RIBB_YERPE
ID RIBB_YERPE Reviewed; 217 AA.
AC Q8ZI56; Q0WJ12;
DT 16-JUN-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 125.
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};
GN OrderedLocusNames=YPO0658, y3520, YP_2973;
OS Yersinia pestis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=632;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CO-92 / Biovar Orientalis;
RX PubMed=11586360; DOI=10.1038/35097083;
RA Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G.,
RA Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L.,
RA Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M.,
RA Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T.,
RA Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S.,
RA Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J.,
RA Stevens K., Whitehead S., Barrell B.G.;
RT "Genome sequence of Yersinia pestis, the causative agent of plague.";
RL Nature 413:523-527(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KIM10+ / Biovar Mediaevalis;
RX PubMed=12142430; DOI=10.1128/jb.184.16.4601-4611.2002;
RA Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P.,
RA Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D.,
RA Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A.,
RA Nilles M.L., Matson J.S., Blattner F.R., Perry R.D.;
RT "Genome sequence of Yersinia pestis KIM.";
RL J. Bacteriol. 184:4601-4611(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=91001 / Biovar Mediaevalis;
RX PubMed=15368893; DOI=10.1093/dnares/11.3.179;
RA Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D.,
RA Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L.,
RA Dai R., Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H.,
RA Wang J., Huang P., Yang R.;
RT "Complete genome sequence of Yersinia pestis strain 91001, an isolate
RT avirulent to humans.";
RL DNA Res. 11:179-197(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_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; AL590842; CAL19335.1; -; Genomic_DNA.
DR EMBL; AE009952; AAM87068.1; -; Genomic_DNA.
DR EMBL; AE017042; AAS63152.1; -; Genomic_DNA.
DR PIR; AE0081; AE0081.
DR RefSeq; WP_002212190.1; NZ_WUCM01000022.1.
DR RefSeq; YP_002345726.1; NC_003143.1.
DR PDB; 3H07; X-ray; 1.95 A; A/B=1-217.
DR PDBsum; 3H07; -.
DR AlphaFoldDB; Q8ZI56; -.
DR SMR; Q8ZI56; -.
DR STRING; 214092.YPO0658; -.
DR PaxDb; Q8ZI56; -.
DR DNASU; 1148467; -.
DR EnsemblBacteria; AAM87068; AAM87068; y3520.
DR EnsemblBacteria; AAS63152; AAS63152; YP_2973.
DR GeneID; 66844174; -.
DR KEGG; ype:YPO0658; -.
DR KEGG; ypk:y3520; -.
DR KEGG; ypm:YP_2973; -.
DR PATRIC; fig|214092.21.peg.917; -.
DR eggNOG; COG0108; Bacteria.
DR HOGENOM; CLU_020273_3_0_6; -.
DR OMA; DAGGLIC; -.
DR UniPathway; UPA00275; UER00399.
DR EvolutionaryTrace; Q8ZI56; -.
DR Proteomes; UP000000815; Chromosome.
DR Proteomes; UP000001019; Chromosome.
DR Proteomes; UP000002490; Chromosome.
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 HAMAP; MF_00180; RibB; 1.
DR InterPro; IPR017945; DHBP_synth_RibB-like_a/b_dom.
DR InterPro; IPR000422; DHBP_synthase_RibB.
DR Pfam; PF00926; DHBP_synthase; 1.
DR SUPFAM; SSF55821; SSF55821; 1.
DR TIGRFAMs; TIGR00506; ribB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Manganese; Metal-binding;
KW Reference proteome; Riboflavin biosynthesis.
FT CHAIN 1..217
FT /note="3,4-dihydroxy-2-butanone 4-phosphate synthase"
FT /id="PRO_0000151820"
FT BINDING 37..38
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 38
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 38
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 42
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 150..154
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 153
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT BINDING 174
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT SITE 136
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT SITE 174
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00180"
FT HELIX 7..9
FT /evidence="ECO:0007829|PDB:3H07"
FT HELIX 12..24
FT /evidence="ECO:0007829|PDB:3H07"
FT STRAND 29..32
FT /evidence="ECO:0007829|PDB:3H07"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:3H07"
FT STRAND 41..46
FT /evidence="ECO:0007829|PDB:3H07"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:3H07"
FT HELIX 52..61
FT /evidence="ECO:0007829|PDB:3H07"
FT STRAND 67..70
FT /evidence="ECO:0007829|PDB:3H07"
FT HELIX 72..77
FT /evidence="ECO:0007829|PDB:3H07"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:3H07"
FT STRAND 106..108
FT /evidence="ECO:0007829|PDB:3H07"
FT HELIX 111..122
FT /evidence="ECO:0007829|PDB:3H07"
FT HELIX 128..130
FT /evidence="ECO:0007829|PDB:3H07"
FT STRAND 131..141
FT /evidence="ECO:0007829|PDB:3H07"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:3H07"
FT HELIX 153..163
FT /evidence="ECO:0007829|PDB:3H07"
FT STRAND 168..176
FT /evidence="ECO:0007829|PDB:3H07"
FT HELIX 185..195
FT /evidence="ECO:0007829|PDB:3H07"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:3H07"
FT HELIX 202..210
FT /evidence="ECO:0007829|PDB:3H07"
SQ SEQUENCE 217 AA; 23360 MW; BFE6BFF6EA409721 CRC64;
MNQTLLSDFG TPVERVERAI DALRNGRGVM VLDDESRENE GDMVFAAEAM TLEQMALTIR
HGSGIVCLCI TDERRQQLDL PMMVTHNSSQ FQTAFTVTIE AAEGVTTGVS AADRLTTIRK
AIADNAKPAD LNRPGHVFPL RGQPGGVLSR RGHTEASIDL ATLAGYKPAG VLCELTNDDG
SMAHAPEVIA FAKLHDMPVV TIDDLAAYLQ SRAKKAS
