ID Q9PES5_XYLFA Unreviewed; 377 AA. AC Q9PES5; DT 01-OCT-2000, integrated into UniProtKB/TrEMBL. DT 01-OCT-2000, sequence version 1. DT 04-NOV-2026, entry version 148. DE RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase {ECO:0000256|ARBA:ARBA00018836, ECO:0000256|HAMAP-Rule:MF_00180}; DE Short=DHBP synthase {ECO:0000256|HAMAP-Rule:MF_00180}; DE EC=4.1.99.12 {ECO:0000256|ARBA:ARBA00012153, ECO:0000256|HAMAP-Rule:MF_00180}; GN Name=ribB {ECO:0000256|HAMAP-Rule:MF_00180}; GN OrderedLocusNames=XF_0953 {ECO:0000313|EMBL:AAF83763.1}; OS Xylella fastidiosa (strain 9a5c). OC Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; OC Lysobacterales; Lysobacteraceae; Xylella. OX NCBI_TaxID=160492 {ECO:0000313|EMBL:AAF83763.1, ECO:0000313|Proteomes:UP000000812}; RN [1] {ECO:0000313|EMBL:AAF83763.1, ECO:0000313|Proteomes:UP000000812} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=9a5c {ECO:0000313|EMBL:AAF83763.1, RC ECO:0000313|Proteomes:UP000000812}; RX PubMed=10910347; DOI=10.1038/35018003; RA Simpson A.J., Reinach F.C., Arruda P., Abreu F.A., Acencio M., RA Alvarenga R., Alves L.M., Araya J.E., Baia G.S., Baptista C.S., RA Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R., RA Bueno M.R., Camargo A.A., Camargo L.E., Carraro D.M., Carrer H., RA Colauto N.B., Colombo C., Costa F.F., Costa M.C., Costa-Neto C.M., RA Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H., RA Facincani A.P., Ferreira A.J., Ferreira V.C., Ferro J.A., Fraga J.S., RA Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H., RA Goldman M.H., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D., RA Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E., RA Laigret F., Lambais M.R., Leite L.C., Lemos E.G., Lemos M.V., Lopes S.A., RA Lopes C.R., Machado J.A., Machado M.A., Madeira A.M., Madeira H.M., RA Marino C.L., Marques M.V., Martins E.A., Martins E.M., Matsukuma A.Y., RA Menck C.F., Miracca E.C., Miyaki C.Y., Monteriro-Vitorello C.B., Moon D.H., RA Nagai M.A., Nascimento A.L., Netto L.E., Nhani A.Jr., Nobrega F.G., RA Nunes L.R., Oliveira M.A., de Oliveira M.C., de Oliveira R.C., RA Palmieri D.A., Paris A., Peixoto B.R., Pereira G.A., Pereira H.A.Jr., RA Pesquero J.B., Quaggio R.B., Roberto P.G., Rodrigues V., de M Rosa A.J., RA de Rosa V.E.Jr., de Sa R.G., Santelli R.V., Sawasaki H.E., da Silva A.C., RA da Silva A.M., da Silva F.R., da Silva W.A.Jr., da Silveira J.F., RA Silvestri M.L., Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., RA Truffi D., Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., RA Verjovski-Almeida S., Vettore A.L., Zago M.A., Zatz M., Meidanis J., RA Setubal J.C.; RT "The genome sequence of the plant pathogen Xylella fastidiosa."; RL Nature 406:151-159(2000). CC -!- FUNCTION: Catalyzes the conversion of D-ribulose 5-phosphate to formate CC and 3,4-dihydroxy-2-butanone 4-phosphate. CC {ECO:0000256|ARBA:ARBA00002284, ECO:0000256|HAMAP-Rule:MF_00180}. 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:0000256|ARBA:ARBA00000141, CC ECO:0000256|HAMAP-Rule:MF_00180}; CC -!- COFACTOR: CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000256|HAMAP- CC Rule:MF_00180}; CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000256|HAMAP- CC Rule:MF_00180}; CC Note=Binds 2 divalent metal cations per subunit. Magnesium or CC manganese. {ECO:0000256|HAMAP-Rule:MF_00180}; CC -!- COFACTOR: CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; CC Evidence={ECO:0000256|ARBA:ARBA00001936}; CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3- CC oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1. CC {ECO:0000256|ARBA:ARBA00004904, ECO:0000256|HAMAP-Rule:MF_00180}. CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00180}. CC -!