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Protein

Oxalate decarboxylase OxdC

Gene

oxdC

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

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

Mn2+Note: 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
Complete GO annotation...

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
Complete GO annotation...

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 – 123Combined sources
Helixi25 – 306Combined sources
Helixi32 – 354Combined sources
Beta strandi49 – 513Combined sources
Helixi52 – 543Combined sources
Beta strandi58 – 603Combined sources
Beta strandi63 – 686Combined sources
Turni70 – 723Combined sources
Beta strandi80 – 867Combined sources
Beta strandi91 – 966Combined sources
Beta strandi101 – 11515Combined sources
Beta strandi121 – 1277Combined sources
Beta strandi130 – 1345Combined sources
Beta strandi140 – 15617Combined sources
Helixi162 – 1643Combined sources
Beta strandi165 – 1673Combined sources
Helixi168 – 1736Combined sources
Helixi177 – 1848Combined sources
Helixi189 – 1913Combined sources
Beta strandi200 – 2023Combined sources
Helixi210 – 2134Combined sources
Beta strandi226 – 2294Combined sources
Helixi230 – 2323Combined sources
Beta strandi236 – 2383Combined sources
Beta strandi241 – 2477Combined sources
Turni248 – 2503Combined sources
Beta strandi258 – 2647Combined sources
Beta strandi268 – 2747Combined sources
Beta strandi276 – 2783Combined sources
Beta strandi280 – 29617Combined sources
Beta strandi299 – 3068Combined sources
Beta strandi309 – 3135Combined sources
Beta strandi318 – 3236Combined sources
Beta strandi325 – 3273Combined sources
Beta strandi329 – 33911Combined sources
Helixi345 – 3506Combined sources
Helixi354 – 3618Combined sources
Helixi365 – 3684Combined sources
Beta strandi377 – 3804Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiO34714.
KOiK01569.
OMAiHARTFNY.
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

        10         20         30         40         50
MKKQNDIPQP IRGDKGATVK IPRNIERDRQ NPDMLVPPET DHGTVSNMKF
60 70 80 90 100
SFSDTHNRLE KGGYAREVTV RELPISENLA SVNMRLKPGA IRELHWHKEA
110 120 130 140 150
EWAYMIYGSA RVTIVDEKGR SFIDDVGEGD LWYFPSGLPH SIQALEEGAE
160 170 180 190 200
FLLVFDDGSF SENSTFQLTD WLAHTPKEVI AANFGVTKEE ISNLPGKEKY
210 220 230 240 250
IFENQLPGSL KDDIVEGPNG EVPYPFTYRL LEQEPIESEG GKVYIADSTN
260 270 280 290 300
FKVSKTIASA LVTVEPGAMR ELHWHPNTHE WQYYISGKAR MTVFASDGHA
310 320 330 340 350
RTFNYQAGDV GYVPFAMGHY VENIGDEPLV FLEIFKDDHY ADVSLNQWLA
360 370 380
MLPETFVQAH LDLGKDFTDV LSKEKHPVVK KKCSK
Length:385
Mass (Da):43,566
Last modified:January 1, 1998 - v1
Checksum:iA301F5A75E53F4FB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
AJ223978 Genomic DNA. Translation: CAA11727.1.
AL009126 Genomic DNA. Translation: CAB15314.1.
PIRiE70047.
RefSeqiNP_391204.1. NC_000964.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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...

Protein-protein interaction databases

STRINGi224308.BSU33240.

Proteomic databases

PaxDbiO34714.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

GenoListiBSU33240. [Micado]

Phylogenomic databases

eggNOGiCOG2140.
HOGENOMiHOG000200624.
InParanoidiO34714.
KOiK01569.
OMAiHARTFNY.
OrthoDBiEOG689HPG.
PhylomeDBiO34714.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiO34714.

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.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: February 4, 2015
This is version 114 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

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 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.