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Serine/threonine-protein kinase KIN28 (EC 2.7.11.23)

 KIN28_YEAST             Reviewed;         306 AA.
P06242; D6VRP2;
01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
01-JAN-1988, sequence version 1.
12-SEP-2018, entry version 195.
RecName: Full=Serine/threonine-protein kinase KIN28;
EC=2.7.11.23;
Name=KIN28; OrderedLocusNames=YDL108W; ORFNames=D2330;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3536482;
Simon M., Seraphin B., Faye G.;
"KIN28, a yeast split gene coding for a putative protein kinase
homologous to CDC28.";
EMBO J. 5:2697-2701(1986).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 96604 / S288c / FY1679;
PubMed=8896274;
DOI=10.1002/(SICI)1097-0061(199609)12:10B<1077::AID-YEA8>3.3.CO;2-Q;
Saiz J.E., Buitrago M.J., Garcia R., Revuelta J.L., del Rey F.;
"The sequence of a 20.3 kb DNA fragment from the left arm of
Saccharomyces cerevisiae chromosome IV contains the KIN28, MSS2, PHO2,
POL3 and DUN1 genes, and six new open reading frames.";
Yeast 12:1077-1084(1996).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169867;
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N.,
Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M.,
Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L.,
Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M.,
Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S.,
Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M.,
Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S.,
Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K.,
Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D.,
Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C.,
Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T.,
Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E.,
Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W.,
Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K.,
Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S.,
Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A.,
Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S.,
Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M.,
Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y.,
Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M.,
Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E.,
Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R.,
Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
Mewes H.-W., Zollner A., Zaccaria P.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
Nature 387:75-78(1997).
[4]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[5]
INTERACTION WITH CCL1.
PubMed=8230216; DOI=10.1006/jmbi.1993.1587;
Valay J.G., Simon M., Faye G.;
"The kin28 protein kinase is associated with a cyclin in Saccharomyces
cerevisiae.";
J. Mol. Biol. 234:307-310(1993).
[6]
SUBUNIT, AND INTERACTION WITH TFB3.
STRAIN=DBY2019;
PubMed=9235928; DOI=10.1074/jbc.272.31.19319;
Feaver W.J., Henry N.L., Wang Z., Wu X., Svejstrup J.Q.,
Bushnell D.A., Friedberg E.C., Kornberg R.D.;
"Genes for Tfb2, Tfb3, and Tfb4 subunits of yeast transcription/repair
factor IIH. Homology to human cyclin-dependent kinase activating
kinase and IIH subunits.";
J. Biol. Chem. 272:19319-19327(1997).
[7]
PHOSPHORYLATION AT THR-162, AND MUTAGENESIS OF THR-162.
PubMed=9774652; DOI=10.1128/MCB.18.11.6365;
Espinoza F.H., Farrell A., Nourse J.L., Chamberlin H.M., Gileadi O.,
Morgan D.O.;
"Cak1 is required for Kin28 phosphorylation and activation in vivo.";
Mol. Cell. Biol. 18:6365-6373(1998).
[8]
PHOSPHORYLATION AT THR-162, AND MUTAGENESIS OF ASP-147; 17-THR-TYR-18
AND THR-162.
PubMed=10373527; DOI=10.1128/MCB.19.7.4774;
Kimmelman J., Kaldis P., Hengartner C.J., Laff G.M., Koh S.S.,
Young R.A., Solomon M.J.;
"Activating phosphorylation of the Kin28p subunit of yeast TFIIH by
Cak1p.";
Mol. Cell. Biol. 19:4774-4787(1999).
[9]
INTERACTION WITH HNT1.
PubMed=10958787; DOI=10.1074/jbc.C000505200;
Korsisaari N., Makela T.P.;
"Interactions of Cdk7 and Kin28 with Hint/PKCI-1 and Hnt1 histidine
triad proteins.";
J. Biol. Chem. 275:34837-34840(2000).
[10]
FUNCTION.
