RIBB_METJA
ID RIBB_METJA Reviewed; 227 AA.
AC Q60364;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase {ECO:0000303|PubMed:12200440};
DE Short=DHBP synthase;
DE Short=DHBPS {ECO:0000303|PubMed:12904291};
DE EC=4.1.99.12 {ECO:0000269|PubMed:12200440};
GN Name=ribB; OrderedLocusNames=MJ0055;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP PROTEIN SEQUENCE OF 1-15, FUNCTION, CATALYTIC ACTIVITY, MASS SPECTROMETRY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, COFACTOR, PATHWAY, AND MUTAGENESIS
RP OF ASP-21; ARG-25; GLU-26; GLU-28; ASP-30; CYS-55; THR-112; ARG-119;
RP ARG-161; HIS-164; THR-165; GLU-166 AND GLU-185.
RX PubMed=12200440; DOI=10.1074/jbc.m206863200;
RA Fischer M., Roemisch W., Schiffmann S., Kelly M., Oschkinat H.,
RA Steinbacher S., Huber R., Eisenreich W., Richter G., Bacher A.;
RT "Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-
RT dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii.";
RL J. Biol. Chem. 277:41410-41416(2002).
RN [3] {ECO:0007744|PDB:1PVW, ECO:0007744|PDB:1PVY}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF WILD-TYPE AND MUTANT SER-147 IN
RP COMPLEXES WITH ZINC; CALCIUM AND D-RIBULOSE 5-PHOSPHATE, AND SUBUNIT.
RX PubMed=12904291; DOI=10.1074/jbc.m307301200;
RA Steinbacher S., Schiffmann S., Richter G., Huber R., Bacher A., Fischer M.;
RT "Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from
RT Methanococcus jannaschii in complex with divalent metal ions and the
RT substrate ribulose 5-phosphate: implications for the catalytic mechanism.";
RL J. Biol. Chem. 278:42256-42265(2003).
RN [4] {ECO:0007744|PDB:1SNN}
RP X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF MUTANT SER-147 IN COMPLEXES WITH
RP ZINC; CALCIUM AND D-RIBULOSE 5-PHOSPHATE, AND SUBUNIT.
RX PubMed=15213409; DOI=10.1107/s0907444904009862;
RA Steinbacher S., Schiffmann S., Bacher A., Fischer M.;
RT "Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from
RT Methanococcus jannaschii in complex with the substrate ribulose 5-
RT phosphate.";
RL Acta Crystallogr. D 60:1338-1340(2004).
CC -!- FUNCTION: Catalyzes the conversion of D-ribulose 5-phosphate to formate
CC and 3,4-dihydroxy-2-butanone 4-phosphate.
CC {ECO:0000269|PubMed:12200440}.
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:12200440};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:18458;
CC Evidence={ECO:0000305|PubMed:12200440};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:12200440};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000305|PubMed:12200440};
CC Note=Requires divalent metal ions, preferentially magnesium, for
CC activity (Probable). Binds 2 divalent metal cations per subunit
CC (PubMed:12904291, PubMed:15213409). Zinc and calcium, which are present
CC in the crystals do not support the enzymatic reaction.
CC {ECO:0000269|PubMed:12904291, ECO:0000269|PubMed:15213409,
CC ECO:0000305|PubMed:12200440, ECO:0000305|PubMed:12904291,
CC ECO:0000305|PubMed:15213409};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=140 uM for ribulose-5-phosphate {ECO:0000269|PubMed:12200440};
CC Vmax=148 nmol/min/mg enzyme {ECO:0000269|PubMed:12200440};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-
CC oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1.
CC {ECO:0000305|PubMed:12200440}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:12200440,
CC ECO:0000269|PubMed:12904291, ECO:0000269|PubMed:15213409}.
CC -!- MASS SPECTROMETRY: Mass=25799; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:12200440};
CC -!- SIMILARITY: Belongs to the DHBP synthase family. {ECO:0000305}.
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DR EMBL; L77117; AAB98035.1; -; Genomic_DNA.
DR PIR; G64306; G64306.
DR RefSeq; WP_010869547.1; NC_000909.1.
DR PDB; 1PVW; X-ray; 2.45 A; A/B/C=1-227.
DR PDB; 1PVY; X-ray; 1.70 A; A/B=1-227.
DR PDB; 1SNN; X-ray; 1.55 A; A/B=1-227.
DR PDBsum; 1PVW; -.
DR PDBsum; 1PVY; -.
DR PDBsum; 1SNN; -.
DR AlphaFoldDB; Q60364; -.
DR SMR; Q60364; -.
DR STRING; 243232.MJ_0055; -.
DR EnsemblBacteria; AAB98035; AAB98035; MJ_0055.
DR GeneID; 1450894; -.
DR KEGG; mja:MJ_0055; -.
DR eggNOG; arCOG01320; Archaea.
DR HOGENOM; CLU_020273_3_2_2; -.
DR InParanoid; Q60364; -.
DR OMA; DAGGLIC; -.
DR OrthoDB; 72536at2157; -.
DR PhylomeDB; Q60364; -.
DR BioCyc; MetaCyc:MON-14603; -.
DR BRENDA; 4.1.99.12; 3260.
DR SABIO-RK; Q60364; -.
