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



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

Synonyms: yfdW

Regulation Summary Diagram: ?

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].

Gene Citations: [Masuda03]

Locations: cytosol

Map Position: [2,490,026 <- 2,491,276] (53.67 centisomes)
Length: 1251 bp / 416 aa

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

In Paralogous Gene Group: 14 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation 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 [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism metabolism of other compounds

Essentiality data for frc 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]

Credits:
Last-Curated ? 13-Feb-2013 by Keseler I , 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.

Reversibility of this reaction is unspecified.

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 75
[UniProt10a]
UniProt: Coenzyme A;
Amino-Acid-Sites-That-Bind 96
[UniProt10a]
UniProt: Coenzyme A;
Amino-Acid-Sites-That-Bind 98
[UniProt10a]
UniProt: Coenzyme A;
Protein-Segment 137 -> 140
[UniProt10]
UniProt: Coenzyme A binding; Sequence Annotation Type: region of interest;
Active-Site 169
[UniProt10a]
UniProt: Nucleophile;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

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

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.

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

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, 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

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

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.

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."

Other References Related to Gene Regulation

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 Sat Dec 20, 2014, BIOCYC14A.