PubMed=10594013; DOI=10.1128/MCB.20.1.104-112.2000;
Rodriguez C.R., Cho E.-J., Keogh M.-C., Moore C.L., Greenleaf A.L.,
Buratowski S.;
"Kin28, the TFIIH-associated carboxy-terminal domain kinase,
facilitates the recruitment of mRNA processing machinery to RNA
polymerase II.";
Mol. Cell. Biol. 20:104-112(2000).
[11]
IDENTIFICATION IN A COMPLEX WITH CCL1 AND TFB3, PHOSPHORYLATION AT
THR-162, AND MUTAGENESIS OF THR-17; LYS-36; GLU-54; ASP-147; THR-162
AND SER-163.
PubMed=11839796; DOI=10.1128/MCB.22.5.1288-1297.2002;
Keogh M.-C., Cho E.-J., Podolny V., Buratowski S.;
"Kin28 is found within TFIIH and a Kin28-Ccl1-Tfb3 trimer complex with
differential sensitivities to T-loop phosphorylation.";
Mol. Cell. Biol. 22:1288-1297(2002).
[12]
INTERACTION WITH HOG1.
PubMed=12743037; DOI=10.1093/emboj/cdg243;
Alepuz P.M., de Nadal E., Zapater M., Ammerer G., Posas F.;
"Osmostress-induced transcription by Hot1 depends on a Hog1-mediated
recruitment of the RNA Pol II.";
EMBO J. 22:2433-2442(2003).
[13]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[14]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[15]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=YAL6B;
PubMed=15665377; DOI=10.1074/mcp.M400219-MCP200;
Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J.,
Mann M., Jensen O.N.;
"Quantitative phosphoproteomics applied to the yeast pheromone
signaling pathway.";
Mol. Cell. Proteomics 4:310-327(2005).
[16]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
[17]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
-!- FUNCTION: Catalytic component of the TFIIK complex (KIN28-CCL1
dimer) which is the protein kinase component of transcription
factor IIH (TFIIH) and phosphorylates the C-terminal domain of RNA
polymerase II during transition from transcription to elongation
after preinitiation complex (PIC) formation, thereby positively
regulating transcription. TFIIH (or factor B) is essential for
both basal and activated transcription, and is involved in
nucleotide excision repair (NER) of damaged DNA. TFIIH has DNA-
dependent ATPase activity and is essential for polymerase II
transcription in vitro. Essential for cell proliferation.
{ECO:0000269|PubMed:10594013}.
-!- CATALYTIC ACTIVITY: ATP + [DNA-directed RNA polymerase] = ADP +
[DNA-directed RNA polymerase] phosphate.
-!- SUBUNIT: CCL1 and KIN28 form the TFIIK complex, a component of the
TFIIH holo complex. Component of a complex consisting of KIN28,
CCL1 and TFB3. Interacts with TFB3. Also interacts with HNT1 and
HOG1. {ECO:0000269|PubMed:10958787, ECO:0000269|PubMed:11839796,
ECO:0000269|PubMed:12743037, ECO:0000269|PubMed:8230216,
ECO:0000269|PubMed:9235928}.
-!- INTERACTION:
P37366:CCL1; NbExp=7; IntAct=EBI-9691, EBI-4385;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
-!- PTM: Phosphorylation of Thr-162 regulates the affinity of
interaction between CCL1, KIN28 and TFB3. Thr-162 phosphorylation
does not vary through the cell cycle and is necessary for full
kinase activity. {ECO:0000269|PubMed:10373527,
ECO:0000269|PubMed:11839796, ECO:0000269|PubMed:9774652}.
-!- MISCELLANEOUS: Present with 4400 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the protein kinase superfamily. CMGC
Ser/Thr protein kinase family. CDC2/CDKX subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X04423; CAA28019.1; -; Genomic_DNA.
EMBL; X95644; CAA64904.1; -; Genomic_DNA.
EMBL; Z74156; CAA98675.1; -; Genomic_DNA.
EMBL; BK006938; DAA11752.1; -; Genomic_DNA.
PIR; A25698; A25698.
