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MetaCyc Enzyme: formyl-CoA transferase

Gene: frc Accession Numbers: G7237 (MetaCyc), b2374, ECK2370

Synonyms: yfdW

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of formyl-CoA transferase = [Frc]2
         formyl-CoA transferase monomer = Frc

Summary:
YfdW (Frc) is a formyl-CoA transferase with sequence and structural similarity to Frc from Oxalobacter formigenes, a strictly anaerobic bacterium found in the mammalian gut [Gruez03, Toyota08]. Unlike the O. formigenes enzyme, the E. coli enzyme shows high substrate specificity [Toyota08].

Crystal structures of apo-YfdW and YfdW with CoA, acetyl-CoA, or both acetyl-CoA and oxalate have been solved. YfdW is a homodimer; the ring-shaped monomers are concatenated like links of a chain [Gruez03, Gogos04].

The enzymatic reaction mechanism is predicted by structural similarity to related enzymes; residue D169 is predicted to catalyze the reaction [Gruez03]. Biochemical data indicates that the kinetic mechanism is ordered bi-bi sequential [Toyota08].

Frc is required during the adaption phase of an oxalate-induced acid tolerance response [Fontenot13]. Expression of frc is increased when the EvgAS two-component regulatory system is overexpressed [Masuda02].

Locations: cytosol

Map Position: [2,490,026 <- 2,491,276]

Molecular Weight of Polypeptide: 45.828 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007828, EchoBASE:EB3897, EcoGene:EG14145, EcoliWiki:b2374, ModBase:P69902, OU-Microarray:b2374, PortEco:frc, PR:PRO_000022685, Pride:P69902, Protein Model Portal:P69902, RefSeq:NP_416875, RegulonDB:G7237, SMR:P69902, String:511145.b2374, UniProt:P69902

Relationship Links: InterPro:IN-FAMILY:IPR003673, InterPro:IN-FAMILY:IPR017659, InterPro:IN-FAMILY:IPR023606, Panther:IN-FAMILY:PTHR11837, PDB:Structure:1PQY, PDB:Structure:1PT5, PDB:Structure:1PT7, PDB:Structure:1PT8, PDB:Structure:1Q6Y, PDB:Structure:1Q7E, Pfam:IN-FAMILY:PF02515

Gene-Reaction Schematic

Gene-Reaction Schematic


GO Terms:
Biological Process:
Inferred from experimentGO:0071468 - cellular response to acidic pH [Fontenot13]
Inferred by computational analysisGO:0008152 - metabolic process [GOA01a]
Inferred by computational analysisGO:0033611 - oxalate catabolic process [UniProtGOA12]
Molecular Function:
Inferred from experimentInferred by computational analysisGO:0033608 - formyl-CoA transferase activity [GOA01, GOA01a, Toyota08]
Inferred by computational analysisGO:0003824 - catalytic activity [GOA01a]
Inferred by computational analysisGO:0008410 - CoA-transferase activity [GOA06]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: metabolismmetabolism of other compounds

Credits:
Imported from EcoCyc 30-Sep-2015 by Paley S, SRI International


Enzymatic reaction of: formyl-CoA transferase

Inferred from experiment

Synonyms: formyl-CoA:oxalate CoA-transferase

EC Number: 2.8.3.16

formyl-CoA + oxalate ⇄ formate + oxalyl-CoA

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Credits:
Imported from EcoCyc 30-Sep-2015 by Paley S, SRI International

Summary:
Oxalate at concentrations above 2.5 mM inhibit the activity [Toyota08].

Inhibitors (Uncompetitive): acetyl-CoA [Toyota08] Inhibitors (Unknown Mechanism): oxalate [Toyota08], coenzyme A [Toyota08]Kinetic Parameters:
Substrate Km (μM) Citations
formyl-CoA 350.0, 352.0 [Toyota08]
oxalate 510.0 [Toyota08, BRENDA14]

Sequence Features

Feature Class Location Citations Comment
Protein-Segment 17 -> 18
Author statement[UniProt15]
UniProt: Coenzyme A binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 38
Inferred from experiment[Gogos04]
UniProt: Coenzyme A.
Protein-Segment 72 -> 75
Author statement[UniProt15]
UniProt: Coenzyme A binding; Sequence Annotation Type: region of interest.
Protein-Segment 96 -> 98
Author statement[UniProt15]
UniProt: Coenzyme A binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 104
Inferred by computational analysis[UniProt15]
UniProt: Coenzyme A.
Protein-Segment 137 -> 140
Author statement[UniProt15]
UniProt: Coenzyme A binding; Sequence Annotation Type: region of interest.
Active-Site 169
Inferred by curator[Gruez03, UniProt15]
UniProt: Nucleophile.
Protein-Segment 248 -> 250
Inferred by curator[UniProt15]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Protein-Segment 273 -> 275
Author statement[UniProt15]
UniProt: Coenzyme A binding; Sequence Annotation Type: region of interest.

History:
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

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

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

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

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Gogos04: Gogos A, Gorman J, Shapiro L (2004). "Structure of Escherichia coli YfdW, a type III CoA transferase." Acta Crystallogr D Biol Crystallogr 60(Pt 3);507-11. PMID: 14993676

Gruez03: Gruez A, Roig-Zamboni V, Valencia C, Campanacci V, Cambillau C (2003). "The crystal structure of the E. coli yfdW gene product reveals a new fold of two interlaced rings identifying a wide family of CoA transferases." J Biol Chem 278(36);34582-6. PMID: 12844490

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

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

Toyota08: Toyota CG, Berthold CL, Gruez A, Jonsson S, Lindqvist Y, Cambillau C, Richards NG (2008). "Differential substrate specificity and kinetic behavior of Escherichia coli YfdW and Oxalobacter formigenes formyl coenzyme A transferase." J Bacteriol 190(7):2556-64. PMID: 18245280

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."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by Pathway Tools version 19.5 (software by SRI International) on Thu Feb 11, 2016, biocyc14.