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O34714

- OXDC_BACSU

UniProt

O34714 - OXDC_BACSU

Protein

Oxalate decarboxylase OxdC

Gene

oxdC

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 110 (01 Oct 2014)
      Sequence version 1 (01 Jan 1998)
      Previous versions | rss
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    Functioni

    Converts oxalate to formate and CO2 in an O(2)-dependent reaction. Can also catalyze minor side reactions: oxalate oxidation to produce H2O2, and oxalate-dependent, H2O(2)-independent dye oxidations.

    Catalytic activityi

    Oxalate = formate + CO2.

    Cofactori

    Binds 2 manganese ions per subunit.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi95 – 951Manganese 1
    Metal bindingi97 – 971Manganese 1
    Metal bindingi101 – 1011Manganese 1
    Metal bindingi140 – 1401Manganese 1
    Metal bindingi273 – 2731Manganese 2
    Metal bindingi275 – 2751Manganese 2
    Metal bindingi280 – 2801Manganese 2
    Metal bindingi319 – 3191Manganese 2
    Active sitei333 – 3331Proton donor

    GO - Molecular functioni

    1. metal ion binding Source: UniProtKB-KW
    2. nutrient reservoir activity Source: InterPro
    3. oxalate decarboxylase activity Source: UniProtKB-EC

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Ligandi

    Manganese, Metal-binding

    Enzyme and pathway databases

    BioCyciBSUB:BSU33240-MONOMER.
    MetaCyc:BSU33240-MONOMER.
    BRENDAi4.1.1.2. 700.
    SABIO-RKO34714.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Oxalate decarboxylase OxdC (EC:4.1.1.2)
    Gene namesi
    Name:oxdC
    Synonyms:yvrK
    Ordered Locus Names:BSU33240
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU33240. [Micado]

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi333 – 3331E → A: 25-fold reduction of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 385385Oxalate decarboxylase OxdCPRO_0000058106Add
    BLAST

    Proteomic databases

    PaxDbiO34714.

    Expressioni

    Inductioni

    Induced by acid pH but not by oxalate. Positively regulated by SigO and its coactivator RsoA.1 Publication

    Interactioni

    Subunit structurei

    Homohexamer.

    Protein-protein interaction databases

    STRINGi224308.BSU33240.

    Structurei

    Secondary structure

    1
    385
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi10 – 123
    Helixi25 – 306
    Helixi32 – 354
    Beta strandi49 – 513
    Helixi52 – 543
    Beta strandi58 – 603
    Beta strandi63 – 686
    Turni70 – 723
    Beta strandi80 – 867
    Beta strandi91 – 999
    Beta strandi101 – 11515
    Beta strandi121 – 1277
    Beta strandi130 – 1345
    Beta strandi140 – 15617
    Helixi162 – 1643
    Beta strandi165 – 1673
    Helixi168 – 1736
    Helixi177 – 1848
    Helixi189 – 1913
    Beta strandi200 – 2023
    Helixi210 – 2134
    Beta strandi226 – 2294
    Helixi230 – 2323
    Beta strandi236 – 2383
    Beta strandi239 – 2479
    Turni248 – 2503
    Beta strandi258 – 2647
    Beta strandi269 – 2746
    Beta strandi276 – 2783
    Beta strandi280 – 29617
    Beta strandi299 – 30810
    Beta strandi310 – 3134
    Beta strandi318 – 3236
    Beta strandi325 – 3273
    Beta strandi329 – 33911
    Helixi345 – 3506
    Helixi354 – 3618
    Helixi365 – 3684
    Beta strandi377 – 3793

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1J58X-ray1.75A1-385[»]
    1L3JX-ray1.90A1-385[»]
    1UW8X-ray2.00A1-385[»]
    2UY8X-ray2.80A1-385[»]
    2UY9X-ray3.10A1-385[»]
    2UYAX-ray2.00A1-385[»]
    2UYBX-ray2.10A1-385[»]
    2V09X-ray1.80A1-385[»]
    3S0MX-ray2.31A6-382[»]
    4METX-ray2.10A/B/C/D1-382[»]
    ProteinModelPortaliO34714.
    SMRiO34714. Positions 8-379.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO34714.

    Family & Domainsi

    Sequence similaritiesi

    To B.subtilis OxdD.Curated

    Phylogenomic databases

    eggNOGiCOG2140.
    HOGENOMiHOG000200624.
    KOiK01569.
    OMAiVEQFPIS.
    OrthoDBiEOG689HPG.
    PhylomeDBiO34714.

