OXDC_BACSU
ID OXDC_BACSU Reviewed; 385 AA.
AC O34714;
DT 06-JUN-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Oxalate decarboxylase OxdC {ECO:0000303|PubMed:11546787};
DE EC=4.1.1.2 {ECO:0000269|PubMed:10960116, ECO:0000269|PubMed:11546787, ECO:0000269|PubMed:12056897};
GN Name=oxdC {ECO:0000303|PubMed:11546787};
GN Synonyms=yvrK {ECO:0000303|PubMed:9639930}; OrderedLocusNames=BSU33240;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9639930; DOI=10.1099/00221287-144-6-1593;
RA Wipat A., Brignell C.S., Guy J.B., Rose M., Emmerson P.T., Harwood C.R.;
RT "The yvsA-yvqA (293 degrees - 289 degrees) region of the Bacillus subtilis
RT chromosome containing genes involved in metal ion uptake and a putative
RT sigma factor.";
RL Microbiology 144:1593-1600(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP PROTEIN SEQUENCE OF 1-15, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND INDUCTION.
RX PubMed=10960116; DOI=10.1128/jb.182.18.5271-5273.2000;
RA Tanner A., Bornemann S.;
RT "Bacillus subtilis YvrK is an acid-induced oxalate decarboxylase.";
RL J. Bacteriol. 182:5271-5273(2000).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP PROBABALE SUBUNIT, AND PROBABLE SUBCELLULAR LOCATION.
RC STRAIN=168;
RX PubMed=11546787; DOI=10.1074/jbc.m107202200;
RA Tanner A., Bowater L., Fairhurst S.A., Bornemann S.;
RT "Oxalate decarboxylase requires manganese and dioxygen for activity.
RT Overexpression and characterization of Bacillus subtilis YvrK and YoaN.";
RL J. Biol. Chem. 276:43627-43634(2001).
RN [5]
RP INDUCTION.
RC STRAIN=168 / CU1065;
RX PubMed=18573182; DOI=10.1111/j.1365-2958.2008.06331.x;
RA MacLellan S.R., Wecke T., Helmann J.D.;
RT "A previously unidentified sigma factor and two accessory proteins regulate
RT oxalate decarboxylase expression in Bacillus subtilis.";
RL Mol. Microbiol. 69:954-967(2008).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS), COFACTOR, FUNCTION, CATALYTIC
RP ACTIVITY, ACTIVE SITE, AND MUTAGENESIS OF ARG-270; GLU-333 AND TYR-340.
RX PubMed=12056897; DOI=10.1021/bi0200965;
RA Anand R., Dorrestein P.C., Kinsland C., Begley T.P., Ealick S.E.;
RT "Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A
RT resolution.";
RL Biochemistry 41:7659-7669(2002).
CC -!- FUNCTION: Converts oxalate to formate and CO(2) in an O(2)-dependent
CC reaction. Can also catalyze minor side reactions: oxalate oxidation to
CC produce H(2)O(2), and oxalate-dependent, H(2)O(2)-independent dye
CC oxidations. {ECO:0000269|PubMed:10960116, ECO:0000269|PubMed:11546787,
CC ECO:0000269|PubMed:12056897}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + oxalate = CO2 + formate; Xref=Rhea:RHEA:16509,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15740, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:30623; EC=4.1.1.2; Evidence={ECO:0000269|PubMed:10960116,
CC ECO:0000269|PubMed:11546787, ECO:0000269|PubMed:12056897};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:11546787, ECO:0000269|PubMed:12056897};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000269|PubMed:12056897};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=15 mM for oxalate {ECO:0000269|PubMed:11546787};
CC Vmax=75 umol/min/mg enzyme {ECO:0000269|PubMed:11546787};
CC pH dependence:
CC Optimum pH is 5.0. {ECO:0000269|PubMed:10960116};
CC -!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:11546787,
CC ECO:0000269|PubMed:12056897}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:11546787}.
CC -!- INDUCTION: Induced by acid pH but not by oxalate (PubMed:10960116).
CC Positively regulated by SigO and its coactivator RsoA
CC (PubMed:18573182). {ECO:0000269|PubMed:10960116,
CC ECO:0000269|PubMed:18573182}.
CC -!- SIMILARITY: To B.subtilis OxdD. {ECO:0000305}.
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DR EMBL; AJ223978; CAA11727.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15314.1; -; Genomic_DNA.
DR PIR; E70047; E70047.
DR RefSeq; NP_391204.1; NC_000964.3.
DR RefSeq; WP_003243476.1; NZ_JNCM01000033.1.
DR PDB; 1J58; X-ray; 1.75 A; A=1-385.
DR PDB; 1L3J; X-ray; 1.90 A; A=1-385.
DR PDB; 1UW8; X-ray; 2.00 A; A=1-385.
DR PDB; 2UY8; X-ray; 2.80 A; A=1-385.
DR PDB; 2UY9; X-ray; 3.10 A; A=1-385.
DR PDB; 2UYA; X-ray; 2.00 A; A=1-385.
DR PDB; 2UYB; X-ray; 2.10 A; A=1-385.
DR PDB; 2V09; X-ray; 1.80 A; A=1-385.
DR PDB; 3S0M; X-ray; 2.31 A; A=6-382.
DR PDB; 4MET; X-ray; 2.10 A; A/B/C/D=1-382.
DR PDB; 5HI0; X-ray; 2.60 A; A=1-385.
DR PDB; 5VG3; X-ray; 1.45 A; A/B/C=1-382.
DR PDB; 6TZP; X-ray; 1.72 A; A=1-385.
DR PDB; 6UFI; X-ray; 1.72 A; A=1-385.
DR PDBsum; 1J58; -.
