RBSK_YEAST
ID RBSK_YEAST Reviewed; 333 AA.
AC P25332; D6VR46;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2004, sequence version 2.
DT 03-AUG-2022, entry version 173.
DE RecName: Full=Ribokinase {ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000303|PubMed:1964349};
DE Short=RK {ECO:0000255|HAMAP-Rule:MF_03215};
DE EC=2.7.1.15 {ECO:0000250|UniProtKB:P0A9J6, ECO:0000255|HAMAP-Rule:MF_03215};
GN Name=RBK1 {ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000303|PubMed:1964349};
GN OrderedLocusNames=YCR036W {ECO:0000312|SGD:S000000632};
GN ORFNames=YCR36W, YCR523;
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].
RC STRAIN=ATCC 96604 / S288c / FY1679;
RX PubMed=1964349; DOI=10.1002/yea.320060609;
RA Thierry A., Fairhead C., Dujon B.;
RT "The complete sequence of the 8.2 kb segment left of MAT on chromosome III
RT reveals five ORFs, including a gene for a yeast ribokinase.";
RL Yeast 6:521-534(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=1574125; DOI=10.1038/357038a0;
RA Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M.,
RA Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G.,
RA Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A.,
RA Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M., Carcano C.,
RA Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M.,
RA Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C.,
RA Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F.,
RA Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C.,
RA Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E.,
RA Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P.,
RA Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J.,
RA Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P.,
RA Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M.,
RA Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P.,
RA Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G.,
RA Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E.,
RA Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F.,
RA Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L.,
RA Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J.,
RA Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M.,
RA Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A.,
RA Richterich P., Roberts A.B., Rodriguez F., Sanz E.,
RA Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J.,
RA Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I.,
RA Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M.,
RA Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M.,
RA Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D.,
RA Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K.,
RA Sgouros J.G.;
RT "The complete DNA sequence of yeast chromosome III.";
RL Nature 357:38-46(1992).
RN [3]
RP SEQUENCE REVISION TO 178 AND 301.
RA Valles G., Volckaerts G.;
RL Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases.
RN [4]
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 [5]
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 [6]
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).
CC -!- FUNCTION: Catalyzes the phosphorylation of ribose at O-5 in a reaction
CC requiring ATP and magnesium. The resulting D-ribose-5-phosphate can
CC then be used either for sythesis of nucleotides, histidine, and
CC tryptophan, or as a component of the pentose phosphate pathway.
CC {ECO:0000255|HAMAP-Rule:MF_03215}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + D-ribose = ADP + D-ribose 5-phosphate + H(+);
CC Xref=Rhea:RHEA:13697, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:47013, ChEBI:CHEBI:78346, ChEBI:CHEBI:456216;
CC EC=2.7.1.15; Evidence={ECO:0000255|HAMAP-Rule:MF_03215};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03215};
CC Note=Requires a divalent cation, most likely magnesium in vivo, as an
CC electrophilic catalyst to aid phosphoryl group transfer. It is the
CC chelate of the metal and the nucleotide that is the actual substrate.
CC {ECO:0000255|HAMAP-Rule:MF_03215};
CC -!- ACTIVITY REGULATION: Activated by a monovalent cation that binds near,
CC but not in, the active site. The most likely occupant of the site in
CC vivo is potassium. Ion binding induces a conformational change that may
CC alter substrate affinity. {ECO:0000255|HAMAP-Rule:MF_03215}.
CC -!- PATHWAY: Carbohydrate metabolism; D-ribose degradation; D-ribose 5-
CC phosphate from beta-D-ribopyranose: step 2/2. {ECO:0000255|HAMAP-
CC Rule:MF_03215}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_03215}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_03215,
CC ECO:0000269|PubMed:14562095}. Nucleus {ECO:0000255|HAMAP-Rule:MF_03215,
CC ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 1780 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the carbohydrate kinase PfkB family. Ribokinase
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_03215}.
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DR EMBL; X56909; CAA40228.1; -; Genomic_DNA.