RefSeq; NP_010175.1; NM_001180167.1.
ProteinModelPortal; P06242; -.
BioGrid; 31954; 550.
ComplexPortal; CPX-1659; General transcription factor complex TFIIH.
ComplexPortal; CPX-1660; General transcription factor complex TFIIK.
DIP; DIP-2259N; -.
IntAct; P06242; 13.
MINT; P06242; -.
STRING; 4932.YDL108W; -.
BindingDB; P06242; -.
ChEMBL; CHEMBL5370; -.
iPTMnet; P06242; -.
MaxQB; P06242; -.
PaxDb; P06242; -.
PRIDE; P06242; -.
EnsemblFungi; YDL108W; YDL108W; YDL108W.
GeneID; 851450; -.
KEGG; sce:YDL108W; -.
EuPathDB; FungiDB:YDL108W; -.
SGD; S000002266; KIN28.
GeneTree; ENSGT00830000128262; -.
HOGENOM; HOG000233024; -.
InParanoid; P06242; -.
KO; K02202; -.
OMA; ADIKAWM; -.
OrthoDB; EOG092C2FL8; -.
BioCyc; YEAST:G3O-29509-MONOMER; -.
BRENDA; 2.7.11.22; 984.
Reactome; R-SCE-113418; Formation of the Early Elongation Complex.
Reactome; R-SCE-5696395; Formation of Incision Complex in GG-NER.
Reactome; R-SCE-674695; RNA Polymerase II Pre-transcription Events.
Reactome; R-SCE-6781823; Formation of TC-NER Pre-Incision Complex.
Reactome; R-SCE-6782135; Dual incision in TC-NER.
Reactome; R-SCE-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
Reactome; R-SCE-6796648; TP53 Regulates Transcription of DNA Repair Genes.
Reactome; R-SCE-6807505; RNA polymerase II transcribes snRNA genes.
Reactome; R-SCE-69202; Cyclin E associated events during G1/S transition.
Reactome; R-SCE-69231; Cyclin D associated events in G1.
Reactome; R-SCE-69273; Cyclin A/B1/B2 associated events during G2/M transition.
Reactome; R-SCE-69656; Cyclin A:Cdk2-associated events at S phase entry.
Reactome; R-SCE-72086; mRNA Capping.
Reactome; R-SCE-73776; RNA Polymerase II Promoter Escape.
Reactome; R-SCE-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
Reactome; R-SCE-75953; RNA Polymerase II Transcription Initiation.
Reactome; R-SCE-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
Reactome; R-SCE-77075; RNA Pol II CTD phosphorylation and interaction with CE.
PRO; PR:P06242; -.
Proteomes; UP000002311; Chromosome IV.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0005675; C:holo TFIIH complex; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0070985; C:TFIIK complex; IDA:SGD.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004693; F:cyclin-dependent protein serine/threonine kinase activity; IBA:GO_Central.
GO; GO:0008353; F:RNA polymerase II carboxy-terminal domain kinase activity; IDA:SGD.
GO; GO:0006370; P:7-methylguanosine mRNA capping; IMP:SGD.
GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
GO; GO:0070816; P:phosphorylation of RNA polymerase II C-terminal domain; IDA:SGD.
GO; GO:1901921; P:phosphorylation of RNA polymerase II C-terminal domain involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex; IMP:SGD.
GO; GO:1903654; P:phosphorylation of RNA polymerase II C-terminal domain serine 5 residues involved in positive regulation of transcription elongation from RNA polymerase II promoter; IMP:SGD.
GO; GO:1900018; P:phosphorylation of RNA polymerase II C-terminal domain serine 5 residues involved in recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex; IMP:SGD.
GO; GO:1905866; P:positive regulation of Atg1/ULK1 kinase complex assembly; IMP:GO_Central.
GO; GO:1904031; P:positive regulation of cyclin-dependent protein kinase activity; IEA:GOC.
GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IDA:SGD.
