YPK3_YEAST
ID YPK3_YEAST Reviewed; 525 AA.
AC P38070; D6VQ29;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 191.
DE RecName: Full=Serine/threonine-protein kinase YPK3 {ECO:0000305|PubMed:20702584};
DE EC=2.7.11.1 {ECO:0000269|PubMed:11062466};
DE AltName: Full=Ribosomal S6 kinase homolog YPK3 {ECO:0000305|PubMed:25767889};
DE Short=S6K homolog YPK3;
GN Name=YPK3 {ECO:0000303|PubMed:20702584};
GN OrderedLocusNames=YBR028C {ECO:0000312|SGD:S000000232}; ORFNames=YBR0312;
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 204508 / S288c;
RX PubMed=8091864; DOI=10.1002/yea.320100010;
RA Smits P.H.M., de Haan M., Maat C., Grivell L.A.;
RT "The complete sequence of a 33 kb fragment on the right arm of chromosome
RT II from Saccharomyces cerevisiae reveals 16 open reading frames, including
RT ten new open reading frames, five previously identified genes and a
RT homologue of the SCO1 gene.";
RL Yeast 10:S75-S80(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA Mewes H.-W., Kleine K.;
RT "Complete DNA sequence of yeast chromosome II.";
RL EMBO J. 13:5795-5809(1994).
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 FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=11062466; DOI=10.1038/81576;
RA Zhu H., Klemic J.F., Chang S., Bertone P., Casamayor A., Klemic K.G.,
RA Smith D., Gerstein M., Reed M.A., Snyder M.;
RT "Analysis of yeast protein kinases using protein chips.";
RL Nat. Genet. 26:283-289(2000).
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).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-90, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=YAL6B;
RX PubMed=15665377; DOI=10.1074/mcp.m400219-mcp200;
RA Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M.,
RA Jensen O.N.;
RT "Quantitative phosphoproteomics applied to the yeast pheromone signaling
RT pathway.";
RL Mol. Cell. Proteomics 4:310-327(2005).
RN [8]
RP PHOSPHORYLATION BY PKA.
RX PubMed=16172400; DOI=10.1073/pnas.0501046102;
RA Budovskaya Y.V., Stephan J.S., Deminoff S.J., Herman P.K.;
RT "An evolutionary proteomics approach identifies substrates of the cAMP-
RT dependent protein kinase.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:13933-13938(2005).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-90, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-105 AND THR-107, AND
RP IDENTIFICATION BY MASS 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 [12]
RP PHOSPHORYLATION BY PKA.
RX PubMed=20702584; DOI=10.1091/mbc.e10-03-0182;
RA Soulard A., Cremonesi A., Moes S., Schutz F., Jeno P., Hall M.N.;
RT "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein
RT kinase A toward some but not all substrates.";
RL Mol. Biol. Cell 21:3475-3486(2010).
RN [13]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [14]
RP FUNCTION.
RX PubMed=25767889; DOI=10.1371/journal.pone.0120250;
RA Gonzalez A., Shimobayashi M., Eisenberg T., Merle D.A., Pendl T.,
RA Hall M.N., Moustafa T.;
RT "TORC1 promotes phosphorylation of ribosomal protein S6 via the AGC kinase
RT Ypk3 in Saccharomyces cerevisiae.";
RL PLoS ONE 10:E0120250-E0120250(2015).
CC -!- FUNCTION: AGC kinase which plays a role in TOR complex 1 (TORC1)
CC signaling pathway which mediates temporal control of cell growth in
CC response to nutrients (PubMed:11062466). Required for phosphorylation
CC of ribosomal protein S6 (RPS6A/RPS6B) at 'Ser-232' and 'Ser-233'
CC (PubMed:25767889). {ECO:0000269|PubMed:11062466,
CC ECO:0000269|PubMed:25767889}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-
CC [protein]; Xref=Rhea:RHEA:17989, Rhea:RHEA-COMP:9863, Rhea:RHEA-
CC COMP:11604, ChEBI:CHEBI:15378, ChEBI:CHEBI:29999, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:83421, ChEBI:CHEBI:456216; EC=2.7.11.1;
CC Evidence={ECO:0000269|PubMed:11062466};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-
CC threonyl-[protein]; Xref=Rhea:RHEA:46608, Rhea:RHEA-COMP:11060,
CC Rhea:RHEA-COMP:11605, ChEBI:CHEBI:15378, ChEBI:CHEBI:30013,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:61977, ChEBI:CHEBI:456216;
CC EC=2.7.11.1; Evidence={ECO:0000269|PubMed:11062466};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
CC -!- PTM: Phosphorylated by PKA in a TORC1-dependent manner. Phosphorylation
CC at PKA consensus sites RRxS/T decreases upon rapamycin treatment.
CC {ECO:0000269|PubMed:16172400, ECO:0000269|PubMed:20702584}.
CC -!- MISCELLANEOUS: Present with 1470 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the protein kinase superfamily. AGC Ser/Thr
CC protein kinase family. S6 kinase subfamily. {ECO:0000305}.
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DR EMBL; X76078; CAA53684.1; -; Genomic_DNA.
DR EMBL; Z35897; CAA84970.1; -; Genomic_DNA.
DR EMBL; BK006936; DAA07149.1; -; Genomic_DNA.
DR PIR; S45884; S45884.
DR RefSeq; NP_009584.1; NM_001178376.1.
DR AlphaFoldDB; P38070; -.
DR SMR; P38070; -.
