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O34714

- OXDC_BACSU

UniProt

O34714 - OXDC_BACSU

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Protein

Oxalate decarboxylase OxdC

Gene

oxdC

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - 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

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-KW
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 – 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.
InParanoidiO34714.
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

        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:
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.
InParanoidi O34714.
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

« 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: October 29, 2014
This is version 111 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