GO; GO:0006360; P:transcription by RNA polymerase I; IMP:SGD.
GO; GO:0006366; P:transcription by RNA polymerase II; IDA:SGD.
InterPro; IPR037770; CDK7.
InterPro; IPR011009; Kinase-like_dom_sf.
InterPro; IPR000719; Prot_kinase_dom.
InterPro; IPR017441; Protein_kinase_ATP_BS.
InterPro; IPR008271; Ser/Thr_kinase_AS.
PANTHER; PTHR24056:SF0; PTHR24056:SF0; 1.
Pfam; PF00069; Pkinase; 1.
SMART; SM00220; S_TKc; 1.
SUPFAM; SSF56112; SSF56112; 1.
PROSITE; PS00107; PROTEIN_KINASE_ATP; 1.
PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
PROSITE; PS00108; PROTEIN_KINASE_ST; 1.
1: Evidence at protein level;
ATP-binding; Cell cycle; Cell division; Complete proteome; Kinase;
Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome;
Serine/threonine-protein kinase; Transcription;
Transcription regulation; Transferase.
CHAIN 1 306 Serine/threonine-protein kinase KIN28.
/FTId=PRO_0000086132.
DOMAIN 7 290 Protein kinase. {ECO:0000255|PROSITE-
ProRule:PRU00159}.
NP_BIND 13 21 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00159}.
ACT_SITE 129 129 Proton acceptor. {ECO:0000255|PROSITE-
ProRule:PRU00159, ECO:0000255|PROSITE-
ProRule:PRU10027}.
BINDING 36 36 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00159}.
MOD_RES 162 162 Phosphothreonine; by CAK.
{ECO:0000269|PubMed:10373527,
ECO:0000269|PubMed:11839796,
ECO:0000269|PubMed:9774652}.
MUTAGEN 17 18 TY->AF: No effect on phosphorylation; no
effect on kinase activity.
{ECO:0000269|PubMed:10373527}.
MUTAGEN 17 17 T->D: Slow growth.
{ECO:0000269|PubMed:11839796}.
MUTAGEN 17 17 T->E,Q,V: Normal growth.
{ECO:0000269|PubMed:11839796}.
MUTAGEN 36 36 K->A: Slow growth.
{ECO:0000269|PubMed:11839796}.
MUTAGEN 54 54 E->Q: Non-viable.
{ECO:0000269|PubMed:11839796}.
MUTAGEN 147 147 D->N: Abolishes kinase activity.
{ECO:0000269|PubMed:10373527,
ECO:0000269|PubMed:11839796}.
MUTAGEN 162 162 T->A: Diminishes phosphorylation; 75-80%
loss in kinase activity; no effect on
survival. {ECO:0000269|PubMed:10373527,
ECO:0000269|PubMed:11839796,
ECO:0000269|PubMed:9774652}.
MUTAGEN 162 162 T->S,D,E: No effect on kinase activity.
{ECO:0000269|PubMed:10373527,
ECO:0000269|PubMed:11839796,
ECO:0000269|PubMed:9774652}.
MUTAGEN 163 163 S->A: Normal growth.
{ECO:0000269|PubMed:11839796}.
SEQUENCE 306 AA; 35247 MW; 763A5720A1D9ACF3 CRC64;
MKVNMEYTKE KKVGEGTYAV VYLGCQHSTG RKIAIKEIKT SEFKDGLDMS AIREVKYLQE
MQHPNVIELI DIFMAYDNLN LVLEFLPTDL EVVIKDKSIL FTPADIKAWM LMTLRGVYHC
HRNFILHRDL KPNNLLFSPD GQIKVADFGL ARAIPAPHEI LTSNVVTRWY RAPELLFGAK
HYTSAIDIWS VGVIFAELML RIPYLPGQND VDQMEVTFRA LGTPTDRDWP EVSSFMTYNK
LQIYPPPSRD ELRKRFIAAS EYALDFMCGM LTMNPQKRWT AVQCLESDYF KELPPPSDPS
SIKIRN


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