RIBBA_ENDTX
ID RIBBA_ENDTX Reviewed; 403 AA.
AC B1H0I0;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 29-APR-2008, sequence version 1.
DT 03-AUG-2022, entry version 81.
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=TGRD_529;
OS Endomicrobium trichonymphae.
OC Bacteria; Elusimicrobia; Endomicrobia; Endomicrobiales; Endomicrobiaceae;
OC Endomicrobium.
OX NCBI_TaxID=1408204;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=18391199; DOI=10.1073/pnas.0801389105;
RA Hongoh Y., Sharma V.K., Prakash T., Noda S., Taylor T.D., Kudo T.,
RA Sakaki Y., Toyoda A., Hattori M., Ohkuma M.;
RT "Complete genome of the uncultured termite group 1 bacteria in a single
RT host protist cell.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:5555-5560(2008).
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; AP009510; BAG14012.1; -; Genomic_DNA.
DR RefSeq; WP_015423537.1; NC_020419.1.
DR RefSeq; YP_001956473.1; NC_020419.1.
DR AlphaFoldDB; B1H0I0; -.
DR SMR; B1H0I0; -.
DR STRING; 471821.TGRD_529; -.
DR EnsemblBacteria; BAG14012; BAG14012; TGRD_529.
DR KEGG; rsd:TGRD_529; -.
DR PATRIC; fig|471821.5.peg.863; -.
DR HOGENOM; CLU_020273_1_2_0; -.
DR OMA; ECRGLIC; -.
DR OrthoDB; 900513at2; -.
DR UniPathway; UPA00275; UER00399.
DR UniPathway; UPA00275; UER00400.
DR Proteomes; UP000001691; 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..403
FT /note="Riboflavin biosynthesis protein RibBA"
FT /id="PRO_1000140369"
FT REGION 1..204
FT /note="DHBP synthase"
FT REGION 205..403
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 403 AA; 44853 MW; 9FF1E288DA7226B2 CRC64;
MKNKVFASIG DAVKDIKVGR MVIVVDDPGR ENEGDLICAA EKASPEVINF MTKYARGLIC
VPMKHERLKE LEIENMVEKP TEKKGCSFTV SVDYKIGTTT GISAYDRSVT VRKLIDKTAK
HEDFARPGHI FPLRCKEGGV LARTGHTEAA VDLVRLAGFY PAGIICEIMN NDGTMARMSD
LIKFAKKHDL HIITIGELVN YRRRTEKFIS EIVNVDLPTR YGDFKLVLFE DLITKDSHIA
VVKGVVKNRQ NVLVRVHSSC ETGDIFHSLR CDCGDQLETA LKAVGEAEQG VVLYIHQEGR
GIGLANKLKA YRLQEKGMDT VEANKALGFD PDLRDYGIGA QMLSELGIKS INLMTNNPGK
INGLESYGLK ITKRVPLEIS PSKSNEKYLK TKKEKMGHML KKV
