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Protein

Formyl-CoA:oxalate CoA-transferase

Gene

frc

Organism
Oxalobacter formigenes
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the catabolism of oxalate and in the adapatation to low pH via the induction of the oxalate-dependent acid tolerance response (ATR). Essential enzyme for the bacterium survival, as it relies on oxalic acid as its sole source of energy. Catalyzes the transfer of the CoA moiety from formyl-CoA to oxalate. It can also use succinate as acceptor.5 Publications

Catalytic activityi

Formyl-CoA + oxalate = formate + oxalyl-CoA.UniRule annotation5 Publications

Enzyme regulationi

Inhibited by the sulfhydryl reagents N-ethylmaleimide and p-chloromercuribenzoate, and by chloride. Competitively inhibited by acetyl-CoA.3 Publications

Kineticsi

Kcat is 5.3 sec(-1) for CoA-transferase activity with formyl-CoA as substrate (with oxalate as acceptor at pH 6.7 and 30 degrees Celsius. Kcat is 149 sec(-1) for CoA-transferase activity with formyl-CoA as substrate (with succinate as acceptor at pH 6.7 and 30 degrees Celsius.PubMed:18245280).

  1. KM=2 µM for formyl-CoA (with oxalate as acceptor at pH 6.7 and 30 degrees Celsius. PubMed:18245280 and 18162462)4 Publications
  2. KM=8 µM for formyl-CoA (with oxalate as acceptor at pH 6.7 and 30 degrees Celsius. PubMed:15213226)4 Publications
  3. KM=16 µM for formyl-CoA (with succinate as acceptor at pH 6.7 and 30 degrees Celsius. PubMed:18245280)4 Publications
  4. KM=0.32 mM for succinate (with formyl-CoA as donor at pH 6.7 and 30 degrees Celsius. PubMed:18245280)4 Publications
  5. KM=2.3 mM for succinate (with formyl-CoA as donor at pH 6.8 and 25 degrees Celsius. PubMed:2361939)4 Publications
  6. KM=3 mM for formyl-CoA (with oxalate as acceptor at pH 6.8 and 25 degrees Celsius. PubMed:2361939)4 Publications
  7. KM=3.9 mM for oxalate (with formyl-CoA as donor at pH 6.7 and 30 degrees Celsius. PubMed:18245280 and 15213226)4 Publications
  8. KM=5.1 mM for oxalate4 Publications
  1. Vmax=6.4 µmol/min/mg enzyme with oxalate as substrate (with formyl-CoA as donor at pH 6.8 and 25 degrees Celsius. PubMed:2361939)4 Publications
  2. Vmax=19.2 µmol/min/mg enzyme with succinate as substrate (with formyl-CoA as donor at pH 6.8 and 25 degrees Celsius. PubMed:2361939)4 Publications
  3. Vmax=29.6 µmol/min/mg enzyme with formyl-CoA as substrate (with oxalate as acceptor at pH 6.8 and 25 degrees Celsius. PubMed:2361939)4 Publications

pH dependencei

Optimum pH is between 6.5 and 7.5.4 Publications

Pathwayi: oxalate degradation

This protein is involved in step 1 of the subpathway that synthesizes CO(2) and formate from oxalate.UniRule annotation
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Formyl-CoA:oxalate CoA-transferase (frc)
  2. Oxalyl-CoA decarboxylase (oxc)
This subpathway is part of the pathway oxalate degradation, which is itself part of Metabolic intermediate degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes CO(2) and formate from oxalate, the pathway oxalate degradation and in Metabolic intermediate degradation.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei38 – 381Coenzyme AUniRule annotation3 Publications
Binding sitei104 – 1041Coenzyme AUniRule annotation3 Publications
Active sitei169 – 1691NucleophileUniRule annotation1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16179.
BRENDAi2.8.3.16. 4478.
UniPathwayiUPA00540; UER00598.

Names & Taxonomyi

Protein namesi
Recommended name:
Formyl-CoA:oxalate CoA-transferase (EC:2.8.3.16UniRule annotation)
Short name:
FCOCT
Alternative name(s):
Formyl-coenzyme A transferaseUniRule annotation
Gene namesi
Name:frcUniRule annotation
OrganismiOxalobacter formigenes
Taxonomic identifieri847 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesOxalobacteraceaeOxalobacter

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi17 – 171Q → A: 45-fold decrease of the catalytic effiency. 1 Publication
Mutagenesisi48 – 481W → F: Little change in the affinity binding and catalytic efficiency, and it does not display major structural changes. 1 Publication
Mutagenesisi48 – 481W → P: Little change in the affinity binding and catalytic efficiency. It exhibits substrate inhibition with oxalate. It does not display major structural changes. 1 Publication
Mutagenesisi169 – 1691D → A: Loss of CoA-transferase activity. 1 Publication
Mutagenesisi169 – 1691D → E: Loss of CoA-transferase activity. 1 Publication
Mutagenesisi169 – 1691D → S: Loss of CoA-transferase activity. 1 Publication
Mutagenesisi259 – 2591G → A: 2.5-fold decrease of the catalytic effiency. 1 Publication
Mutagenesisi260 – 2601G → A: 25-fold decrease of the catalytic effiency. Reduction of the affinity binding for both formyl-CoA and oxalate. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved
Chaini2 – 428427Formyl-CoA:oxalate CoA-transferasePRO_0000194720Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation5 Publications

Protein-protein interaction databases

STRINGi556269.OFBG_01036.

