ID RIBB_VIBCH Reviewed; 218 AA.
AC Q9KKP2;
DT 30-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 27-MAR-2024, entry version 106.
DE RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase {ECO:0000255|HAMAP-Rule:MF_00180};
DE Short=DHBP synthase {ECO:0000255|HAMAP-Rule:MF_00180};
DE EC=4.1.99.12 {ECO:0000255|HAMAP-Rule:MF_00180};
GN Name=ribB {ECO:0000255|HAMAP-Rule:MF_00180}; OrderedLocusNames=VC_A1060;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=243277;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX PubMed=10952301; DOI=10.1038/35020000;
RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT cholerae.";
RL Nature 406:477-483(2000).
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_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:0000255|HAMAP-Rule:MF_00180};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00180};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00180};
CC Note=Binds 2 divalent metal cations per subunit. Magnesium or
CC manganese. {ECO:0000255|HAMAP-Rule:MF_00180};
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_00180}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00180}.
CC -!- SIMILARITY: Belongs to the DHBP synthase family. {ECO:0000255|HAMAP-
CC Rule:MF_00180}.
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DR EMBL; AE003853; AAF96954.1; -; Genomic_DNA.
DR PIR; B82384; B82384.
DR RefSeq; NP_233442.1; NC_002506.1.
DR RefSeq; WP_001076646.1; NZ_LT906615.1.
DR PDB; 4P6C; X-ray; 1.86 A; A/B=1-218.
DR PDB; 4P6D; X-ray; 1.59 A; A/B=1-218.
DR PDB; 4P6P; X-ray; 1.86 A; A/B=1-218.
DR PDB; 4P77; X-ray; 2.04 A; A/B=1-218.
DR PDB; 4P8E; X-ray; 2.04 A; A/B=1-218.
DR PDB; 4P8J; X-ray; 1.96 A; A/B=1-218.
DR PDB; 7UEZ; X-ray; 1.08 A; A/B=1-218.
DR PDB; 7UF0; X-ray; 1.80 A; A=1-218.
DR PDB; 7UF1; X-ray; 1.95 A; A=1-218.
DR PDB; 7UF2; X-ray; 2.00 A; A=1-218.
DR PDB; 7UF3; X-ray; 2.00 A; A=1-218.
DR PDB; 7UF4; X-ray; 2.20 A; A=1-218.
DR PDB; 7UF5; X-ray; 2.10 A; A=1-218.
DR PDBsum; 4P6C; -.
DR PDBsum; 4P6D; -.
DR PDBsum; 4P6P; -.
DR PDBsum; 4P77; -.
DR PDBsum; 4P8E; -.
DR PDBsum; 4P8J; -.
DR PDBsum; 7UEZ; -.
DR PDBsum; 7UF0; -.
DR PDBsum; 7UF1; -.
DR PDBsum; 7UF2; -.
DR PDBsum; 7UF3; -.
DR PDBsum; 7UF4; -.
DR PDBsum; 7UF5; -.
DR AlphaFoldDB; Q9KKP2; -.
DR SMR; Q9KKP2; -.
DR STRING; 243277.VC_A1060; -.
DR DNASU; 2612048; -.
DR EnsemblBacteria; AAF96954; AAF96954; VC_A1060.
DR KEGG; vch:VC_A1060; -.
DR PATRIC; fig|243277.26.peg.3666; -.
DR eggNOG; COG0108; Bacteria.
DR HOGENOM; CLU_020273_3_0_6; -.
DR BRENDA; 4.1.99.12; 15862.
DR UniPathway; UPA00275; UER00399.
DR Proteomes; UP000000584; Chromosome 2.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IBA:GO_Central.
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; IBA:GO_Central.
DR Gene3D; 3.90.870.10; DHBP synthase; 1.
DR HAMAP; MF_00180; RibB; 1.
DR InterPro; IPR017945; DHBP_synth_RibB-like_a/b_dom.
DR InterPro; IPR000422; DHBP_synthase_RibB.
DR NCBIfam; TIGR00506; ribB; 1.
DR PANTHER; PTHR21327:SF38; 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE; 1.
DR PANTHER; PTHR21327; GTP CYCLOHYDROLASE II-RELATED; 1.
DR Pfam; PF00926; DHBP_synthase; 1.
DR SUPFAM; SSF55821; YrdC/RibB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Manganese; Metal-binding;
KW Reference proteome; Riboflavin biosynthesis.
FT CHAIN 1..218
FT /note="3,4-dihydroxy-2-butanone 4-phosphate synthase"
FT /id="PRO_0000151813"
FT BINDING 38..39
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 39
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 39
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 43
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 151..155
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 154
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 175
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT SITE 137
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT SITE 175
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT HELIX 3..7
FT /evidence="ECO:0007829|PDB:7UF0"
FT HELIX 8..10
FT /evidence="ECO:0007829|PDB:7UEZ"
FT HELIX 13..25
FT /evidence="ECO:0007829|PDB:7UEZ"
FT STRAND 30..36
FT /evidence="ECO:0007829|PDB:7UEZ"
FT STRAND 43..48
FT /evidence="ECO:0007829|PDB:7UEZ"
FT HELIX 53..62
FT /evidence="ECO:0007829|PDB:7UEZ"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:7UEZ"
FT HELIX 73..78
FT /evidence="ECO:0007829|PDB:7UEZ"
FT STRAND 83..87
FT /evidence="ECO:0007829|PDB:4P6P"
FT STRAND 90..92
FT /evidence="ECO:0007829|PDB:7UF4"
FT STRAND 100..105
FT /evidence="ECO:0007829|PDB:7UEZ"
FT STRAND 107..109
FT /evidence="ECO:0007829|PDB:7UEZ"
FT HELIX 112..123
FT /evidence="ECO:0007829|PDB:7UEZ"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:7UEZ"
FT STRAND 132..142
FT /evidence="ECO:0007829|PDB:7UEZ"
FT HELIX 147..149
FT /evidence="ECO:0007829|PDB:7UEZ"
FT HELIX 154..165
FT /evidence="ECO:0007829|PDB:7UEZ"
FT STRAND 171..177
FT /evidence="ECO:0007829|PDB:7UEZ"
FT STRAND 181..183
FT /evidence="ECO:0007829|PDB:4P6D"
FT HELIX 186..196
FT /evidence="ECO:0007829|PDB:7UEZ"
FT STRAND 200..202
FT /evidence="ECO:0007829|PDB:7UEZ"
FT HELIX 203..213
FT /evidence="ECO:0007829|PDB:7UEZ"
SQ SEQUENCE 218 AA; 23567 MW; 69E4167C234999F0 CRC64;
MNQSSLLAEF GDPITRVENA LQALREGRGV LLLDDEDREN EGDIIYAVES LTTAQMALMI
RECSGIVCLC LTEAQADRLA LPPMVVNNNS ANQTAFTVSI EAKHGVTTGV SAQDRVTTIK
TAANPQAKPE DLARPGHVFP LRARAGGVLA RRGHTEGTVD LMQMAGLQPA GVLCELTNPD
GSMAKTPEII EFGKLHNMPV LTIEDMVQYR IQFDLKLA
//
