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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)DescriptionActionsGraphical viewLength
    Binding sitei32Substrate; via amide nitrogenBy similarity1
    Binding sitei118SubstrateBy similarity1
    Binding sitei158ADP1 Publication1
    Binding sitei220ADP1 Publication1
    Binding sitei280ADP1 Publication1
    Binding sitei302ADP1 Publication1
    Binding sitei322ADP; via amide nitrogen1 Publication1
    Binding sitei355Substrate1
    Binding sitei372Thiamine pyrophosphate1 Publication1
    Metal bindingi447Magnesium1 Publication1
    Metal bindingi474Magnesium1 Publication1
    Metal bindingi476Magnesium; via carbonyl oxygen1 Publication1
    Binding sitei478Thiamine pyrophosphate; via amide nitrogen1 Publication1

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG14143. oxc.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000908241 – 564Oxalyl-CoA decarboxylaseAdd BLAST564

    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 interactors.
    DIPiDIP-48075N.
    IntActiP0AFI0. 6 interactors.
    MINTiMINT-7717811.
    STRINGi511145.b2373.

    Structurei

    Secondary structure

    1564
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi7 – 9Combined sources3
    Helixi10 – 20Combined sources11
    Beta strandi25 – 28Combined sources4
    Turni32 – 34Combined sources3
    Helixi35 – 43Combined sources9
    Beta strandi47 – 50Combined sources4
    Helixi54 – 68Combined sources15
    Beta strandi72 – 76Combined sources5
    Helixi79 – 95Combined sources17
    Beta strandi99 – 105Combined sources7
    Helixi108 – 112Combined sources5
    Helixi123 – 127Combined sources5
    Helixi128 – 130Combined sources3
    Beta strandi131 – 136Combined sources6
    Helixi140 – 142Combined sources3
    Helixi143 – 155Combined sources13
    Beta strandi156 – 158Combined sources3
    Beta strandi161 – 167Combined sources7
    Helixi168 – 172Combined sources5
    Beta strandi174 – 176Combined sources3
    Helixi177 – 182Combined sources6
    Beta strandi188 – 191Combined sources4
    Beta strandi194 – 196Combined sources3
    Helixi198 – 210Combined sources13
    Beta strandi212 – 218Combined sources7
    Helixi220 – 225Combined sources6
    Helixi228 – 238Combined sources11
    Beta strandi242 – 244Combined sources3
    Helixi246 – 248Combined sources3
    Helixi261 – 263Combined sources3
    Helixi264 – 270Combined sources7
    Beta strandi272 – 278Combined sources7
    Helixi283 – 288Combined sources6
    Turni289 – 291Combined sources3
    Beta strandi297 – 303Combined sources7
    Helixi305 – 307Combined sources3
    Beta strandi310 – 312Combined sources3
    Beta strandi315 – 320Combined sources6
    Helixi322 – 335Combined sources14
    Helixi342 – 363Combined sources22
    Beta strandi368 – 370Combined sources3
    Helixi372 – 383Combined sources12
    Beta strandi390 – 396Combined sources7
    Helixi397 – 405Combined sources9
    Beta strandi410 – 412Combined sources3
    Beta strandi414 – 417Combined sources4
    Turni418 – 421Combined sources4
    Helixi426 – 437Combined sources12
    Beta strandi441 – 446Combined sources6
    Helixi447 – 451Combined sources5
    Helixi454 – 456Combined sources3
    Helixi457 – 462Combined sources6
    Beta strandi467 – 473Combined sources7
    Beta strandi475 – 478Combined sources4
    Helixi502 – 509Combined sources8
    Beta strandi512 – 516Combined sources5
    Helixi519 – 532Combined sources14
    Beta strandi536 – 542Combined sources7

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP0AFI0.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni261 – 265Substrate bindingCurated5
    Regioni396 – 398Thiamine pyrophosphate binding3
    Regioni403 – 404Substrate binding2
    Regioni421 – 423Thiamine pyrophosphate binding3
    Regioni448 – 449Thiamine pyrophosphate binding2
    Regioni550 – 552Substrate bindingBy similarity3

    Sequence similaritiesi

    Belongs to the TPP enzyme family.Curated

    Phylogenomic databases

    eggNOGiENOG4105CFN. Bacteria.
    COG0028. LUCA.
    HOGENOMiHOG000053808.
    InParanoidiP0AFI0.
    KOiK01577.
    OMAiFRHEQHA.
    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2Q27X-ray2.12A/B1-564[»]
    2Q28X-ray1.74A/B1-564[»]
    2Q29X-ray1.82A/B1-564[»]
    ProteinModelPortaliP0AFI0.
    SMRiP0AFI0.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260862. 15 interactors.
    DIPiDIP-48075N.
    IntActiP0AFI0. 6 interactors.
    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.
    OMAiFRHEQHA.
    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...

    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: November 2, 2016
    This is version 90 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.