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RIBBA_BACFR
ID   RIBBA_BACFR             Reviewed;         404 AA.
AC   Q64YT3;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   25-OCT-2004, sequence version 1.
DT   03-AUG-2022, entry version 93.
DE   RecName: Full=Riboflavin biosynthesis protein RibBA {ECO:0000255|HAMAP-Rule:MF_01283};
DE   Includes:
DE     RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase {ECO:0000255|HAMAP-Rule:MF_01283};
DE              Short=DHBP synthase {ECO:0000255|HAMAP-Rule:MF_01283};
DE              EC=4.1.99.12 {ECO:0000255|HAMAP-Rule:MF_01283};
DE   Includes:
DE     RecName: Full=GTP cyclohydrolase-2 {ECO:0000255|HAMAP-Rule:MF_01283};
DE              EC=3.5.4.25 {ECO:0000255|HAMAP-Rule:MF_01283};
DE     AltName: Full=GTP cyclohydrolase II {ECO:0000255|HAMAP-Rule:MF_01283};
GN   Name=ribBA {ECO:0000255|HAMAP-Rule:MF_01283}; OrderedLocusNames=BF0594;
OS   Bacteroides fragilis (strain YCH46).
OC   Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae;
OC   Bacteroides.
OX   NCBI_TaxID=295405;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=YCH46;
RX   PubMed=15466707; DOI=10.1073/pnas.0404172101;
RA   Kuwahara T., Yamashita A., Hirakawa H., Nakayama H., Toh H., Okada N.,
RA   Kuhara S., Hattori M., Hayashi T., Ohnishi Y.;
RT   "Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions
RT   regulating cell surface adaptation.";
RL   Proc. Natl. Acad. Sci. U.S.A. 101:14919-14924(2004).
CC   -!- FUNCTION: Catalyzes the conversion of D-ribulose 5-phosphate to formate
CC       and 3,4-dihydroxy-2-butanone 4-phosphate. {ECO:0000255|HAMAP-
CC       Rule:MF_01283}.
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_01283}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate +
CC         formate + H(+); Xref=Rhea:RHEA:18457, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:15740, ChEBI:CHEBI:58121, ChEBI:CHEBI:58830;
CC         EC=4.1.99.12; Evidence={ECO:0000255|HAMAP-Rule:MF_01283};
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_01283};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01283};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01283};
CC       Note=Binds 2 divalent metal cations per subunit. Magnesium or
CC       manganese. {ECO:0000255|HAMAP-Rule:MF_01283};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01283};
CC       Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_01283};
CC   -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-
CC       oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1.
CC       {ECO:0000255|HAMAP-Rule:MF_01283}.
CC   -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC       ribitylamino)uracil from GTP: step 1/4. {ECO:0000255|HAMAP-
CC       Rule:MF_01283}.
CC   -!- SIMILARITY: In the N-terminal section; belongs to the DHBP synthase
CC       family. {ECO:0000255|HAMAP-Rule:MF_01283}.
CC   -!- SIMILARITY: In the C-terminal section; belongs to the GTP
CC       cyclohydrolase II family. {ECO:0000255|HAMAP-Rule:MF_01283}.
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DR   EMBL; AP006841; BAD47343.1; -; Genomic_DNA.
DR   RefSeq; WP_005784515.1; NZ_UYXF01000037.1.
DR   RefSeq; YP_097877.1; NC_006347.1.
DR   AlphaFoldDB; Q64YT3; -.
DR   SMR; Q64YT3; -.
DR   STRING; 295405.BF0594; -.
DR   EnsemblBacteria; BAD47343; BAD47343; BF0594.
DR   GeneID; 66330368; -.
DR   KEGG; bfr:BF0594; -.
DR   PATRIC; fig|295405.11.peg.612; -.
DR   HOGENOM; CLU_020273_1_2_10; -.
DR   OMA; ECRGLIC; -.
DR   UniPathway; UPA00275; UER00399.
DR   UniPathway; UPA00275; UER00400.
DR   Proteomes; UP000002197; Chromosome.
