RIBBA_BACVZ
ID RIBBA_BACVZ Reviewed; 398 AA.
AC A7Z675;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 23-OCT-2007, sequence version 1.
DT 03-AUG-2022, entry version 98.
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};
GN OrderedLocusNames=RBAM_021400;
OS Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42)
OS (Bacillus amyloliquefaciens subsp. plantarum).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus amyloliquefaciens group.
OX NCBI_TaxID=326423;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42;
RX PubMed=17704766; DOI=10.1038/nbt1325;
RA Chen X.H., Koumoutsi A., Scholz R., Eisenreich A., Schneider K.,
RA Heinemeyer I., Morgenstern B., Voss B., Hess W.R., Reva O., Junge H.,
RA Voigt B., Jungblut P.R., Vater J., Suessmuth R., Liesegang H.,
RA Strittmatter A., Gottschalk G., Borriss R.;
RT "Comparative analysis of the complete genome sequence of the plant growth-
RT promoting bacterium Bacillus amyloliquefaciens FZB42.";
RL Nat. Biotechnol. 25:1007-1014(2007).
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; CP000560; ABS74501.1; -; Genomic_DNA.
DR RefSeq; WP_003153371.1; NC_009725.2.
DR AlphaFoldDB; A7Z675; -.
DR SMR; A7Z675; -.
DR STRING; 326423.RBAM_021400; -.
DR PRIDE; A7Z675; -.
DR EnsemblBacteria; ABS74501; ABS74501; RBAM_021400.
DR GeneID; 66325895; -.
DR KEGG; bay:RBAM_021400; -.
DR HOGENOM; CLU_020273_1_2_9; -.
DR OMA; ECRGLIC; -.
DR UniPathway; UPA00275; UER00399.
DR UniPathway; UPA00275; UER00400.
DR Proteomes; UP000001120; 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..398
FT /note="Riboflavin biosynthesis protein RibBA"
FT /id="PRO_1000067413"
FT REGION 1..199
FT /note="DHBP synthase"
FT REGION 200..398
FT /note="GTP cyclohydrolase II"
FT ACT_SITE 328
FT /note="Proton acceptor; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT ACT_SITE 330
FT /note="Nucleophile; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 26..27
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 27
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 27
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 31
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 138..142
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 141
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 162
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 251..255
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 256
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 269
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 272
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 294..296
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 316
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 351
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 356
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT SITE 124
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT SITE 162
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
SQ SEQUENCE 398 AA; 44170 MW; 7D5B923E23FA5745 CRC64;
MFHPIEEALE ALKKGEVIIV VDDEDRENEG DFVALAEHAT PEVVNFMATH GRGLICTPLS
EDIAGRLDLH PMVDHNTDSH ETAFTVSIDH RLTKTGISAQ ERSFTIQALL NEESVSDDFQ
RPGHIFPLIA KKGGVLKRAG HTEAAVDLAK ACGSQGAGVI CEIMNEDGTM ARVPELAEIA
ERHQLKMITI KDLIEYRYNI TTLVNREVDI TLPTDFGTFR VYGYTNEVDG KEHLAFVMGD
VPFNSEPVLV RVHSECLTGD VFASHRCDCG PQLHAALAQI AEEGRGVLLY LRQEGRGIGL
INKLKAYRLQ EQGYDTVEAN EALGFLPDLR NYGIGAQILR DLGVQHMKLL TNNPRKIAGL
EGYGLSISER VPLQMEASEH NKQYLQTKMK KLGHLLHF
