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Protein

Oxalyl-CoA decarboxylase

Gene

oxc

Organism
Escherichia coli (strain K12)
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). Catalyzes the decarboxylation of oxalyl-CoA to yield carbon dioxide and formyl-CoA.1 Publication

Catalytic activityi

Oxalyl-CoA = formyl-CoA + CO2.1 Publication

Cofactori

Protein has several cofactor binding sites:
  • Mg2+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication
  • thiamine diphosphate1 PublicationNote: Binds 1 thiamine pyrophosphate per subunit.1 Publication

Enzyme regulationi

Activated by ADP.1 Publication

Kineticsi

Kcat is 69.7 sec(-1) for decarboxylase activity with oxalyl-CoA as substrate (with 300 µM ADP at pH 6.5 and 30 degrees Celsius). Kcat is 60.7 sec(-1) for decarboxylase activity with oxalyl-CoA as substrate (at pH 6.5 and 30 degrees Celsius).

  1. KM=3.17 µM for oxalyl-CoA (with 300 µM ADP at pH 6.5 and 30 degrees Celsius)1 Publication
  2. KM=4.8 µM for oxalyl-CoA (at pH 6.5 and 30 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is between 5.5 and 7.1 Publication

    Pathwayi: oxalate degradation

    This protein is involved in step 2 of the subpathway that synthesizes CO(2) and formate from oxalate.
    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 sitei32 – 321Substrate; via amide nitrogenBy similarity
    Binding sitei118 – 1181SubstrateBy similarity
    Binding sitei158 – 1581ADP1 Publication
    Binding sitei220 – 2201ADP1 Publication
    Binding sitei280 – 2801ADP1 Publication
    Binding sitei302 – 3021ADP1 Publication
    Binding sitei322 – 3221ADP; via amide nitrogen1 Publication
    Binding sitei355 – 3551Substrate
    Binding sitei372 – 3721Thiamine pyrophosphate1 Publication
    Metal bindingi447 – 4471Magnesium1 Publication
    Metal bindingi474 – 4741Magnesium1 Publication
    Metal bindingi476 – 4761Magnesium; via carbonyl oxygen1 Publication
    Binding sitei478 – 4781Thiamine pyrophosphate; via amide nitrogen1 Publication

    GO - Molecular functioni

    • ADP binding Source: EcoCyc
    • identical protein binding Source: IntAct
    • magnesium ion binding Source: UniProtKB
    • oxalyl-CoA decarboxylase activity Source: EcoCyc
    • thiamine pyrophosphate binding Source: EcoCyc

    GO - Biological processi

    • cellular response to acidic pH Source: EcoCyc
    • oxalate catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding, Nucleotide-binding, Thiamine pyrophosphate

    Enzyme and pathway databases

    BioCyciEcoCyc:G7236-MONOMER.
    ECOL316407:JW2370-MONOMER.
    MetaCyc:G7236-MONOMER.
    BRENDAi4.1.1.8. 2026.
    UniPathwayiUPA00540; UER00599.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Oxalyl-CoA decarboxylase (EC:4.1.1.8)
    Gene namesi
    Name:oxc
    Synonyms:yfdU
    Ordered Locus Names:b2373, JW2370
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG14143. oxc.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 564564Oxalyl-CoA decarboxylasePRO_0000090824Add
    BLAST

    Proteomic databases

    PaxDbiP0AFI0.
    PRIDEiP0AFI0.

    Expressioni

    Inductioni

    By the acid response regulator EvgA.1 Publication

    Interactioni

    Subunit structurei

    Homotetramer; dimer of dimers.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself4EBI-557143,EBI-557143

    GO - Molecular functioni

    • identical protein binding Source: IntAct

    Protein-protein interaction databases

    BioGridi4260862. 15 interactions.
    DIPiDIP-48075N.
    IntActiP0AFI0. 6 interactions.
    MINTiMINT-7717811.
    STRINGi511145.b2373.