DR   GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IEA:UniProtKB-UniRule.
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:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0030145; F:manganese ion binding; 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   HAMAP; MF_00180; RibB; 1.
DR   HAMAP; MF_01283; RibBA; 1.
DR   InterPro; IPR017945; DHBP_synth_RibB-like_a/b_dom.
DR   InterPro; IPR000422; DHBP_synthase_RibB.
DR   InterPro; IPR032677; GTP_cyclohydro_II.
DR   InterPro; IPR000926; RibA.
DR   InterPro; IPR036144; RibA-like_sf.
DR   InterPro; IPR016299; Riboflavin_synth_RibBA.
DR   Pfam; PF00926; DHBP_synthase; 1.
DR   Pfam; PF00925; GTP_cyclohydro2; 1.
DR   SUPFAM; SSF142695; SSF142695; 1.
DR   SUPFAM; SSF55821; SSF55821; 1.
DR   TIGRFAMs; TIGR00505; ribA; 1.
DR   TIGRFAMs; TIGR00506; ribB; 1.
PE   3: Inferred from homology;
KW   GTP-binding; Hydrolase; Lyase; Magnesium; Manganese; Metal-binding;
KW   Multifunctional enzyme; Nucleotide-binding; Riboflavin biosynthesis; Zinc.
FT   CHAIN           1..404
FT                   /note="Riboflavin biosynthesis protein RibBA"
FT                   /id="PRO_1000165247"
FT   REGION          1..204
FT                   /note="DHBP synthase"
FT   REGION          205..404
FT                   /note="GTP cyclohydrolase II"
FT   ACT_SITE        332
FT                   /note="Proton acceptor; for GTP cyclohydrolase activity"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   ACT_SITE        334
FT                   /note="Nucleophile; for GTP cyclohydrolase activity"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         30..31
FT                   /ligand="D-ribulose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:58121"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         31
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         31
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         35
FT                   /ligand="D-ribulose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:58121"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         143..147
FT                   /ligand="D-ribulose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:58121"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         146
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         167
FT                   /ligand="D-ribulose 5-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:58121"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         255..259
FT                   /ligand="GTP"
FT                   /ligand_id="ChEBI:CHEBI:37565"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         260
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         271
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         273
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         276
FT                   /ligand="GTP"
FT                   /ligand_id="ChEBI:CHEBI:37565"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         298..300
FT                   /ligand="GTP"
FT                   /ligand_id="ChEBI:CHEBI:37565"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         320
FT                   /ligand="GTP"
FT                   /ligand_id="ChEBI:CHEBI:37565"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         355
FT                   /ligand="GTP"
FT                   /ligand_id="ChEBI:CHEBI:37565"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   BINDING         360
FT                   /ligand="GTP"
FT                   /ligand_id="ChEBI:CHEBI:37565"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   SITE            129
FT                   /note="Essential for DHBP synthase activity"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT   SITE            167
FT                   /note="Essential for DHBP synthase activity"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
SQ   SEQUENCE   404 AA;  45101 MW;  F456056CAA89C843 CRC64;
     MEPIRLNTIE EAIADFKEGN FVIVVDDEDR ENEGDFIIAA EKITPEKVNF MLTHGRGVLC
     APITEERCAE LELDMQVSSN TSIYETPFTV TVDLLEGCTT GVSMHDRAMT IRALADPKTK
     PADLGRPGHI NPLRARSRGV LRRAGHTEAS VDLAKLAGLY PAAALIEIIN EDGTMARLPQ
     LVEVARRFGL KIISIKDLIA YRLQMESIVD RGVEVDMPTQ FGHFRLIPFR QKSNGMEHIA
     LIKGTWDTDE PILVRVHSSC MTGDIFGSCR CECGEQLHKA MEMIEAAGKG VIVYMNQEGR
     GIGLMNKIAA YKLQEEGYDT VDANLHLGFD ADERDYGVGA QILREIGVKK MKLMTNNPVK
     RIGLEAYGLE ITENVGIEIK PNPYNERYLK TKKDRMGHTL HFNK
 
 
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