DR EMBL; X59720; CAA42303.2; -; Genomic_DNA.
DR EMBL; BK006937; DAA07515.1; -; Genomic_DNA.
DR PIR; S12918; KIBYRB.
DR RefSeq; NP_009965.2; NM_001178750.1.
DR AlphaFoldDB; P25332; -.
DR SMR; P25332; -.
DR BioGRID; 31019; 122.
DR DIP; DIP-4990N; -.
DR IntAct; P25332; 2.
DR STRING; 4932.YCR036W; -.
DR MaxQB; P25332; -.
DR PaxDb; P25332; -.
DR PRIDE; P25332; -.
DR EnsemblFungi; YCR036W_mRNA; YCR036W; YCR036W.
DR GeneID; 850402; -.
DR KEGG; sce:YCR036W; -.
DR SGD; S000000632; RBK1.
DR VEuPathDB; FungiDB:YCR036W; -.
DR eggNOG; KOG2855; Eukaryota.
DR GeneTree; ENSGT00390000005743; -.
DR HOGENOM; CLU_027634_2_0_1; -.
DR InParanoid; P25332; -.
DR OMA; IPWRDEL; -.
DR BioCyc; YEAST:YCR036W-MON; -.
DR Reactome; R-SCE-71336; Pentose phosphate pathway.
DR UniPathway; UPA00916; UER00889.
DR PRO; PR:P25332; -.
DR Proteomes; UP000002311; Chromosome III.
DR RNAct; P25332; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004747; F:ribokinase activity; ISS:SGD.
DR GO; GO:0019303; P:D-ribose catabolic process; ISS:SGD.
DR CDD; cd01174; ribokinase; 1.
DR Gene3D; 3.40.1190.20; -; 1.
DR HAMAP; MF_01987; Ribokinase; 1.
DR InterPro; IPR002173; Carboh/pur_kinase_PfkB_CS.
DR InterPro; IPR011877; D_ribokin.
DR InterPro; IPR011611; PfkB_dom.
DR InterPro; IPR002139; Ribo/fructo_kinase.
DR InterPro; IPR029056; Ribokinase-like.
DR Pfam; PF00294; PfkB; 1.
DR PRINTS; PR00990; RIBOKINASE.
DR SUPFAM; SSF53613; SSF53613; 1.
DR PROSITE; PS00584; PFKB_KINASES_2; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Carbohydrate metabolism; Cytoplasm; Kinase; Magnesium;
KW Metal-binding; Nucleotide-binding; Nucleus; Potassium; Reference proteome;
KW Transferase.
FT CHAIN 1..333
FT /note="Ribokinase"
FT /id="PRO_0000080094"
FT ACT_SITE 283
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 10..12
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 38..42
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 149
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 193
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 248..253
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 277
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 279
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 282..283
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 283
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 313
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 316
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 318
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT BINDING 322
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03215"
FT CONFLICT 178
FT /note="A -> T (in Ref. 1; CAA40228)"
FT /evidence="ECO:0000305"
FT CONFLICT 301
FT /note="T -> M (in Ref. 1; CAA40228)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 333 AA; 36924 MW; 226B44DA7E458B95 CRC64;
MGITVIGSLN YDLDTFTDRL PNAGETFRAN HFETHAGGKG LNQAAAIGKL KNPSSRYSVR
MIGNVGNDTF GKQLKDTLSD CGVDITHVGT YEGINTGTAT ILIEEKAGGQ NRILIVEGAN
SKTIYDPKQL CEIFPEGKEE EEYVVFQHEI PDPLSIIKWI HANRPNFQIV YNPSPFKAMP
KKDWELVDLL VVNEIEGLQI VESVFDNELV EEIREKIKDD FLGEYRKICE LLYEKLMNRK
KRGIVVMTLG SRGVLFCSHE SPEVQFLPAI QNVSVVDTTG AGDTFLGGLV TQLYQGETLS
TAIKFSTLAS SLTIQRKGAA ESMPLYKDVQ KDA
