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Protein

Oxalyl-CoA decarboxylase

Gene

oxc

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 decarboxylation of oxalyl-CoA to yield carbon dioxide and formyl-CoA.2 Publications

Catalytic activityi

Oxalyl-CoA = formyl-CoA + CO2.2 Publications

Cofactori

Protein has several cofactor binding sites:

Enzyme regulationi

Inhibited by CoA and activated by ADP.

Kineticsi

Kcat is 88 sec(-1) for decarboxylase activity with oxalyl-CoA as substrate (at pH 6.7 and 30 degrees Celsius).

  1. KM=23 µM for oxalyl-CoA (at pH 6.7 and 30 degrees Celsius)2 Publications

    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 sitei34 – 341Substrate; via amide nitrogen
    Binding sitei120 – 1201Substrate
    Binding sitei160 – 1601ADP2 Publications
    Binding sitei222 – 2221ADP2 Publications
    Binding sitei282 – 2821ADP2 Publications
    Binding sitei306 – 3061ADP2 Publications
    Binding sitei326 – 3261ADP; via amide nitrogen2 Publications
    Binding sitei358 – 3581SubstrateBy similarity
    Binding sitei377 – 3771Thiamine pyrophosphate2 Publications
    Metal bindingi452 – 4521Magnesium2 Publications
    Metal bindingi479 – 4791Magnesium2 Publications
    Metal bindingi481 – 4811Magnesium; via carbonyl oxygen2 Publications
    Binding sitei483 – 4831Thiamine pyrophosphate2 Publications

    GO - Molecular functioni

    • ADP binding Source: UniProtKB
    • magnesium ion binding Source: UniProtKB
    • oxalyl-CoA decarboxylase activity Source: UniProtKB
    • thiamine pyrophosphate binding Source: UniProtKB

    GO - Biological processi

    • 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

    BioCyciMetaCyc:MONOMER-16180.
    BRENDAi4.1.1.8. 4478.
    SABIO-RKP40149.
    UniPathwayiUPA00540; UER00599.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Oxalyl-CoA decarboxylase (EC:4.1.1.8)
    Gene namesi
    Name:oxc
    OrganismiOxalobacter formigenes
    Taxonomic identifieri847 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesOxalobacteraceaeOxalobacter

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi56 – 561E → A: Loss of the decarboxylase activity. The mutant forms a dimer and not a tetramer. 1 Publication
    Mutagenesisi120 – 1201Y → A: 3-fold reduction in the affinity binding and strong reduction in the catalytic efficiency for oxalyl-CoA. 1 Publication
    Mutagenesisi120 – 1201Y → F: 2 and 12-fold reduction in the affinity binding and in the catalytic efficiency for oxalyl-CoA, respectively. 1 Publication
    Mutagenesisi121 – 1211E → A: 2-fold reduction in the affinity binding and strong reduction in the catalytic efficiency for oxalyl-CoA. 1 Publication
    Mutagenesisi121 – 1211E → Q: Slight increase of the affinity binding and strong reduction in the catalytic efficiency for oxalyl-CoA. 1 Publication
    Mutagenesisi483 – 4831Y → A: Does not affect oxalyl-CoA binding, but it strongly reduces the catalytic efficiency for oxalyl-CoA. 1 Publication
    Mutagenesisi483 – 4831Y → F: 2-fold reduction in the affinity binding and strong reduction in the catalytic efficiency for oxalyl-CoA. 1 Publication
    Mutagenesisi553 – 5531S → A: Does not affect oxalyl-CoA binding, but it reduces 7-fold the catalytic efficiency for oxalyl-CoA. 1 Publication
    Mutagenesisi555 – 5551R → A: 3-fold reduction in the affinity binding for oxalyl-CoA, but it does not affect the catalytic efficiency. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 568568Oxalyl-CoA decarboxylasePRO_0000090823Add
    BLAST

    Post-translational modificationi

    The N-terminus is blocked.

    Interactioni

    Subunit structurei

    Homotetramer; dimer of dimers.2 Publications

    Protein-protein interaction databases

    DIPiDIP-29437N.
    STRINGi556269.OFBG_01523.

