protein homodimerization activity Inferred from experiment [Mullins13]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism unassigned reversible reactions

Essentiality data for yfdE knockouts: ?

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

Credits:
Created 19-Aug-2013 by Keseler I , SRI International
Last-Curated ? 19-Aug-2013 by Keseler I , SRI International


Enzymatic reaction of: acetyl-CoA:oxalate CoA-transferase

EC Number: 2.8.3.19

acetyl-CoA + oxalate <=> oxalyl-CoA + acetate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Alternative Substrates for acetyl-CoA: formyl-CoA [Mullins13 ]

Alternative Substrates for oxalyl-CoA: formyl-CoA [Mullins13 ]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
acetyl-CoA
17.0
11.0
[Mullins13]
oxalate
22000.0
15.0
[Mullins13]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 294
[Utsumi94, UniProt10]
Alternate sequence: I → T; UniProt: (in Ref. 4; D14008);
Sequence-Conflict 333
[Utsumi94, UniProt10]
Alternate sequence: Q → E; UniProt: (in Ref. 4; D14008);
Sequence-Conflict 357
[Utsumi94, UniProt10]
Alternate sequence: A → T; UniProt: (in Ref. 4; D14008);
Sequence-Conflict 368
[Utsumi94, UniProt10]
Alternate sequence: L → S; UniProt: (in Ref. 4; D14008);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
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

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Masuda02: Masuda N, Church GM (2002). "Escherichia coli gene expression responsive to levels of the response regulator EvgA." J Bacteriol 184(22);6225-34. PMID: 12399493

Masuda03: Masuda N, Church GM (2003). "Regulatory network of acid resistance genes in Escherichia coli." Mol Microbiol 48(3);699-712. PMID: 12694615

Mullins13: Mullins EA, Sullivan KL, Kappock TJ (2013). "Function and X-Ray crystal structure of Escherichia coli YfdE." PLoS One 8(7);e67901. PMID: 23935849

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

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

Utsumi94: Utsumi R, Katayama S, Taniguchi M, Horie T, Ikeda M, Igaki S, Nakagawa H, Miwa A, Tanabe H, Noda M (1994). "Newly identified genes involved in the signal transduction of Escherichia coli K-12." Gene 1994;140(1);73-7. PMID: 8125343

Other References Related to Gene Regulation

Fontenot13: Fontenot EM, Ezelle KE, Gabreski LN, Giglio ER, McAfee JM, Mills AC, Qureshi MN, Salmon KM, Toyota CG (2013). "YfdW and YfdU are required for oxalate-induced acid tolerance in Escherichia coli K-12." J Bacteriol 195(7);1446-55. PMID: 23335415

Itou09: Itou J, Eguchi Y, Utsumi R (2009). "Molecular mechanism of transcriptional cascade initiated by the EvgS/EvgA system in Escherichia coli K-12." Biosci Biotechnol Biochem 73(4);870-8. PMID: 19352034


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 18.5 on Wed Dec 17, 2014, biocyc13.