DR UniPathway; UPA00275; UER00399.
DR EvolutionaryTrace; Q60364; -.
DR Proteomes; UP000000805; 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; Direct protein sequencing; Lyase; Magnesium; Manganese;
KW Metal-binding; Reference proteome; Riboflavin biosynthesis.
FT CHAIN 1..227
FT /note="3,4-dihydroxy-2-butanone 4-phosphate synthase"
FT /id="PRO_0000151825"
FT BINDING 25..26
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:12904291,
FT ECO:0000269|PubMed:15213409, ECO:0007744|PDB:1PVY,
FT ECO:0007744|PDB:1SNN"
FT BINDING 26
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000305|PubMed:12904291,
FT ECO:0000305|PubMed:15213409, ECO:0007744|PDB:1PVY,
FT ECO:0007744|PDB:1SNN"
FT BINDING 26
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000305|PubMed:12904291,
FT ECO:0000305|PubMed:15213409, ECO:0007744|PDB:1PVY,
FT ECO:0007744|PDB:1SNN"
FT BINDING 30
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:12904291,
FT ECO:0000269|PubMed:15213409, ECO:0007744|PDB:1PVY,
FT ECO:0007744|PDB:1SNN"
FT BINDING 161..165
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:12904291,
FT ECO:0000269|PubMed:15213409, ECO:0007744|PDB:1PVY,
FT ECO:0007744|PDB:1SNN"
FT BINDING 164
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000305|PubMed:12904291,
FT ECO:0000305|PubMed:15213409, ECO:0007744|PDB:1PVY,
FT ECO:0007744|PDB:1SNN"
FT SITE 147
FT /note="Essential for catalytic activity"
FT SITE 185
FT /note="Essential for catalytic activity"
FT MUTAGEN 21
FT /note="D->E,N: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 21
FT /note="D->S: Reduces activity 70-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 25
FT /note="R->E,K: Reduces activity 50-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 26
FT /note="E->D,Q,S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 28
FT /note="E->D,S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 28
FT /note="E->Q: Reduces activity 23-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 30
FT /note="D->E,N: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 30
FT /note="D->S: Reduces activity 30-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 55
FT /note="C->G: Reduces activity 70-fold. Increases Km for
FT ribulose-5-phosphate 7-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 55
FT /note="C->S: Reduces activity 30-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 112
FT /note="T->A: Reduces activity 50-fold. Increases Km for
FT ribulose-5-phosphate 10-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 119
FT /note="R->S: Reduces activity 8-fold. Increases Km for
FT ribulose-5-phosphate 8-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 147
FT /note="H->S: Reduces activity 10-fold."
FT MUTAGEN 161
FT /note="R->S: Reduces activity 10-fold. Increases Km for
FT ribulose-5-phosphate 7-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 164
FT /note="H->N,S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 165
FT /note="T->A: Reduces activity by 2-fold. Increases Km for
FT ribulose-5-phosphate 8-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 165
FT /note="T->S: Reduces activity by 3-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 166
FT /note="E->S: Increases Km for ribulose-5-phosphate 8-fold."
FT /evidence="ECO:0000269|PubMed:12200440"
FT MUTAGEN 185
FT /note="E->D,Q,S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12200440"
FT HELIX 3..12
FT /evidence="ECO:0007829|PDB:1SNN"
FT STRAND 17..20
FT /evidence="ECO:0007829|PDB:1SNN"
FT TURN 23..26
FT /evidence="ECO:0007829|PDB:1SNN"
FT STRAND 29..34
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 35..37
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 40..49
FT /evidence="ECO:0007829|PDB:1SNN"
FT STRAND 51..58
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 60..66
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 71..78
FT /evidence="ECO:0007829|PDB:1SNN"
FT TURN 79..81
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 83..87
FT /evidence="ECO:0007829|PDB:1SNN"
FT STRAND 96..98
FT /evidence="ECO:0007829|PDB:1SNN"
FT STRAND 101..107
FT /evidence="ECO:0007829|PDB:1SNN"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 116..131
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 138..141
FT /evidence="ECO:0007829|PDB:1SNN"
FT STRAND 142..152
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 164..174
FT /evidence="ECO:0007829|PDB:1SNN"
FT STRAND 179..187
FT /evidence="ECO:0007829|PDB:1SNN"
FT STRAND 191..193
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 196..206
FT /evidence="ECO:0007829|PDB:1SNN"
FT STRAND 210..212
FT /evidence="ECO:0007829|PDB:1SNN"
FT HELIX 213..219
FT /evidence="ECO:0007829|PDB:1SNN"
SQ SEQUENCE 227 AA; 25797 MW; 0718EE5B4247995D CRC64;
MNNVEKAIEA LKKGEIILVY DSDEREGETD MVVASQFITP EHIRIMRKDA GGLICTALHP
DICNKLGIPF MVDILEFASQ KFKVLRELYP NDIPYDEKSS FSITINHRKT FTGITDNDRA
FTIKKLAELV KEGRFNDFGK EFRSPGHVTL LRAAEGLVKN RQGHTEMTVA LAELANLVPI
TTICEMMGDD GNAMSKNETK RYAEKHNLIY LSGEEIINYY LDKYLKD
