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 27-MAR-2024, entry version 157. 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}; GN OrderedLocusNames=BSU33240; OS Bacillus subtilis (strain 168). OC Bacteria; Bacillota; 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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; 224308-BSU33240; -. 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 OrthoDB; 1973590at2; -. DR PhylomeDB; O34714; -. DR BioCyc; BSUB:BSU33240-MONOMER; -. DR BioCyc; MetaCyc:BSU33240-MONOMER; -. 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 CDD; cd20305; cupin_OxDC_C; 1. DR CDD; cd20304; cupin_OxDC_N; 1. DR Gene3D; 2.60.120.10; Jelly Rolls; 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 NCBIfam; TIGR03404; bicupin_oxalic; 1. DR PANTHER; PTHR35848:SF6; CUPIN 2 CONSERVED BARREL DOMAIN-CONTAINING PROTEIN; 1. DR PANTHER; PTHR35848; OXALATE-BINDING PROTEIN; 1. DR Pfam; PF00190; Cupin_1; 2. DR SMART; SM00835; Cupin_1; 2. DR SUPFAM; SSF51182; RmlC-like cupins; 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 //