RIBB_ECOLI
ID RIBB_ECOLI Reviewed; 217 AA.
AC P0A7J0; P24199; Q2M9F9;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase {ECO:0000303|PubMed:11687623, ECO:0000303|PubMed:1597419};
DE Short=DHBP synthase;
DE Short=DHBPS {ECO:0000303|PubMed:11687623};
DE EC=4.1.99.12 {ECO:0000269|PubMed:1597419};
GN Name=ribB; Synonyms=htrP; OrderedLocusNames=b3041, JW3009;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1917833; DOI=10.1128/jb.173.19.5999-6008.1991;
RA Raina S., Mabey L., Georgopoulos C.;
RT "The Escherichia coli htrP gene product is essential for bacterial growth
RT at high temperatures: mapping, cloning, sequencing, and transcriptional
RT regulation of htrP.";
RL J. Bacteriol. 173:5999-6008(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1314093; DOI=10.1016/0167-4781(92)90535-8;
RA Yang T.-P., Depew R.E.;
RT "Nucleotide sequence of a region duplicated in Escherichia coli toc
RT mutants.";
RL Biochim. Biophys. Acta 1130:227-228(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-39, MASS
RP SPECTROMETRY, CATALYTIC ACTIVITY, AND FUNCTION.
RC STRAIN=K12;
RX PubMed=1597419; DOI=10.1128/jb.174.12.4050-4056.1992;
RA Richter G., Volk R., Krieger C., Laham H.-W., Roethlisberger U., Bacher A.;
RT "Biosynthesis of riboflavin: cloning, sequencing, and expression of the
RT gene coding for 3,4-dihydroxy-2-butanone 4-phosphate synthase of
RT Escherichia coli.";
RL J. Bacteriol. 174:4050-4056(1992).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP STRUCTURE BY NMR, COFACTOR, MUTAGENESIS OF ASP-33; GLU-35; ARG-37; GLU-38;
RP GLU-40; ASP-42; CYS-67; THR-107; SER-110; ASP-113; THR-117; HIS-136;
RP ARG-150; HIS-153; GLU-155 AND GLU-174, AND SUBUNIT.
RX PubMed=11687623; DOI=10.1073/pnas.231323598;
RA Kelly M.J.S., Ball L.J., Krieger C., Yu Y., Fischer M., Schiffmann S.,
RA Schmieder P., Kuehne R., Bermel W., Bacher A., Richter G., Oschkinat H.;
RT "The NMR structure of the 47-kDa dimeric enzyme 3,4-dihydroxy-2-butanone-4-
RT phosphate synthase and ligand binding studies reveal the location of the
RT active site.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:13025-13030(2001).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS), AND SUBUNIT.
RX PubMed=11342130; DOI=10.1016/s0969-2126(00)00550-5;
RA Liao D.-I., Calabrese J.C., Wawrzak Z., Viitanen P.V., Jordan D.B.;
RT "Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of
RT riboflavin biosynthesis.";
RL Structure 9:11-18(2001).
CC -!- FUNCTION: Catalyzes the conversion of D-ribulose 5-phosphate to formate
CC and 3,4-dihydroxy-2-butanone 4-phosphate. {ECO:0000269|PubMed:1597419}.
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:0000269|PubMed:1597419};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:18458;
CC Evidence={ECO:0000305|PubMed:1597419};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11687623};
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:0000269|PubMed:11687623};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-
CC oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11342130,
CC ECO:0000269|PubMed:11687623}.
CC -!- INTERACTION:
CC P0A7J0; P0A7J0: ribB; NbExp=4; IntAct=EBI-553653, EBI-553653;
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Peripheral membrane
CC protein {ECO:0000305}.
CC -!- INDUCTION: Is expressed at all temperatures, but accumulation of
CC transcripts decline with raising temperature. Thus, its expression is
CC repressed by heat shock.
CC -!- MASS SPECTROMETRY: Mass=23352; Mass_error=2; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:1597419};
CC -!- SIMILARITY: Belongs to the DHBP synthase family. {ECO:0000305}.
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DR EMBL; M64472; AAA23996.1; -; Genomic_DNA.
DR EMBL; M77129; AAA71879.1; -; Genomic_DNA.
DR EMBL; X66720; CAA47252.1; -; Genomic_DNA.
DR EMBL; U28377; AAA69209.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76077.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77097.1; -; Genomic_DNA.
DR PIR; A38159; A38159.
DR RefSeq; NP_417513.1; NC_000913.3.
DR RefSeq; WP_001076997.1; NZ_STEB01000001.1.
DR PDB; 1G57; X-ray; 1.40 A; A/B=3-217.
DR PDB; 1G58; X-ray; 1.55 A; A/B=3-217.
DR PDB; 1IEZ; NMR; -; A=1-217.
DR PDBsum; 1G57; -.
DR PDBsum; 1G58; -.
DR PDBsum; 1IEZ; -.
DR AlphaFoldDB; P0A7J0; -.
DR SMR; P0A7J0; -.
DR BioGRID; 4260672; 53.
DR BioGRID; 851843; 1.
DR DIP; DIP-35934N; -.
DR IntAct; P0A7J0; 26.
DR STRING; 511145.b3041; -.
DR jPOST; P0A7J0; -.
DR PaxDb; P0A7J0; -.