DR PDBsum; 1L3J; -.
DR PDBsum; 1UW8; -.
DR PDBsum; 2UY8; -.
DR PDBsum; 2UY9; -.
DR PDBsum; 2UYA; -.
DR PDBsum; 2UYB; -.
DR PDBsum; 2V09; -.
DR PDBsum; 3S0M; -.
DR PDBsum; 4MET; -.
DR PDBsum; 5HI0; -.
DR PDBsum; 5VG3; -.
DR PDBsum; 6TZP; -.
DR PDBsum; 6UFI; -.
DR AlphaFoldDB; O34714; -.
DR SMR; O34714; -.
DR STRING; 224308.BSU33240; -.
DR DrugBank; DB01942; Formic acid.
DR jPOST; O34714; -.
DR PaxDb; O34714; -.
DR PRIDE; O34714; -.
DR EnsemblBacteria; CAB15314; CAB15314; BSU_33240.
DR GeneID; 938620; -.
DR KEGG; bsu:BSU33240; -.
DR PATRIC; fig|224308.179.peg.3608; -.
DR eggNOG; COG2140; Bacteria.
DR InParanoid; O34714; -.
DR OMA; HARTFNY; -.
DR PhylomeDB; O34714; -.
DR BioCyc; BSUB:BSU33240-MON; -.
DR BioCyc; MetaCyc:BSU33240-MON; -.
DR BRENDA; 4.1.1.2; 658.
DR SABIO-RK; O34714; -.
DR EvolutionaryTrace; O34714; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0046564; F:oxalate decarboxylase activity; IEA:UniProtKB-EC.
DR GO; GO:0033609; P:oxalate metabolic process; IEA:InterPro.
DR Gene3D; 2.60.120.10; -; 2.
DR InterPro; IPR017774; Bicupin_oxalate_deCO2ase/Oxase.
DR InterPro; IPR006045; Cupin_1.
DR InterPro; IPR014710; RmlC-like_jellyroll.
DR InterPro; IPR011051; RmlC_Cupin_sf.
DR Pfam; PF00190; Cupin_1; 2.
DR SMART; SM00835; Cupin_1; 2.
DR SUPFAM; SSF51182; SSF51182; 1.
DR TIGRFAMs; TIGR03404; bicupin_oxalic; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Decarboxylase; Direct protein sequencing; Lyase;
KW Manganese; Metal-binding; Reference proteome.
FT CHAIN 1..385
FT /note="Oxalate decarboxylase OxdC"
FT /id="PRO_0000058106"
FT DOMAIN 50..192
FT /note="Cupin type-1 1"
FT /evidence="ECO:0000255"
FT DOMAIN 228..369
FT /note="Cupin type-1 2"
FT /evidence="ECO:0000255"
FT REGION 24..47
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 333
FT /note="Proton donor"
FT /evidence="ECO:0000269|PubMed:12056897"
FT BINDING 95
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12056897"
FT BINDING 97
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12056897"
FT BINDING 101
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12056897"
FT BINDING 140
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12056897"
FT BINDING 273
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12056897"
FT BINDING 275
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12056897"
FT BINDING 280
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12056897"
FT BINDING 319
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12056897"
FT MUTAGEN 270
FT /note="R->E: Leads to a 20-fold reduction of CO(2)
FT production."
FT /evidence="ECO:0000269|PubMed:12056897"
FT MUTAGEN 333
FT /note="E->A: Leads to a 25-fold reduction of activity and a
FT 4-fold reduction of CO(2) production."
FT /evidence="ECO:0000269|PubMed:12056897"
FT MUTAGEN 340
FT /note="Y->F: Leads to a 13-fold reduction of CO(2)
FT production."
FT /evidence="ECO:0000269|PubMed:12056897"
FT STRAND 10..12
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 25..30
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 32..35
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 49..51
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 58..60
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 63..68
FT /evidence="ECO:0007829|PDB:5VG3"
FT TURN 70..72
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 80..86
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 91..96
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 101..115
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 121..127
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 130..134
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 140..156
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 162..164
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 165..167
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 168..173
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 177..184
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 189..191
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 200..202
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 210..213
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 226..229
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 230..232
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 236..238
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 241..246
FT /evidence="ECO:0007829|PDB:5VG3"
FT TURN 248..250
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 258..264
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 268..274
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 276..278
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 280..296
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 299..306
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 309..313
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 318..323
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 325..327
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 329..339
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 345..350
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 354..361
FT /evidence="ECO:0007829|PDB:5VG3"
FT HELIX 365..368
FT /evidence="ECO:0007829|PDB:5VG3"
FT STRAND 377..380
FT /evidence="ECO:0007829|PDB:5VG3"
SQ SEQUENCE 385 AA; 43566 MW; A301F5A75E53F4FB CRC64;
MKKQNDIPQP IRGDKGATVK IPRNIERDRQ NPDMLVPPET DHGTVSNMKF SFSDTHNRLE
KGGYAREVTV RELPISENLA SVNMRLKPGA IRELHWHKEA EWAYMIYGSA RVTIVDEKGR
SFIDDVGEGD LWYFPSGLPH SIQALEEGAE FLLVFDDGSF SENSTFQLTD WLAHTPKEVI
AANFGVTKEE ISNLPGKEKY IFENQLPGSL KDDIVEGPNG EVPYPFTYRL LEQEPIESEG
GKVYIADSTN FKVSKTIASA LVTVEPGAMR ELHWHPNTHE WQYYISGKAR MTVFASDGHA
RTFNYQAGDV GYVPFAMGHY VENIGDEPLV FLEIFKDDHY ADVSLNQWLA MLPETFVQAH
LDLGKDFTDV LSKEKHPVVK KKCSK
