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O34714 (OXDC_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 107. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Oxalate decarboxylase OxdC

EC=4.1.1.2
Gene names
Name:oxdC
Synonyms:yvrK
Ordered Locus Names:BSU33240
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length385 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

Oxalate = formate + CO2.

Cofactor

Binds 2 manganese ions per subunit.

Subunit structure

Homohexamer.

Subcellular location

Cytoplasm.

Induction

Induced by acid pH but not by oxalate. Positively regulated by SigO and its coactivator RsoA. Ref.5

Sequence similarities

To B.subtilis OxdD.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 385385Oxalate decarboxylase OxdC
PRO_0000058106

Sites

Active site3331Proton donor
Metal binding951Manganese 1
Metal binding971Manganese 1
Metal binding1011Manganese 1
Metal binding1401Manganese 1
Metal binding2731Manganese 2
Metal binding2751Manganese 2
Metal binding2801Manganese 2
Metal binding3191Manganese 2

Experimental info

Mutagenesis3331E → A: 25-fold reduction of activity. Ref.6

Secondary structure

......................................................................... 385
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O34714 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: A301F5A75E53F4FB

FASTA38543,566
        10         20         30         40         50         60 
MKKQNDIPQP IRGDKGATVK IPRNIERDRQ NPDMLVPPET DHGTVSNMKF SFSDTHNRLE 

        70         80         90        100        110        120 
KGGYAREVTV RELPISENLA SVNMRLKPGA IRELHWHKEA EWAYMIYGSA RVTIVDEKGR 

       130        140        150        160        170        180 
SFIDDVGEGD LWYFPSGLPH SIQALEEGAE FLLVFDDGSF SENSTFQLTD WLAHTPKEVI 

       190        200        210        220        230        240 
AANFGVTKEE ISNLPGKEKY IFENQLPGSL KDDIVEGPNG EVPYPFTYRL LEQEPIESEG 

       250        260        270        280        290        300 
GKVYIADSTN FKVSKTIASA LVTVEPGAMR ELHWHPNTHE WQYYISGKAR MTVFASDGHA 

       310        320        330        340        350        360 
RTFNYQAGDV GYVPFAMGHY VENIGDEPLV FLEIFKDDHY ADVSLNQWLA MLPETFVQAH 

       370        380 
LDLGKDFTDV LSKEKHPVVK KKCSK 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ223978 Genomic DNA. Translation: CAA11727.1.
AL009126 Genomic DNA. Translation: CAB15314.1.
PIRE70047.
RefSeqNP_391204.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalO34714.
SMRO34714. Positions 8-379.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING224308.BSU33240.

Proteomic databases

PaxDbO34714.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB15314; CAB15314; BSU33240.
GeneID938620.
KEGGbsu:BSU33240.
PATRIC18978646. VBIBacSub10457_3486.

Organism-specific databases

GenoListBSU33240. [Micado]

Phylogenomic databases

eggNOGCOG2140.
HOGENOMHOG000200624.
KOK01569.
OMAITDSTNF.
OrthoDBEOG689HPG.
ProtClustDBCLSK2301483.

Enzyme and pathway databases

BioCycBSUB:BSU33240-MONOMER.
MetaCyc:BSU33240-MONOMER.
BRENDA4.1.1.2. 700.
SABIO-RKO34714.

Family and domain databases

Gene3D2.60.120.10. 2 hits.
InterProIPR017774. Bicupin_oxalate_deCO2ase/Oxase.
IPR006045. Cupin_1.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view]
PfamPF00190. Cupin_1. 2 hits.
[Graphical view]
SMARTSM00835. Cupin_1. 2 hits.
[Graphical view]
SUPFAMSSF51182. SSF51182. 1 hit.
TIGRFAMsTIGR03404. bicupin_oxalic. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceO34714.

Entry information

Entry nameOXDC_BACSU
AccessionPrimary (citable) accession number: O34714
Entry history
Integrated into UniProtKB/Swiss-Prot: June 6, 2002
Last sequence update: January 1, 1998
Last modified: April 16, 2014
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList