O34714 (OXDC_BACSU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Oxalate decarboxylase OxdC
EC=4.1.1.2

Gene names

Name:	oxdC
Synonyms:	yvrK
Ordered Locus Names:	BSU33240

Organism

Bacillus subtilis (strain 168) [Reference proteome] [HAMAP]

Taxonomic identifier

224308 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › Bacillus subtilis group › Bacillus subtilis › Bacillus subtilis subsp. subtilis

Protein attributes

Sequence length	385 AA.
Sequence status	Complete.
Protein existence	Evidence 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

Keywords
Cellular component	Cytoplasm
Ligand	Manganese Metal-binding
Molecular function	Decarboxylase Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nutrient reservoir activity Inferred from electronic annotation. Source: InterPro oxalate decarboxylase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 385

385

Oxalate decarboxylase OxdC

PRO_0000058106

Sites

Active site

333

1

Proton donor

Metal binding

95

1

Manganese 1

Metal binding

97

1

Manganese 1

Metal binding

101

1

Manganese 1

Metal binding

140

1

Manganese 1

Metal binding

273

1

Manganese 2

Metal binding

275

1

Manganese 2

Metal binding

280

1

Manganese 2

Metal binding

319

1

Manganese 2

Experimental info

Mutagenesis

333

1

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

Secondary structure

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385

Helix Strand Turn

Details...

Beta strand

10 – 12

3

Helix

25 – 30

6

Helix

32 – 35

4

Beta strand

49 – 51

3

Helix

52 – 54

3

Beta strand

58 – 60

3

Beta strand

63 – 68

6

Turn

70 – 72

3

Beta strand

80 – 86

7

Beta strand

91 – 99

9

Beta strand

101 – 115

15

Beta strand

121 – 127

7

Beta strand

130 – 134

5

Beta strand

140 – 156

17

Helix

162 – 164

3

Beta strand

165 – 167

3

Helix

168 – 173

6

Helix

177 – 184

8

Helix

189 – 191

3

Beta strand

200 – 202

3

Helix

210 – 213

4

Beta strand

226 – 229

4

Helix

230 – 232

3

Beta strand

236 – 238

3

Beta strand

239 – 247

9

Turn

248 – 250

3

Beta strand

258 – 264

7

Beta strand

269 – 274

6

Beta strand

276 – 278

3

Beta strand

280 – 296

17

Beta strand

299 – 308

10

Beta strand

310 – 313

4

Beta strand

318 – 323

6

Beta strand

325 – 327

3

Beta strand

329 – 339

11

Helix

345 – 350

6

Helix

354 – 361

8

Helix

365 – 368

4

Beta strand

377 – 379

3

Sequences

	Sequence		Length	Mass (Da)
	O34714 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: A301F5A75E53F4FB	FASTA	385	43,566
	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

References

	« Hide 'large scale' referencesShow '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. , 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.

PIR

E70047.

RefSeq

NP_391204.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

O34714.

SMR

O34714. Positions 8-379.

ModBase

Search...

Protein-protein interaction databases

STRING

224308.BSU33240.

Proteomic databases

PaxDb

O34714.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

CAB15314; CAB15314; BSU33240.

GeneID

938620.

KEGG

bsu:BSU33240.

PATRIC

18978646. VBIBacSub10457_3486.

Organism-specific databases

GenoList

BSU33240. [Micado]

Phylogenomic databases

eggNOG

COG2140.

HOGENOM

HOG000200624.

KO

K01569.

OMA

GHARTFN.

ProtClustDB

CLSK2301483.

Enzyme and pathway databases

BioCyc

BSUB:BSU33240-MONOMER.
MetaCyc:BSU33240-MONOMER.

BRENDA

4.1.1.2. 700.

SABIO-RK

O34714.

Family and domain databases

Gene3D

2.60.120.10. 2 hits.

InterPro

IPR017774. Bicupin_oxalate_deCO2ase/Oxase.
IPR006045. Cupin_1.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view]

Pfam

PF00190. Cupin_1. 2 hits.
[Graphical view]

SMART

SM00835. Cupin_1. 2 hits.
[Graphical view]

SUPFAM

SSF51182. RmlC_like_cupin. 1 hit.

TIGRFAMs

TIGR03404. bicupin_oxalic. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

O34714.

Entry information

Entry name

OXDC_BACSU

Accession

Primary (citable) accession number: O34714

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 6, 2002
Last sequence update:	January 1, 1998
Last modified:	May 1, 2013
This is version 103 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program