RIBA_VIBPA
ID RIBA_VIBPA Reviewed; 198 AA.
AC Q87NE7;
DT 30-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2003, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=GTP cyclohydrolase-2 {ECO:0000255|HAMAP-Rule:MF_00179};
DE EC=3.5.4.25 {ECO:0000255|HAMAP-Rule:MF_00179};
DE AltName: Full=GTP cyclohydrolase II {ECO:0000255|HAMAP-Rule:MF_00179};
GN Name=ribA {ECO:0000255|HAMAP-Rule:MF_00179}; OrderedLocusNames=VP1921;
OS Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=223926;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RIMD 2210633;
RX PubMed=12620739; DOI=10.1016/s0140-6736(03)12659-1;
RA Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K.,
RA Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S.,
RA Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.;
RT "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism
RT distinct from that of V. cholerae.";
RL Lancet 361:743-749(2003).
CC -!- FUNCTION: Catalyzes the conversion of GTP to 2,5-diamino-6-
CC ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and
CC pyrophosphate. {ECO:0000255|HAMAP-Rule:MF_00179}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GTP + 4 H2O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-
CC pyrimidine + formate + 3 H(+) + 2 phosphate; Xref=Rhea:RHEA:23704,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15740,
CC ChEBI:CHEBI:37565, ChEBI:CHEBI:43474, ChEBI:CHEBI:58614; EC=3.5.4.25;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00179};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00179};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00179};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 1/4. {ECO:0000255|HAMAP-
CC Rule:MF_00179}.
CC -!- SIMILARITY: Belongs to the GTP cyclohydrolase II family.
CC {ECO:0000255|HAMAP-Rule:MF_00179}.
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DR EMBL; BA000031; BAC60184.1; -; Genomic_DNA.
DR RefSeq; NP_798300.1; NC_004603.1.
DR RefSeq; WP_005490705.1; NC_004603.1.
DR AlphaFoldDB; Q87NE7; -.
DR SMR; Q87NE7; -.
DR STRING; 223926.28806913; -.
DR EnsemblBacteria; BAC60184; BAC60184; BAC60184.
DR GeneID; 1189428; -.
DR KEGG; vpa:VP1921; -.
DR PATRIC; fig|223926.6.peg.1836; -.
DR eggNOG; COG0807; Bacteria.
DR HOGENOM; CLU_020273_2_1_6; -.
DR OMA; DERDYTV; -.
DR UniPathway; UPA00275; UER00400.
DR Proteomes; UP000002493; Chromosome 1.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003935; F:GTP cyclohydrolase II activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd00641; GTP_cyclohydro2; 1.
DR Gene3D; 3.40.50.10990; -; 1.
DR HAMAP; MF_00179; RibA; 1.
DR InterPro; IPR032677; GTP_cyclohydro_II.
DR InterPro; IPR000926; RibA.
DR InterPro; IPR036144; RibA-like_sf.
DR Pfam; PF00925; GTP_cyclohydro2; 1.
DR SUPFAM; SSF142695; SSF142695; 1.
DR TIGRFAMs; TIGR00505; ribA; 1.
PE 3: Inferred from homology;
KW GTP-binding; Hydrolase; Metal-binding; Nucleotide-binding;
KW Reference proteome; Riboflavin biosynthesis; Zinc.
FT CHAIN 1..198
FT /note="GTP cyclohydrolase-2"
FT /id="PRO_0000151779"
FT ACT_SITE 128
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00179"
FT ACT_SITE 130
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00179"
FT BINDING 52..56
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00179"
FT BINDING 57
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00179"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00179"
FT BINDING 70
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00179"
FT BINDING 73
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00179"
FT BINDING 94..96
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00179"
FT BINDING 116
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00179"
FT BINDING 151
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00179"
FT BINDING 156
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00179"
SQ SEQUENCE 198 AA; 22308 MW; A351795D61D44A1A CRC64;
MAEVRARVDF KVGAKSNIDA EILSFRGLKT DKEHVAVIFK QADQTQDTPL VRMHSECLTG
DVFHSSRCDC GEQLEETIQR MGESGGVILY LRQEGRGIGL YNKIDAYRLQ SQGMNTYEAN
NHLGFDDDLR DFTEAAQMLE ALGIKKIRLV TNNPKKIREL AEYGIEIVEV VNTSAHIKDG
NENYLRAKVS HGKHNLKV
