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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)DescriptionActionsGraphical viewLength
    Binding sitei34Substrate; via amide nitrogen1
    Binding sitei120Substrate1
    Binding sitei160ADP2 Publications1
    Binding sitei222ADP2 Publications1
    Binding sitei282ADP2 Publications1
    Binding sitei306ADP2 Publications1
    Binding sitei326ADP; via amide nitrogen2 Publications1
    Binding sitei358SubstrateBy similarity1
    Binding sitei377Thiamine pyrophosphate2 Publications1
    Metal bindingi452Magnesium2 Publications1
    Metal bindingi479Magnesium2 Publications1
    Metal bindingi481Magnesium; via carbonyl oxygen2 Publications1
    Binding sitei483Thiamine pyrophosphate2 Publications1

    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)DescriptionActionsGraphical viewLength
    Mutagenesisi56E → A: Loss of the decarboxylase activity. The mutant forms a dimer and not a tetramer. 1 Publication1
    Mutagenesisi120Y → A: 3-fold reduction in the affinity binding and strong reduction in the catalytic efficiency for oxalyl-CoA. 1 Publication1
    Mutagenesisi120Y → F: 2 and 12-fold reduction in the affinity binding and in the catalytic efficiency for oxalyl-CoA, respectively. 1 Publication1
    Mutagenesisi121E → A: 2-fold reduction in the affinity binding and strong reduction in the catalytic efficiency for oxalyl-CoA. 1 Publication1
    Mutagenesisi121E → Q: Slight increase of the affinity binding and strong reduction in the catalytic efficiency for oxalyl-CoA. 1 Publication1
    Mutagenesisi483Y → A: Does not affect oxalyl-CoA binding, but it strongly reduces the catalytic efficiency for oxalyl-CoA. 1 Publication1
    Mutagenesisi483Y → F: 2-fold reduction in the affinity binding and strong reduction in the catalytic efficiency for oxalyl-CoA. 1 Publication1
    Mutagenesisi553S → A: Does not affect oxalyl-CoA binding, but it reduces 7-fold the catalytic efficiency for oxalyl-CoA. 1 Publication1
    Mutagenesisi555R → A: 3-fold reduction in the affinity binding for oxalyl-CoA, but it does not affect the catalytic efficiency. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000908231 – 568Oxalyl-CoA decarboxylaseAdd BLAST568

    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

    1568
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi9 – 11Combined sources3
    Helixi12 – 22Combined sources11
    Beta strandi27 – 30Combined sources4
    Turni34 – 36Combined sources3
    Helixi37 – 45Combined sources9
    Beta strandi49 – 52Combined sources4
    Helixi56 – 70Combined sources15
    Beta strandi74 – 78Combined sources5
    Helixi81 – 97Combined sources17
    Beta strandi101 – 107Combined sources7
    Helixi110 – 114Combined sources5
    Helixi125 – 128Combined sources4
    Helixi130 – 132Combined sources3
    Beta strandi133 – 138Combined sources6
    Helixi142 – 144Combined sources3
    Helixi145 – 157Combined sources13
    Beta strandi158 – 160Combined sources3
    Beta strandi163 – 169Combined sources7
    Helixi171 – 174Combined sources4
    Beta strandi176 – 178Combined sources3
    Helixi179 – 185Combined sources7
    Beta strandi190 – 193Combined sources4
    Helixi200 – 211Combined sources12
    Beta strandi214 – 220Combined sources7
    Helixi222 – 227Combined sources6
    Helixi230 – 240Combined sources11
    Beta strandi244 – 246Combined sources3
    Helixi248 – 250Combined sources3
    Helixi263 – 265Combined sources3
    Helixi266 – 272Combined sources7
    Beta strandi274 – 280Combined sources7
    Helixi285 – 290Combined sources6
    Helixi293 – 295Combined sources3
    Beta strandi301 – 307Combined sources7
    Helixi309 – 311Combined sources3
    Beta strandi314 – 316Combined sources3
    Beta strandi319 – 324Combined sources6
    Helixi326 – 337Combined sources12
    Helixi345 – 367Combined sources23
    Helixi377 – 390Combined sources14
    Beta strandi393 – 401Combined sources9
    Helixi402 – 410Combined sources9
    Beta strandi419 – 422Combined sources4
    Turni423 – 426Combined sources4
    Helixi431 – 442Combined sources12
    Beta strandi446 – 451Combined sources6
    Helixi452 – 456Combined sources5
    Helixi459 – 461Combined sources3
    Helixi462 – 467Combined sources6
    Beta strandi472 – 483Combined sources12
    Helixi505 – 510Combined sources6
    Turni511 – 513Combined sources3
    Beta strandi515 – 521Combined sources7
    Helixi522 – 535Combined sources14
    Beta strandi539 – 545Combined sources7
    Helixi554 – 559Combined sources6

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP40149.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni263 – 267Substrate binding5
    Regioni401 – 403Thiamine pyrophosphate binding3
    Regioni408 – 409Substrate binding2
    Regioni426 – 428Thiamine pyrophosphate binding3
    Regioni453 – 454Thiamine pyrophosphate binding2
    Regioni553 – 555Substrate binding3

    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
    PDB 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.
    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 2, 2016
    This is version 89 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.