    Structurei

    Secondary structure

    1
    568
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 113Combined sources
    Helixi12 – 2211Combined sources
    Beta strandi27 – 304Combined sources
    Turni34 – 363Combined sources
    Helixi37 – 459Combined sources
    Beta strandi49 – 524Combined sources
    Helixi56 – 7015Combined sources
    Beta strandi74 – 785Combined sources
    Helixi81 – 9717Combined sources
    Beta strandi101 – 1077Combined sources
    Helixi110 – 1145Combined sources
    Helixi125 – 1284Combined sources
    Helixi130 – 1323Combined sources
    Beta strandi133 – 1386Combined sources
    Helixi142 – 1443Combined sources
    Helixi145 – 15713Combined sources
    Beta strandi158 – 1603Combined sources
    Beta strandi163 – 1697Combined sources
    Helixi171 – 1744Combined sources
    Beta strandi176 – 1783Combined sources
    Helixi179 – 1857Combined sources
    Beta strandi190 – 1934Combined sources
    Helixi200 – 21112Combined sources
    Beta strandi214 – 2207Combined sources
    Helixi222 – 2276Combined sources
    Helixi230 – 24011Combined sources
    Beta strandi244 – 2463Combined sources
    Helixi248 – 2503Combined sources
    Helixi263 – 2653Combined sources
    Helixi266 – 2727Combined sources
    Beta strandi274 – 2807Combined sources
    Helixi285 – 2906Combined sources
    Helixi293 – 2953Combined sources
    Beta strandi301 – 3077Combined sources
    Helixi309 – 3113Combined sources
    Beta strandi314 – 3163Combined sources
    Beta strandi319 – 3246Combined sources
    Helixi326 – 33712Combined sources
    Helixi345 – 36723Combined sources
    Helixi377 – 39014Combined sources
    Beta strandi393 – 4019Combined sources
    Helixi402 – 4109Combined sources
    Beta strandi419 – 4224Combined sources
    Turni423 – 4264Combined sources
    Helixi431 – 44212Combined sources
    Beta strandi446 – 4516Combined sources
    Helixi452 – 4565Combined sources
    Helixi459 – 4613Combined sources
    Helixi462 – 4676Combined sources
    Beta strandi472 – 48312Combined sources
    Helixi505 – 5106Combined sources
    Turni511 – 5133Combined sources
    Beta strandi515 – 5217Combined sources
    Helixi522 – 53514Combined sources
    Beta strandi539 – 5457Combined sources
    Helixi554 – 5596Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2C31X-ray1.73A/B1-568[»]
    2JI6X-ray2.06A/B1-568[»]
    2JI7X-ray1.82A/B1-568[»]
    2JI8X-ray2.15A/B1-568[»]
    2JI9X-ray2.20A/B1-568[»]
    2JIBX-ray2.20A/B1-568[»]
    ProteinModelPortaliP40149.
    SMRiP40149. Positions 7-565.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP40149.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni263 – 2675Substrate binding
    Regioni401 – 4033Thiamine pyrophosphate binding
    Regioni408 – 4092Substrate binding
    Regioni426 – 4283Thiamine pyrophosphate binding
    Regioni453 – 4542Thiamine pyrophosphate binding
    Regioni553 – 5553Substrate binding

    Sequence similaritiesi

    Belongs to the TPP enzyme family.Curated

    Phylogenomic databases

    eggNOGiENOG4105CFN. Bacteria.
    COG0028. LUCA.

    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.

    P40149-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSNDDNVELT DGFHVLIDAL KMNDIDTMYG VVGIPITNLA RMWQDDGQRF
    60 70 80 90 100
    YSFRHEQHAG YAASIAGYIE GKPGVCLTVS APGFLNGVTS LAHATTNCFP
    110 120 130 140 150
    MILLSGSSER EIVDLQQGDY EEMDQMNVAR PHCKASFRIN SIKDIPIGIA
    160 170 180 190 200
    RAVRTAVSGR PGGVYVDLPA KLFGQTISVE EANKLLFKPI DPAPAQIPAE
    210 220 230 240 250
    DAIARAADLI KNAKRPVIML GKGAAYAQCD DEIRALVEET GIPFLPMGMA
    260 270 280 290 300
    KGLLPDNHPQ SAAATRAFAL AQCDVCVLIG ARLNWLMQHG KGKTWGDELK
    310 320 330 340 350
    KYVQIDIQAN EMDSNQPIAA PVVGDIKSAV SLLRKALKGA PKADAEWTGA
    360 370 380 390 400
    LKAKVDGNKA KLAGKMTAET PSGMMNYSNS LGVVRDFMLA NPDISLVNEG
    410 420 430 440 450
    ANALDNTRMI VDMLKPRKRL DSGTWGVMGI GMGYCVAAAA VTGKPVIAVE
    460 470 480 490 500
    GDSAFGFSGM ELETICRYNL PVTVIIMNNG GIYKGNEADP QPGVISCTRL
    510 520 530 540 550
    TRGRYDMMME AFGGKGYVAN TPAELKAALE EAVASGKPCL INAMIDPDAG
    560
    VESGRIKSLN VVSKVGKK
    Length:568
    Mass (Da):60,684
    Last modified:February 1, 1995 - v1
    Checksum:iE33DB2E0064497D1
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M77128 Genomic DNA. Translation: AAA53683.1.
    PIRiA55219.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M77128 Genomic DNA. Translation: AAA53683.1.
    PIRiA55219.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2C31X-ray1.73A/B1-568[»]
    2JI6X-ray2.06A/B1-568[»]
    2JI7X-ray1.82A/B1-568[»]
    2JI8X-ray2.15A/B1-568[»]
    2JI9X-ray2.20A/B1-568[»]
    2JIBX-ray2.20A/B1-568[»]
    ProteinModelPortaliP40149.
    SMRiP40149. Positions 7-565.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-29437N.
    STRINGi556269.OFBG_01523.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Phylogenomic databases

    eggNOGiENOG4105CFN. Bacteria.
    COG0028. LUCA.

    Enzyme and pathway databases

    UniPathwayiUPA00540; UER00599.
    BioCyciMetaCyc:MONOMER-16180.
    BRENDAi4.1.1.8. 4478.
    SABIO-RKP40149.

    Miscellaneous databases

    EvolutionaryTraceiP40149.

    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_OXAFO
    AccessioniPrimary (citable) accession number: P40149
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: November 11, 2015
    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, 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.