DR PRIDE; P0A7J0; -.
DR EnsemblBacteria; AAC76077; AAC76077; b3041.
DR EnsemblBacteria; BAE77097; BAE77097; BAE77097.
DR GeneID; 66673060; -.
DR GeneID; 947526; -.
DR KEGG; ecj:JW3009; -.
DR KEGG; eco:b3041; -.
DR PATRIC; fig|1411691.4.peg.3690; -.
DR EchoBASE; EB0460; -.
DR eggNOG; COG0108; Bacteria.
DR HOGENOM; CLU_020273_3_0_6; -.
DR InParanoid; P0A7J0; -.
DR OMA; DAGGLIC; -.
DR PhylomeDB; P0A7J0; -.
DR BioCyc; EcoCyc:DIOHBUTANONEPSYN-MON; -.
DR BioCyc; MetaCyc:DIOHBUTANONEPSYN-MON; -.
DR BRENDA; 4.1.99.12; 2026.
DR UniPathway; UPA00275; UER00399.
DR EvolutionaryTrace; P0A7J0; -.
DR PRO; PR:P0A7J0; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IMP:EcoCyc.
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; Cell membrane; Direct protein sequencing; Lyase; Magnesium;
KW Manganese; Membrane; Metal-binding; Reference proteome;
KW Riboflavin biosynthesis; Stress response.
FT CHAIN 1..217
FT /note="3,4-dihydroxy-2-butanone 4-phosphate synthase"
FT /id="PRO_0000151797"
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 SITE 136
FT /note="Essential for catalytic activity"
FT SITE 174
FT /note="Essential for catalytic activity"
FT MUTAGEN 33
FT /note="D->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 35
FT /note="E->S: Reduces activity by 85%."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 37
FT /note="R->E: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 38
FT /note="E->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 40
FT /note="E->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 42
FT /note="D->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 67
FT /note="C->S: Reduces activity by 80%."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 107
FT /note="T->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 110
FT /note="S->A: Reduces activity by 85%."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 113
FT /note="D->S: Reduces activity by 88%."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 117
FT /note="T->A: Reduces activity by 75%."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 136
FT /note="H->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 150
FT /note="R->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 153
FT /note="H->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 155
FT /note="E->S: Reduces activity by 83%."
FT /evidence="ECO:0000269|PubMed:11687623"
FT MUTAGEN 174
FT /note="E->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11687623"
FT CONFLICT 120..123
FT /note="AAIA -> SDS (in Ref. 1; AAA23996)"
FT /evidence="ECO:0000305"
FT CONFLICT 211..217
FT /note="AHERKAS -> HMSVKPAENRCLIYCLNQETEVVAGFGFYFSLLCKMLIPLL
FT FL (in Ref. 1; AAA23996)"
FT /evidence="ECO:0000305"
FT HELIX 6..9
FT /evidence="ECO:0007829|PDB:1G57"
FT HELIX 12..24
FT /evidence="ECO:0007829|PDB:1G57"
FT STRAND 29..33
FT /evidence="ECO:0007829|PDB:1G57"
FT STRAND 34..36
FT /evidence="ECO:0007829|PDB:1IEZ"
FT STRAND 40..46
FT /evidence="ECO:0007829|PDB:1G57"
FT TURN 47..49
FT /evidence="ECO:0007829|PDB:1G57"
FT HELIX 52..61
FT /evidence="ECO:0007829|PDB:1G57"
FT STRAND 67..70
FT /evidence="ECO:0007829|PDB:1G57"
FT HELIX 72..77
FT /evidence="ECO:0007829|PDB:1G57"
FT STRAND 90..92
FT /evidence="ECO:0007829|PDB:1IEZ"
FT STRAND 95..97
FT /evidence="ECO:0007829|PDB:1G57"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:1G57"
FT STRAND 106..108
FT /evidence="ECO:0007829|PDB:1G57"
FT HELIX 111..122
FT /evidence="ECO:0007829|PDB:1G57"
FT HELIX 128..130
FT /evidence="ECO:0007829|PDB:1G57"
FT STRAND 131..141
FT /evidence="ECO:0007829|PDB:1G57"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:1G57"
FT HELIX 153..163
FT /evidence="ECO:0007829|PDB:1G57"
FT STRAND 170..176
FT /evidence="ECO:0007829|PDB:1G57"
FT STRAND 180..182
FT /evidence="ECO:0007829|PDB:1G57"
FT HELIX 185..194
FT /evidence="ECO:0007829|PDB:1G57"
FT STRAND 198..201
FT /evidence="ECO:0007829|PDB:1G57"
FT HELIX 202..212
FT /evidence="ECO:0007829|PDB:1G57"
SQ SEQUENCE 217 AA; 23353 MW; 6833C120A1442608 CRC64;
MNQTLLSSFG TPFERVENAL AALREGRGVM VLDDEDRENE GDMIFPAETM TVEQMALTIR
HGSGIVCLCI TEDRRKQLDL PMMVENNTSA YGTGFTVTIE AAEGVTTGVS AADRITTVRA
AIADGAKPSD LNRPGHVFPL RAQAGGVLTR GGHTEATIDL MTLAGFKPAG VLCELTNDDG
TMARAPECIE FANKHNMALV TIEDLVAYRQ AHERKAS