    Family and domain databases

    Gene3Di2.60.120.10. 2 hits.
    InterProiIPR017774. Bicupin_oxalate_deCO2ase/Oxase.
    IPR006045. Cupin_1.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view]
    PfamiPF00190. Cupin_1. 2 hits.
    [Graphical view]
    SMARTiSM00835. Cupin_1. 2 hits.
    [Graphical view]
    SUPFAMiSSF51182. SSF51182. 1 hit.
    TIGRFAMsiTIGR03404. bicupin_oxalic. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    O34714-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKKQNDIPQP IRGDKGATVK IPRNIERDRQ NPDMLVPPET DHGTVSNMKF    50
    SFSDTHNRLE KGGYAREVTV RELPISENLA SVNMRLKPGA IRELHWHKEA 100
    EWAYMIYGSA RVTIVDEKGR SFIDDVGEGD LWYFPSGLPH SIQALEEGAE 150
    FLLVFDDGSF SENSTFQLTD WLAHTPKEVI AANFGVTKEE ISNLPGKEKY 200
    IFENQLPGSL KDDIVEGPNG EVPYPFTYRL LEQEPIESEG GKVYIADSTN 250
    FKVSKTIASA LVTVEPGAMR ELHWHPNTHE WQYYISGKAR MTVFASDGHA 300
    RTFNYQAGDV GYVPFAMGHY VENIGDEPLV FLEIFKDDHY ADVSLNQWLA 350
    MLPETFVQAH LDLGKDFTDV LSKEKHPVVK KKCSK 385
    Length:385
    Mass (Da):43,566
    Last modified:January 1, 1998 - v1
    Checksum:iA301F5A75E53F4FB
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ223978 Genomic DNA. Translation: CAA11727.1.
    AL009126 Genomic DNA. Translation: CAB15314.1.
    PIRiE70047.
    RefSeqiNP_391204.1. NC_000964.3.

    Genome annotation databases

    EnsemblBacteriaiCAB15314; CAB15314; BSU33240.
    GeneIDi938620.
    KEGGibsu:BSU33240.
    PATRICi18978646. VBIBacSub10457_3486.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ223978 Genomic DNA. Translation: CAA11727.1 .
    AL009126 Genomic DNA. Translation: CAB15314.1 .
    PIRi E70047.
    RefSeqi NP_391204.1. NC_000964.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1J58 X-ray 1.75 A 1-385 [» ]
    1L3J X-ray 1.90 A 1-385 [» ]
    1UW8 X-ray 2.00 A 1-385 [» ]
    2UY8 X-ray 2.80 A 1-385 [» ]
    2UY9 X-ray 3.10 A 1-385 [» ]
    2UYA X-ray 2.00 A 1-385 [» ]
    2UYB X-ray 2.10 A 1-385 [» ]
    2V09 X-ray 1.80 A 1-385 [» ]
    3S0M X-ray 2.31 A 6-382 [» ]
    4MET X-ray 2.10 A/B/C/D 1-382 [» ]
    ProteinModelPortali O34714.
    SMRi O34714. Positions 8-379.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU33240.

    Proteomic databases

    PaxDbi O34714.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB15314 ; CAB15314 ; BSU33240 .
    GeneIDi 938620.
    KEGGi bsu:BSU33240.
    PATRICi 18978646. VBIBacSub10457_3486.

    Organism-specific databases

    GenoListi BSU33240. [Micado ]

    Phylogenomic databases

    eggNOGi COG2140.
    HOGENOMi HOG000200624.
    KOi K01569.
    OMAi VEQFPIS.
    OrthoDBi EOG689HPG.
    PhylomeDBi O34714.

    Enzyme and pathway databases

    BioCyci BSUB:BSU33240-MONOMER.
    MetaCyc:BSU33240-MONOMER.
    BRENDAi 4.1.1.2. 700.
    SABIO-RK O34714.

    Miscellaneous databases

    EvolutionaryTracei O34714.

    Family and domain databases

    Gene3Di 2.60.120.10. 2 hits.
    InterProi IPR017774. Bicupin_oxalate_deCO2ase/Oxase.
    IPR006045. Cupin_1.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view ]
    Pfami PF00190. Cupin_1. 2 hits.
    [Graphical view ]
    SMARTi SM00835. Cupin_1. 2 hits.
    [Graphical view ]
    SUPFAMi SSF51182. SSF51182. 1 hit.
    TIGRFAMsi TIGR03404. bicupin_oxalic. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The yvsA-yvqA (293 degrees - 289 degrees) region of the Bacillus subtilis chromosome containing genes involved in metal ion uptake and a putative sigma factor."
      Wipat A., Brignell C.S., Guy J.B., Rose M., Emmerson P.T., Harwood C.R.
      Microbiology 144:1593-1600(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    3. "Bacillus subtilis YvrK is an acid-induced oxalate decarboxylase."
      Tanner A., Bornemann S.
      J. Bacteriol. 182:5271-5273(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-15, CHARACTERIZATION.
    4. "Oxalate decarboxylase requires manganese and dioxygen for activity. Overexpression and characterization of Bacillus subtilis YvrK and YoaN."
      Tanner A., Bowater L., Fairhurst S.A., Bornemann S.
      J. Biol. Chem. 276:43627-43634(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
      Strain: 168.
    5. "A previously unidentified sigma factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis."
      MacLellan S.R., Wecke T., Helmann J.D.
      Mol. Microbiol. 69:954-967(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
      Strain: 168 / CU1065.
    6. "Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution."
      Anand R., Dorrestein P.C., Kinsland C., Begley T.P., Ealick S.E.
      Biochemistry 41:7659-7669(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS), MUTAGENESIS OF GLU-333.

    Entry informationi

    Entry nameiOXDC_BACSU
    AccessioniPrimary (citable) accession number: O34714
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 6, 2002
    Last sequence update: January 1, 1998
    Last modified: October 1, 2014
    This is version 110 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, Direct protein sequencing, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references

    External Data

    Dasty 3