RIB3_YEAST
ID RIB3_YEAST Reviewed; 208 AA.
AC Q99258; D6VTB0;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 166.
DE RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase;
DE Short=DHBP synthase;
DE EC=4.1.99.12 {ECO:0000305|PubMed:7559556};
GN Name=RIB3; OrderedLocusNames=YDR487C; ORFNames=D8035.30;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Garcia-Ramirez J.J., Santos M.A., Revuelta J.L.;
RT "Cloning and sequencing of the RIB3 gene from Saccharomyces cerevisiae.";
RL Submitted (JAN-1995) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=7559556; DOI=10.1074/jbc.270.40.23801;
RA Garcia-Ramirez J.J., Santos M.A., Revuelta J.L.;
RT "The Saccharomyces cerevisiae RIB4 gene codes for 6,7-dimethyl-8-
RT ribityllumazine synthase involved in riboflavin biosynthesis. Molecular
RT characterization of the gene and purification of the encoded protein.";
RL J. Biol. Chem. 270:23801-23807(1995).
RN [6]
RP SUBCELLULAR LOCATION.
RX PubMed=12595523; DOI=10.1074/jbc.m300593200;
RA Jin C., Barrientos A., Tzagoloff A.;
RT "Yeast dihydroxybutanone phosphate synthase, an enzyme of the riboflavin
RT biosynthetic pathway, has a second unrelated function in expression of
RT mitochondrial respiration.";
RL J. Biol. Chem. 278:14698-14703(2003).
RN [7]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [8]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-3, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [10]
RP GLUTATHIONYLATION AT CYS-56.
RX PubMed=21565288; DOI=10.1016/j.jprot.2011.04.018;
RA McDonagh B., Requejo R., Fuentes-Almagro C.A., Ogueta S., Barcena J.A.,
RA Padilla C.A.;
RT "Thiol redox proteomics identifies differential targets of cytosolic and
RT mitochondrial glutaredoxin-2 isoforms in Saccharomyces cerevisiae.
RT Reversible S-glutathionylation of DHBP synthase (RIB3).";
RL J. Proteomics 74:2487-2497(2011).
CC -!- FUNCTION: Catalyzes the conversion of D-ribulose 5-phosphate to formate
CC and 3,4-dihydroxy-2-butanone 4-phosphate (Probable). Has also an
CC unrelated function in expression of mitochondrial respiration
CC (PubMed:12595523). {ECO:0000269|PubMed:12595523,
CC ECO:0000305|PubMed:7559556}.
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:0000305|PubMed:7559556};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 2 divalent metal cations per subunit. Magnesium or
CC manganese. {ECO:0000250};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-
CC oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12595523,
CC ECO:0000269|PubMed:14562095}. Nucleus {ECO:0000269|PubMed:14562095}.
CC Mitochondrion intermembrane space {ECO:0000269|PubMed:12595523}.
CC -!- PTM: S-glutathionylation of Cys-56 is reversible and dependent on the
CC cytoplasmic isoform of glutaredoxin-2. {ECO:0000269|PubMed:21565288}.
CC -!- MISCELLANEOUS: Present with 5460 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the DHBP synthase family. {ECO:0000305}.
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DR EMBL; Z21619; CAA79743.1; -; Genomic_DNA.
DR EMBL; U33050; AAB64927.1; -; Genomic_DNA.
DR EMBL; AY557810; AAS56136.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12320.1; -; Genomic_DNA.
DR PIR; S50973; S50973.
DR RefSeq; NP_010775.1; NM_001180795.1.
DR AlphaFoldDB; Q99258; -.
DR SMR; Q99258; -.
DR BioGRID; 32539; 18.
DR DIP; DIP-4316N; -.
DR IntAct; Q99258; 1.
DR MINT; Q99258; -.
DR STRING; 4932.YDR487C; -.
DR iPTMnet; Q99258; -.
DR MaxQB; Q99258; -.
DR PaxDb; Q99258; -.
DR PRIDE; Q99258; -.
DR EnsemblFungi; YDR487C_mRNA; YDR487C; YDR487C.
DR GeneID; 852098; -.
DR KEGG; sce:YDR487C; -.
DR SGD; S000002895; RIB3.
DR VEuPathDB; FungiDB:YDR487C; -.
DR eggNOG; KOG1284; Eukaryota.
DR GeneTree; ENSGT00940000176677; -.
DR HOGENOM; CLU_020273_3_0_1; -.
DR InParanoid; Q99258; -.
DR OMA; DAGGLIC; -.
DR BioCyc; YEAST:MON3O-89; -.
DR UniPathway; UPA00275; UER00399.
DR PRO; PR:Q99258; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q99258; protein.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IMP:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009060; P:aerobic respiration; IMP:SGD.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IMP:SGD.
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 Cytoplasm; Glutathionylation; Lyase; Magnesium; Manganese; Metal-binding;
KW Mitochondrion; Nucleus; Phosphoprotein; Reference proteome;
KW Riboflavin biosynthesis.
FT CHAIN 1..208
FT /note="3,4-dihydroxy-2-butanone 4-phosphate synthase"
FT /id="PRO_0000151829"
FT BINDING 27
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q8TG90"
FT BINDING 27
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q8TG90"
FT BINDING 31
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250|UniProtKB:Q5A3V6"
FT BINDING 88
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250|UniProtKB:Q5A3V6"
FT BINDING 145..149
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250|UniProtKB:Q5A3V6"
FT BINDING 148
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q8TG90"
FT SITE 131
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000250"
FT SITE 169
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000250"
FT MOD_RES 3
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 56
FT /note="S-glutathionyl cysteine; by GRX2"
FT /evidence="ECO:0000269|PubMed:21565288"
SQ SEQUENCE 208 AA; 22568 MW; ECA30183FAFCBA9E CRC64;
MFTPIDQAIE HFKQNKFVIV MDDAGRENEG DLICAAENVS TEQMAFLVRH SSGYVCAPMT
NAIADKLDLP LLRTGMKFES NDDDRHGTAY TITVDVAQGT TTGISAHDRS MTCRALADSS
STPKSFLKPG HICPLRAADG GVLQRRGHTE AGVDLCKLSG LSPVAVIGEL VNDDEQGTMM
RLNDCQAFGK KHGIPLISIE ELAQYLKK
