RIBBA_STAAR
ID RIBBA_STAAR Reviewed; 393 AA.
AC Q6GFT5;
DT 22-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 105.
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}; Synonyms=ribA;
GN OrderedLocusNames=SAR1851;
OS Staphylococcus aureus (strain MRSA252).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=282458;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MRSA252;
RX PubMed=15213324; DOI=10.1073/pnas.0402521101;
RA Holden M.T.G., Feil E.J., Lindsay J.A., Peacock S.J., Day N.P.J.,
RA Enright M.C., Foster T.J., Moore C.E., Hurst L., Atkin R., Barron A.,
RA Bason N., Bentley S.D., Chillingworth C., Chillingworth T., Churcher C.,
RA Clark L., Corton C., Cronin A., Doggett J., Dowd L., Feltwell T., Hance Z.,
RA Harris B., Hauser H., Holroyd S., Jagels K., James K.D., Lennard N.,
RA Line A., Mayes R., Moule S., Mungall K., Ormond D., Quail M.A.,
RA Rabbinowitsch E., Rutherford K.M., Sanders M., Sharp S., Simmonds M.,
RA Stevens K., Whitehead S., Barrell B.G., Spratt B.G., Parkhill J.;
RT "Complete genomes of two clinical Staphylococcus aureus strains: evidence
RT for the rapid evolution of virulence and drug resistance.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:9786-9791(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; BX571856; CAG40842.1; -; Genomic_DNA.
DR RefSeq; WP_001159032.1; NC_002952.2.
DR AlphaFoldDB; Q6GFT5; -.
DR SMR; Q6GFT5; -.
DR KEGG; sar:SAR1851; -.
DR HOGENOM; CLU_020273_1_2_9; -.
DR OMA; ECRGLIC; -.
DR OrthoDB; 900513at2; -.
DR UniPathway; UPA00275; UER00399.
DR UniPathway; UPA00275; UER00400.
DR Proteomes; UP000000596; 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..393
FT /note="Riboflavin biosynthesis protein RibBA"
FT /id="PRO_0000151736"
FT REGION 1..200
FT /note="DHBP synthase"
FT REGION 201..393
FT /note="GTP cyclohydrolase II"
FT ACT_SITE 325
FT /note="Proton acceptor; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT ACT_SITE 327
FT /note="Nucleophile; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 27..28
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 28
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 28
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 32
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 139..143
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 142
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 163
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 249..253
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 254
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 265
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 267
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 270
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 291..293
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 313
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 348
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 353
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT SITE 125
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT SITE 163
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
SQ SEQUENCE 393 AA; 44192 MW; ABEE7512A8B72AE9 CRC64;
MQFDNIDSAL MALKNGETII VVDDENRENE GDLVAVTEWM NDNTINFMAK EARGLICAPV
SKDIAQRLDL VQMVDDNSDI FGTQFTVSID HVDTTTGISA YERTLTAKKL IDPSSEAKDF
NRPGHLFPLV AQDKGVLARN GHTEAAVDLA KLTGAKPAGV ICEIMNDDGT MAKGQDLQKF
KEKHKLKMIT IDDLIEYRKK LEPEIEFKAK VKMPTDFGTF DMYGFKATYT DEEIVVLTKG
AIRQHENVRL HSACLTGDIF HSQRCDCGAQ LESSMKYINE HGGMIIYLPQ EGRGIGLLNK
LRAYELIEQG YDTVTANLAL GFDEDLRDYH IAAQILKYFN IEHINLLSNN PSKFEGLKQY
GIDIAERIEV IVPETVHNHD YMETKKIKMG HLI
