PYRF_BACSU
ID PYRF_BACSU Reviewed; 239 AA.
AC P25971;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1992, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Orotidine 5'-phosphate decarboxylase;
DE EC=4.1.1.23;
DE AltName: Full=OMP decarboxylase;
DE Short=OMPDCase;
DE Short=OMPdecase;
GN Name=pyrF; OrderedLocusNames=BSU15550;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1709162; DOI=10.1016/s0021-9258(18)31559-x;
RA Quinn C.L., Stephenson B.T., Switzer R.L.;
RT "Functional organization and nucleotide sequence of the Bacillus subtilis
RT pyrimidine biosynthetic operon.";
RL J. Biol. Chem. 266:9113-9127(1991).
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 X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH UMP, AND SUBUNIT.
RX PubMed=10681442; DOI=10.1073/pnas.259441296;
RA Appleby T.C., Kinsland C., Begley T.P., Ealick S.E.;
RT "The crystal structure and mechanism of orotidine 5'-monophosphate
RT decarboxylase.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:2005-2010(2000).
CC -!- FUNCTION: Catalyzes the decarboxylation of orotidine 5'-monophosphate
CC (OMP) to uridine 5'-monophosphate (UMP).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + orotidine 5'-phosphate = CO2 + UMP;
CC Xref=Rhea:RHEA:11596, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:57538, ChEBI:CHEBI:57865; EC=4.1.1.23;
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC UMP from orotate: step 2/2.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10681442}.
CC -!- SIMILARITY: Belongs to the OMP decarboxylase family. Type 1 subfamily.
CC {ECO:0000305}.
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DR EMBL; M59757; AAA21273.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13429.1; -; Genomic_DNA.
DR PIR; I39845; I39845.
DR RefSeq; NP_389438.1; NC_000964.3.
DR RefSeq; WP_003232107.1; NZ_JNCM01000035.1.
DR PDB; 1DBT; X-ray; 2.40 A; A/B/C=1-239.
DR PDBsum; 1DBT; -.
DR AlphaFoldDB; P25971; -.
DR SMR; P25971; -.
DR IntAct; P25971; 1.
DR MINT; P25971; -.
DR STRING; 224308.BSU15550; -.
DR DrugBank; DB03685; Uridine monophosphate.
DR PaxDb; P25971; -.
DR PRIDE; P25971; -.
DR EnsemblBacteria; CAB13429; CAB13429; BSU_15550.
DR GeneID; 935960; -.
DR KEGG; bsu:BSU15550; -.
DR PATRIC; fig|224308.179.peg.1694; -.
DR eggNOG; COG0284; Bacteria.
DR InParanoid; P25971; -.
DR OMA; NFKIFLD; -.
DR PhylomeDB; P25971; -.
DR BioCyc; BSUB:BSU15550-MON; -.
DR BioCyc; MetaCyc:BSU15550-MON; -.
DR BRENDA; 4.1.1.23; 658.
DR UniPathway; UPA00070; UER00120.
DR EvolutionaryTrace; P25971; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0004590; F:orotidine-5'-phosphate decarboxylase activity; IBA:GO_Central.
DR GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IBA:GO_Central.
DR GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_01200_B; OMPdecase_type1_B; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR014732; OMPdecase.
DR InterPro; IPR018089; OMPdecase_AS.
DR InterPro; IPR001754; OMPdeCOase_dom.
DR InterPro; IPR011060; RibuloseP-bd_barrel.
DR PANTHER; PTHR32119:SF2; PTHR32119:SF2; 1.
DR Pfam; PF00215; OMPdecase; 1.
DR SMART; SM00934; OMPdecase; 1.
DR SUPFAM; SSF51366; SSF51366; 1.
DR TIGRFAMs; TIGR01740; pyrF; 1.
DR PROSITE; PS00156; OMPDECASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Decarboxylase; Lyase; Pyrimidine biosynthesis;
KW Reference proteome.
FT CHAIN 1..239
FT /note="Orotidine 5'-phosphate decarboxylase"
FT /id="PRO_0000134527"
FT ACT_SITE 62
FT /note="Proton donor"
FT BINDING 11
FT /ligand="substrate"
FT BINDING 33
FT /ligand="substrate"
FT BINDING 60..69
FT /ligand="substrate"
FT BINDING 123
FT /ligand="substrate"
FT BINDING 185
FT /ligand="substrate"
FT BINDING 194
FT /ligand="substrate"
FT BINDING 214
FT /ligand="substrate"
FT BINDING 215
FT /ligand="substrate"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 15..21
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 23..25
FT /evidence="ECO:0007829|PDB:1DBT"
FT STRAND 31..34
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 36..42
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 44..52
FT /evidence="ECO:0007829|PDB:1DBT"
FT STRAND 56..63
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 67..78
FT /evidence="ECO:0007829|PDB:1DBT"
FT TURN 79..81
FT /evidence="ECO:0007829|PDB:1DBT"
FT STRAND 83..88
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 93..106
FT /evidence="ECO:0007829|PDB:1DBT"
FT STRAND 115..119
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 127..132
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 140..153
FT /evidence="ECO:0007829|PDB:1DBT"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 163..165
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 166..169
FT /evidence="ECO:0007829|PDB:1DBT"
FT TURN 170..172
FT /evidence="ECO:0007829|PDB:1DBT"
FT STRAND 178..181
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 200..205
FT /evidence="ECO:0007829|PDB:1DBT"
FT STRAND 209..213
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 215..218
FT /evidence="ECO:0007829|PDB:1DBT"
FT HELIX 223..235
FT /evidence="ECO:0007829|PDB:1DBT"
SQ SEQUENCE 239 AA; 25992 MW; DB1743714ED052E7 CRC64;
MKNNLPIIAL DFASAEETLA FLAPFQQEPL FVKVGMELFY QEGPSIVKQL KERNCELFLD
LKLHDIPTTV NKAMKRLASL GVDLVNVHAA GGKKMMQAAL EGLEEGTPAG KKRPSLIAVT
QLTSTSEQIM KDELLIEKSL IDTVVHYSKQ AEESGLDGVV CSVHEAKAIY QAVSPSFLTV
TPGIRMSEDA ANDQVRVATP AIAREKGSSA IVVGRSITKA EDPVKAYKAV RLEWEGIKS