    Structurei

    Secondary structure

    1
    564
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi7 – 93Combined sources
    Helixi10 – 2011Combined sources
    Beta strandi25 – 284Combined sources
    Turni32 – 343Combined sources
    Helixi35 – 439Combined sources
    Beta strandi47 – 504Combined sources
    Helixi54 – 6815Combined sources
    Beta strandi72 – 765Combined sources
    Helixi79 – 9517Combined sources
    Beta strandi99 – 1057Combined sources
    Helixi108 – 1125Combined sources
    Helixi123 – 1275Combined sources
    Helixi128 – 1303Combined sources
    Beta strandi131 – 1366Combined sources
    Helixi140 – 1423Combined sources
    Helixi143 – 15513Combined sources
    Beta strandi156 – 1583Combined sources
    Beta strandi161 – 1677Combined sources
    Helixi168 – 1725Combined sources
    Beta strandi174 – 1763Combined sources
    Helixi177 – 1826Combined sources
    Beta strandi188 – 1914Combined sources
    Beta strandi194 – 1963Combined sources
    Helixi198 – 21013Combined sources
    Beta strandi212 – 2187Combined sources
    Helixi220 – 2256Combined sources
    Helixi228 – 23811Combined sources
    Beta strandi242 – 2443Combined sources
    Helixi246 – 2483Combined sources
    Helixi261 – 2633Combined sources
    Helixi264 – 2707Combined sources
    Beta strandi272 – 2787Combined sources
    Helixi283 – 2886Combined sources
    Turni289 – 2913Combined sources
    Beta strandi297 – 3037Combined sources
    Helixi305 – 3073Combined sources
    Beta strandi310 – 3123Combined sources
    Beta strandi315 – 3206Combined sources
    Helixi322 – 33514Combined sources
    Helixi342 – 36322Combined sources
    Beta strandi368 – 3703Combined sources
    Helixi372 – 38312Combined sources
    Beta strandi390 – 3967Combined sources
    Helixi397 – 4059Combined sources
    Beta strandi410 – 4123Combined sources
    Beta strandi414 – 4174Combined sources
    Turni418 – 4214Combined sources
    Helixi426 – 43712Combined sources
    Beta strandi441 – 4466Combined sources
    Helixi447 – 4515Combined sources
    Helixi454 – 4563Combined sources
    Helixi457 – 4626Combined sources
    Beta strandi467 – 4737Combined sources
    Beta strandi475 – 4784Combined sources
    Helixi502 – 5098Combined sources
    Beta strandi512 – 5165Combined sources
    Helixi519 – 53214Combined sources
    Beta strandi536 – 5427Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2Q27X-ray2.12A/B1-564[»]
    2Q28X-ray1.74A/B1-564[»]
    2Q29X-ray1.82A/B1-564[»]
    ProteinModelPortaliP0AFI0.
    SMRiP0AFI0. Positions 5-554.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AFI0.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni261 – 2655Substrate bindingCurated
    Regioni396 – 3983Thiamine pyrophosphate binding
    Regioni403 – 4042Substrate binding
    Regioni421 – 4233Thiamine pyrophosphate binding
    Regioni448 – 4492Thiamine pyrophosphate binding
    Regioni550 – 5523Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the TPP enzyme family.Curated

    Phylogenomic databases

    eggNOGiENOG4105CFN. Bacteria.
    COG0028. LUCA.
    HOGENOMiHOG000053808.
    InParanoidiP0AFI0.
    KOiK01577.
    OMAiGIPYLPM.
    OrthoDBiEOG6FNHKQ.
    PhylomeDBiP0AFI0.