DR BioGRID; 32730; 91.
DR DIP; DIP-4629N; -.
DR IntAct; P38070; 6.
DR MINT; P38070; -.
DR STRING; 4932.YBR028C; -.
DR iPTMnet; P38070; -.
DR MaxQB; P38070; -.
DR PaxDb; P38070; -.
DR PRIDE; P38070; -.
DR EnsemblFungi; YBR028C_mRNA; YBR028C; YBR028C.
DR GeneID; 852316; -.
DR KEGG; sce:YBR028C; -.
DR SGD; S000000232; YPK3.
DR VEuPathDB; FungiDB:YBR028C; -.
DR eggNOG; KOG0598; Eukaryota.
DR GeneTree; ENSGT00940000167362; -.
DR HOGENOM; CLU_000288_63_5_1; -.
DR InParanoid; P38070; -.
DR OMA; KGSIFAM; -.
DR BioCyc; YEAST:G3O-29007-MON; -.
DR Reactome; R-SCE-166208; mTORC1-mediated signalling.
DR Reactome; R-SCE-198693; AKT phosphorylates targets in the nucleus.
DR Reactome; R-SCE-198753; ERK/MAPK targets.
DR Reactome; R-SCE-375165; NCAM signaling for neurite out-growth.
DR PRO; PR:P38070; -.
DR Proteomes; UP000002311; Chromosome II.
DR RNAct; P38070; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0106310; F:protein serine kinase activity; IEA:RHEA.
DR GO; GO:0004674; F:protein serine/threonine kinase activity; IDA:SGD.
DR GO; GO:0004711; F:ribosomal protein S6 kinase activity; IBA:GO_Central.
DR GO; GO:0018105; P:peptidyl-serine phosphorylation; IDA:SGD.
DR GO; GO:0046777; P:protein autophosphorylation; IDA:SGD.
DR GO; GO:0031929; P:TOR signaling; IBA:GO_Central.
DR CDD; cd05123; STKc_AGC; 1.
DR InterPro; IPR000961; AGC-kinase_C.
DR InterPro; IPR011009; Kinase-like_dom_sf.
DR InterPro; IPR017892; Pkinase_C.
DR InterPro; IPR000719; Prot_kinase_dom.
DR InterPro; IPR017441; Protein_kinase_ATP_BS.
DR InterPro; IPR008271; Ser/Thr_kinase_AS.
DR InterPro; IPR045270; STKc_AGC.
DR Pfam; PF00069; Pkinase; 1.
DR Pfam; PF00433; Pkinase_C; 1.
DR SMART; SM00133; S_TK_X; 1.
DR SMART; SM00220; S_TKc; 1.
DR SUPFAM; SSF56112; SSF56112; 1.
DR PROSITE; PS51285; AGC_KINASE_CTER; 1.
DR PROSITE; PS00107; PROTEIN_KINASE_ATP; 1.
DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
DR PROSITE; PS00108; PROTEIN_KINASE_ST; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; Kinase; Nucleotide-binding; Phosphoprotein;
KW Reference proteome; Serine/threonine-protein kinase; Transferase.
FT CHAIN 1..525
FT /note="Serine/threonine-protein kinase YPK3"
FT /id="PRO_0000086073"
FT DOMAIN 128..424
FT /note="Protein kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT DOMAIN 445..524
FT /note="AGC-kinase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00618"
FT REGION 170..193
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 277
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159,
FT ECO:0000255|PROSITE-ProRule:PRU10027"
FT BINDING 134..142
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT BINDING 157
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT MOD_RES 90
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:15665377,
FT ECO:0007744|PubMed:17330950"
FT MOD_RES 105
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 107
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 321
FT /note="Phosphoserine; by PKH1 or PKH2"
FT /evidence="ECO:0000250|UniProtKB:Q12706"
FT MOD_RES 490
FT /note="Phosphothreonine; by TORC1"
FT /evidence="ECO:0000250|UniProtKB:Q12706"
FT MOD_RES 513
FT /note="Phosphoserine; by TORC1"
FT /evidence="ECO:0000250|UniProtKB:Q12706"
SQ SEQUENCE 525 AA; 59591 MW; B8FFE61A44067677 CRC64;
MIFSLDEELH RVSLDDKKND IKVDYSSAIY NDINHEQGSS ITYEESINHL SVHSNAIPLN
GMSPAHRMRR RSSAYSKFPI LTPPNTRRFS ITGSDAMRTN TNRLSITPQD IISSNIGENE
LSRNLHDFKP VRVLGQGAYG KVLLVKDVNT SKLYAMKQLR KAEILISQTA TDSKREDEDK
NDGNNNDNDD GLSKRLERTF AERSILSEIE HPNIVKLFYS FHDNSKLYLL LQYIPGGELF
YHLKEHGTLD ETTVSFYAAE ISCALRFLHT KGVVYRDLKP ENCLLNQRGH LVLTDFGLSK
KSANDSAVDE EDPENVNALY SIIGTPEYCA PEILLGKAYS QNCDWYSLGC LLYDMLVGKP
PYTGSNHKVI INKIQQNKQG PKIPFYLSEG MKDILNALLK KETAKRWNVD KYWAKTGANN
KPTKSKKKKS GAARTSLFTE HFIFRKIDWK LLESGQLQKT TLGPIVPVIT DLELAENFDT
EFTSMSYEET YTDSKPININ SVSKSPDMFK GFSYKASGSY LEKYF