Structurei

Secondary structure

1
428
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni4 – 74Combined sources
Beta strandi9 – 124Combined sources
Helixi18 – 2811Combined sources
Beta strandi32 – 387Combined sources
Turni39 – 413Combined sources
Helixi44 – 474Combined sources
Helixi58 – 614Combined sources
Turni62 – 665Combined sources
Beta strandi68 – 725Combined sources
Beta strandi74 – 763Combined sources
Helixi77 – 8913Combined sources
Beta strandi91 – 955Combined sources
Helixi101 – 1044Combined sources
Helixi109 – 1157Combined sources
Beta strandi120 – 1278Combined sources
Turni132 – 1354Combined sources
Helixi140 – 1467Combined sources
Turni147 – 1493Combined sources
Helixi150 – 1523Combined sources
Helixi169 – 19022Combined sources
Beta strandi195 – 1995Combined sources
Helixi200 – 2078Combined sources
Helixi209 – 22113Combined sources
Helixi228 – 2303Combined sources
Turni232 – 2343Combined sources
Turni238 – 2403Combined sources
Helixi245 – 2473Combined sources
Beta strandi261 – 2688Combined sources
Turni270 – 2745Combined sources
Beta strandi279 – 2835Combined sources
Helixi286 – 2883Combined sources
Helixi289 – 2957Combined sources
Helixi299 – 3013Combined sources
Turni305 – 3073Combined sources
Helixi310 – 3134Combined sources
Turni314 – 3163Combined sources
Helixi317 – 32610Combined sources
Turni327 – 3304Combined sources
Helixi333 – 34210Combined sources
Beta strandi347 – 3493Combined sources
Helixi353 – 3575Combined sources
Helixi360 – 3645Combined sources
Beta strandi367 – 3715Combined sources
Turni374 – 3763Combined sources
Beta strandi379 – 3824Combined sources
Beta strandi385 – 3906Combined sources
Turni401 – 4044Combined sources
Helixi405 – 4117Combined sources
Helixi416 – 4249Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1P5HX-ray2.20A/B1-428[»]
1P5RX-ray2.50A/B1-428[»]
1T3ZX-ray2.30A/B2-428[»]
1T4CX-ray2.61A/B2-428[»]
1VGQX-ray2.13A/B2-428[»]
1VGRX-ray2.10A/B2-428[»]
2VJKX-ray1.97A/B1-428[»]
2VJLX-ray2.00A/B1-428[»]
2VJMX-ray1.89A/B1-428[»]
2VJNX-ray2.00A/B1-428[»]
2VJOX-ray2.20A/B1-428[»]
2VJPX-ray1.95A/B1-428[»]
2VJQX-ray1.80A/B/C/D1-428[»]
ProteinModelPortaliO06644.
SMRiO06644. Positions 2-428.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO06644.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni15 – 184Coenzyme A binding
Regioni72 – 754Coenzyme A binding
Regioni96 – 983Coenzyme A binding
Regioni137 – 1404Coenzyme A binding
Regioni260 – 2623Substrate binding

Sequence similaritiesi

Belongs to the CaiB/BaiF CoA-transferase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C04. Bacteria.
COG1804. LUCA.
KOiK07749.

Family and domain databases

Gene3Di3.40.50.10540. 2 hits.
HAMAPiMF_00742. Formyl_CoA_transfer.
InterProiIPR003673. CoA-Trfase_fam_III.
IPR023606. CoA-Trfase_III_dom.
IPR017659. Formyl_CoA_transfer.
[Graphical view]
PfamiPF02515. CoA_transf_3. 2 hits.
[Graphical view]
SUPFAMiSSF89796. SSF89796. 1 hit.
TIGRFAMsiTIGR03253. oxalate_frc. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O06644-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKPLDGINV LDFTHVQAGP ACTQMMGFLG ANVIKIERRG SGDMTRGWLQ
60 70 80 90 100
DKPNVDSLYF TMFNCNKRSI ELDMKTPEGK ELLEQMIKKA DVMVENFGPG
110 120 130 140 150
ALDRMGFTWE YIQELNPRVI LASVKGYAEG HANEHLKVYE NVAQCSGGAA
160 170 180 190 200
ATTGFWDGPP TVSGAALGDS NSGMHLMIGI LAALEMRHKT GRGQKVAVAM
210 220 230 240 250
QDAVLNLVRI KLRDQQRLER TGILAEYPQA QPNFAFDRDG NPLSFDNITS
260 270 280 290 300
VPRGGNAGGG GQPGWMLKCK GWETDADSYV YFTIAANMWP QICDMIDKPE
310 320 330 340 350
WKDDPAYNTF EGRVDKLMDI FSFIETKFAD KDKFEVTEWA AQYGIPCGPV
360 370 380 390 400
MSMKELAHDP SLQKVGTVVE VVDEIRGNHL TVGAPFKFSG FQPEITRAPL
410 420
LGEHTDEVLK ELGLDDAKIK ELHAKQVV
Length:428
Mass (Da):47,327
Last modified:January 23, 2007 - v3
Checksum:i386E87C19EA0C8AC
GO

Mass spectrometryi

Molecular mass is 47196 Da from positions 1 - 428. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82167 Genomic DNA. Translation: AAC45298.1.

