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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: GO:0071468 - cellular response to acidic pH Inferred from experiment [Fontenot13]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0033611 - oxalate catabolic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0033608 - formyl-CoA transferase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Toyota08]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0008410 - CoA-transferase activity Inferred by computational analysis [GOA06]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism metabolism of other compounds

Credits:
Imported from EcoCyc 27-Jan-2015 by Paley S , SRI International


Enzymatic reaction of: formyl-CoA transferase

Synonyms: formyl-CoA:oxalate CoA-transferase

EC Number: 2.8.3.16

formyl-CoA + oxalate <=> formate + oxalyl-CoA

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

The reaction is favored in the direction shown.

Credits:
Imported from EcoCyc 27-Jan-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, BRENDA14]
oxalate
510.0
[Toyota08, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 17 -> 18
[UniProt10]
UniProt: Coenzyme A binding; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 38
[Gogos04, UniProt14]
UniProt: Coenzyme A.
Protein-Segment 72 -> 75
[UniProt14]
UniProt: Coenzyme A binding; Sequence Annotation Type: region of interest.
Protein-Segment 96 -> 98
[UniProt14]
UniProt: Coenzyme A binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 104
[UniProt14]
UniProt: Coenzyme A.
Protein-Segment 137 -> 140
[UniProt10]
UniProt: Coenzyme A binding; Sequence Annotation Type: region of interest;
Active-Site 169
[UniProt10a]
UniProt: Nucleophile;
Protein-Segment 248 -> 250
[UniProt14]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Protein-Segment 273 -> 275
[UniProt14]
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." http://www.brenda-enzymes.org.

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. 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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

UniProtGOA11a: 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 SRI International Pathway Tools version 19.0 on Sun Apr 26, 2015, biocyc11.