    Family and domain databases

    Gene3Di3.40.50.1220. 1 hit.
    3.40.50.970. 2 hits.
    InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
    IPR017660. Oxalyl-CoA_decarboxylase.
    IPR029061. THDP-binding.
    IPR012000. Thiamin_PyroP_enz_cen_dom.
    IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
    IPR011766. TPP_enzyme-bd_C.
    [Graphical view]
    PfamiPF02775. TPP_enzyme_C. 1 hit.
    PF00205. TPP_enzyme_M. 1 hit.
    PF02776. TPP_enzyme_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF52467. SSF52467. 1 hit.
    SSF52518. SSF52518. 2 hits.
    TIGRFAMsiTIGR03254. oxalate_oxc. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P0AFI0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSDQLQMTDG MHIIVEALKQ NNIDTIYGVV GIPVTDMARH AQAEGIRYIG
    60 70 80 90 100
    FRHEQSAGYA AAASGFLTQK PGICLTVSAP GFLNGLTALA NATVNGFPMI
    110 120 130 140 150
    MISGSSDRAI VDLQQGDYEE LDQMNAAKPY AKAAFRVNQP QDLGIALARA
    160 170 180 190 200
    IRVSVSGRPG GVYLDLPANV LAATMEKDEA LTTIVKVENP SPALLPCPKS
    210 220 230 240 250
    VTSAISLLAK AERPLIILGK GAAYSQADEQ LREFIESAQI PFLPMSMAKG
    260 270 280 290 300
    ILEDTHPLSA AAARSFALAN ADVVMLVGAR LNWLLAHGKK GWAADTQFIQ
    310 320 330 340 350
    LDIEPQEIDS NRPIAVPVVG DIASSMQGML AELKQNTFTT PLVWRDILNI
    360 370 380 390 400
    HKQQNAQKMH EKLSTDTQPL NYFNALSAVR DVLRENQDIY LVNEGANTLD
    410 420 430 440 450
    NARNIIDMYK PRRRLDCGTW GVMGIGMGYA IGASVTSGSP VVAIEGDSAF
    460 470 480 490 500
    GFSGMEIETI CRYNLPVTIV IFNNGGIYRG DGVDLSGAGA PSPTDLLHHA
    510 520 530 540 550
    RYDKLMDAFR GVGYNVTTTD ELRHALTTGI QSRKPTIINV VIDPAAGTES
    560
    GHITKLNPKQ VAGN
    Length:564
    Mass (Da):60,581
    Last modified:December 20, 2005 - v1
    Checksum:i94418B2BE7D40C17
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC75432.1.
    AP009048 Genomic DNA. Translation: BAA16245.1.
    PIRiB65011.
    RefSeqiNP_416874.1. NC_000913.3.
    WP_001283490.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75432; AAC75432; b2373.
    BAA16245; BAA16245; BAA16245.
    GeneIDi946845.
    KEGGiecj:JW2370.
    eco:b2373.
    PATRICi32120125. VBIEscCol129921_2471.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC75432.1.
    AP009048 Genomic DNA. Translation: BAA16245.1.
    PIRiB65011.
    RefSeqiNP_416874.1. NC_000913.3.
    WP_001283490.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2Q27X-ray2.12A/B1-564[»]
    2Q28X-ray1.74A/B1-564[»]
    2Q29X-ray1.82A/B1-564[»]
    ProteinModelPortaliP0AFI0.
    SMRiP0AFI0. Positions 5-554.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260862. 15 interactions.
    DIPiDIP-48075N.
    IntActiP0AFI0. 6 interactions.
    MINTiMINT-7717811.
    STRINGi511145.b2373.

    Proteomic databases

    PaxDbiP0AFI0.
    PRIDEiP0AFI0.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75432; AAC75432; b2373.
    BAA16245; BAA16245; BAA16245.
    GeneIDi946845.
    KEGGiecj:JW2370.
    eco:b2373.
    PATRICi32120125. VBIEscCol129921_2471.

    Organism-specific databases

    EchoBASEiEB3895.
    EcoGeneiEG14143. oxc.

    Phylogenomic databases

    eggNOGiENOG4105CFN. Bacteria.
    COG0028. LUCA.
    HOGENOMiHOG000053808.
    InParanoidiP0AFI0.
    KOiK01577.
    OMAiGIPYLPM.
    OrthoDBiEOG6FNHKQ.
    PhylomeDBiP0AFI0.

    Enzyme and pathway databases

    UniPathwayiUPA00540; UER00599.
    BioCyciEcoCyc:G7236-MONOMER.
    ECOL316407:JW2370-MONOMER.
    MetaCyc:G7236-MONOMER.
    BRENDAi4.1.1.8. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP0AFI0.
    PROiP0AFI0.

    Family and domain databases

    Gene3Di3.40.50.1220. 1 hit.
    3.40.50.970. 2 hits.
    InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
    IPR017660. Oxalyl-CoA_decarboxylase.
    IPR029061. THDP-binding.
    IPR012000. Thiamin_PyroP_enz_cen_dom.
    IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
    IPR011766. TPP_enzyme-bd_C.
    [Graphical view]
    PfamiPF02775. TPP_enzyme_C. 1 hit.
    PF00205. TPP_enzyme_M. 1 hit.
    PF02776. TPP_enzyme_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF52467. SSF52467. 1 hit.
    SSF52518. SSF52518. 2 hits.
    TIGRFAMsiTIGR03254. oxalate_oxc. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "YfdW and YfdU are required for oxalate-induced acid tolerance in Escherichia coli K-12."
      Fontenot E.M., Ezelle K.E., Gabreski L.N., Giglio E.R., McAfee J.M., Mills A.C., Qureshi M.N., Salmon K.M., Toyota C.G.
      J. Bacteriol. 195:1446-1455(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    5. "New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli."
      Werther T., Zimmer A., Wille G., Golbik R., Weiss M.S., Konig S.
      FEBS J. 277:2628-2640(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.74 ANGSTROMS) IN COMPLEX WITH THIAMINE PYROPHOSPHATE; SUBSTRATE ANALOGS; ADP AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, COFACTOR, SUBUNIT.

    Entry informationi

    Entry nameiOXC_ECOLI
    AccessioniPrimary (citable) accession number: P0AFI0
    Secondary accession number(s): P78093, P78194, P78195
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 20, 2005
    Last sequence update: December 20, 2005
    Last modified: January 20, 2016
    This is version 87 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.