- SIMILARITY: Belongs to the DHBP synthase family. {ECO:0000256|HAMAP- CC Rule:MF_00180}. CC -!- SIMILARITY: In the C-terminal section; belongs to the GTP CC cyclohydrolase II family. {ECO:0000256|ARBA:ARBA00008976}. CC -!- SIMILARITY: In the N-terminal section; belongs to the DHBP synthase CC family. {ECO:0000256|ARBA:ARBA00005520}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AE003849; AAF83763.1; -; Genomic_DNA. DR PIR; B82741; B82741. DR RefSeq; WP_010893472.1; NC_002488.3. DR AlphaFoldDB; Q9PES5; -. DR STRING; 160492.XF_0953; -. DR KEGG; xfa:XF_0953; -. DR eggNOG; COG0108; Bacteria. DR eggNOG; COG0807; Bacteria. DR HOGENOM; CLU_020273_1_2_6; -. DR OMA; AAIHCTE; -. DR UniPathway; UPA00275; UER00399. DR Proteomes; UP000000812; Chromosome. DR GO; GO:0005829; C:cytosol; IEA:TreeGrafter. DR GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IEA:UniProtKB-UniRule. DR GO; GO:0003935; F:GTP cyclohydrolase II activity; IEA:TreeGrafter. 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:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniRule. DR FunFam; 3.90.870.10:FF:000001; Riboflavin biosynthesis protein RibBA; 1. DR Gene3D; 3.90.870.10; DHBP synthase; 1. DR Gene3D; 3.40.50.10990; GTP cyclohydrolase II; 1. DR HAMAP; MF_00180; RibB; 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; IPR036144; RibA-like_sf. DR NCBIfam; TIGR00506; ribB; 1. DR PANTHER; PTHR21327:SF34; 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE; 1. DR PANTHER; PTHR21327; GTP CYCLOHYDROLASE II-RELATED; 1. DR Pfam; PF00926; DHBP_synthase; 1. DR Pfam; PF00925; GTP_cyclohydro2; 1. DR PIRSF; PIRSF001259; RibA; 1. DR SUPFAM; SSF142695; RibA-like; 1. DR SUPFAM; SSF55821; YrdC/RibB; 1. PE 3: Inferred from homology; KW Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_00180}; KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00180}; KW Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|HAMAP-Rule:MF_00180}; KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP- KW Rule:MF_00180}; Reference proteome {ECO:0000313|Proteomes:UP000000812}; KW Riboflavin biosynthesis {ECO:0000256|ARBA:ARBA00022619, ECO:0000256|HAMAP- KW Rule:MF_00180}. FT DOMAIN 209..363 FT /note="GTP cyclohydrolase II" FT /evidence="ECO:0000259|Pfam:PF00925" FT BINDING 28..29 FT /ligand="D-ribulose 5-phosphate" FT /ligand_id="ChEBI:CHEBI:58121" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180" FT BINDING 29 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180" FT BINDING 29 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180" FT BINDING 33 FT /ligand="D-ribulose 5-phosphate" FT /ligand_id="ChEBI:CHEBI:58121" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180" FT BINDING 141..145 FT /ligand="D-ribulose 5-phosphate" FT /ligand_id="ChEBI:CHEBI:58121" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180" FT BINDING 144 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180" FT SITE 127 FT /note="Essential for catalytic activity" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180" FT SITE 165 FT /note="Essential for catalytic activity" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180" SQ SEQUENCE 377 AA; 41057 MW; B5ECE9BC194CCA41 CRC64; MNSFAAVPVL IEEIRAGRMV VIVDDEDREN EGDLIMAAEL VAPKDINFMV THARGLVCLS LTRERCAQIG LSPMVQRNTT RFQTNFTVSI EAAEGLTTGI SAYDRAHTIR TAVRPNAKPS DLHQPGHIFP LIAQPGGVLT RAGHTEAAND LPMLAGLEPA GVLVEIMNAD GTMARRPQLE VFAQQHGLKI GSIADLIAYR LANEHTVERV DERVIETEYG SFLLVTYRDR IAHDLHFALV RGTLDASIPT LVRVQVENPL ADMLHWRRED FGVAASDALR MIAAAERGVM VVLAAPRDSD ALLARLRREP EVVSNVKDVG QWRRNGAGGQ ILADLGLGKL RVLGTPRRQI ALAGFGLEVL EYVECRGGAP VAPQGVD //