Genome annotation databases

KEGGiag:AAC45298.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82167 Genomic DNA. Translation: AAC45298.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1P5HX-ray2.20A/B1-428[»]
1P5RX-ray2.50A/B1-428[»]
1T3ZX-ray2.30A/B2-428[»]
1T4CX-ray2.61A/B2-428[»]
1VGQX-ray2.13A/B2-428[»]
1VGRX-ray2.10A/B2-428[»]
2VJKX-ray1.97A/B1-428[»]
2VJLX-ray2.00A/B1-428[»]
2VJMX-ray1.89A/B1-428[»]
2VJNX-ray2.00A/B1-428[»]
2VJOX-ray2.20A/B1-428[»]
2VJPX-ray1.95A/B1-428[»]
2VJQX-ray1.80A/B/C/D1-428[»]
ProteinModelPortaliO06644.
SMRiO06644. Positions 2-428.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi556269.OFBG_01036.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGiag:AAC45298.

Phylogenomic databases

eggNOGiENOG4105C04. Bacteria.
COG1804. LUCA.
KOiK07749.

Enzyme and pathway databases

UniPathwayiUPA00540; UER00598.
BioCyciMetaCyc:MONOMER-16179.
BRENDAi2.8.3.16. 4478.

Miscellaneous databases

EvolutionaryTraceiO06644.

Family and domain databases

Gene3Di3.40.50.10540. 2 hits.
HAMAPiMF_00742. Formyl_CoA_transfer.
InterProiIPR003673. CoA-Trfase_fam_III.
IPR023606. CoA-Trfase_III_dom.
IPR017659. Formyl_CoA_transfer.
[Graphical view]
PfamiPF02515. CoA_transf_3. 2 hits.
[Graphical view]
SUPFAMiSSF89796. SSF89796. 1 hit.
TIGRFAMsiTIGR03253. oxalate_frc. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "DNA sequencing and expression of the formyl coenzyme A transferase gene, frc, from Oxalobacter formigenes."
    Sidhu H., Ogden S.D., Lung H.-Y., Luttge B.G., Baetz A.L., Peck A.B.
    J. Bacteriol. 179:3378-3381(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF N-TERMINUS, FUNCTION, CATALYTIC ACTIVITY.
    Strain: OxB.
  2. "Purification and characterization of formyl-coenzyme A transferase from Oxalobacter formigenes."
    Baetz A.L., Allison M.J.
    J. Bacteriol. 172:3537-3540(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBCELLULAR LOCATION, SUBSTRATE SPECIFICITY, SUBUNIT.
    Strain: OxB.
  3. "Formyl-CoA transferase encloses the CoA binding site at the interface of an interlocked dimer."
    Ricagno S., Jonsson S., Richards N., Lindqvist Y.
    EMBO J. 22:3210-3219(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH COENZYME A, SUBUNIT.
  4. "Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes."
    Jonsson S., Ricagno S., Lindqvist Y., Richards N.G.
    J. Biol. Chem. 279:36003-36012(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 2-428 OF MUTANTS ALA-169; GLU-169; SER-169 IN COMPLEX WITH COENZYME A, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-169, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM, SUBUNIT.
  5. "Differential substrate specificity and kinetic behavior of Escherichia coli YfdW and Oxalobacter formigenes formyl coenzyme A transferase."
    Toyota C.G., Berthold C.L., Gruez A., Jonsson S., Lindqvist Y., Cambillau C., Richards N.G.
    J. Bacteriol. 190:2556-2564(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF MUTANTS PRO-48 AND PHE-48, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF TRP-48, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBSTRATE SPECIFICITY, SUBUNIT.
  6. "Reinvestigation of the catalytic mechanism of formyl-CoA transferase, a class III CoA-transferase."
    Berthold C.L., Toyota C.G., Richards N.G., Lindqvist Y.
    J. Biol. Chem. 283:6519-6529(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS) OF MUTANTS ALA-17 AND ALA-260 IN COMPLEX WITH COENZYME A AND SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLN-17; GLY-259 AND GLY-260, BIOPHYSICOCHEMICAL PROPERTIES, MASS SPECTROMETRY, ENZYME REGULATION, REACTION MECHANISM, SUBUNIT.

Entry informationi

Entry nameiFCTA_OXAFO
AccessioniPrimary (citable) accession number: O06644
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 20, 2002
Last sequence update: January 23, 2007
Last modified: April 13, 2016
This is version 100 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.