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Protein

Serine/threonine-protein kinase KIN28

Gene

KIN28

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.1 Publication

Catalytic activityi

ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei36 – 361ATPPROSITE-ProRule annotation
Active sitei129 – 1291Proton acceptorPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi13 – 219ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

  • 7-methylguanosine mRNA capping Source: SGD
  • cell cycle Source: UniProtKB-KW
  • cell division Source: UniProtKB-KW
  • phosphorylation of RNA polymerase II C-terminal domain Source: SGD
  • phosphorylation of RNA polymerase II C-terminal domain involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex Source: SGD
  • phosphorylation of RNA polymerase II C-terminal domain serine 5 residues involved in recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex Source: SGD
  • positive regulation of transcription from RNA polymerase II promoter Source: SGD
  • transcription from RNA polymerase II promoter Source: SGD
  • transcription from RNA polymerase I promoter Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Serine/threonine-protein kinase, Transferase

Keywords - Biological processi

Cell cycle, Cell division, Transcription, Transcription regulation

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29509-MONOMER.
BRENDAi2.7.11.22. 984.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-5696395. Formation of Incision Complex in GG-NER.
R-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-SCE-69202. Cyclin E associated events during G1/S transition.
R-SCE-69273. Cyclin A/B1 associated events during G2/M transition.
R-SCE-69656. Cyclin A:Cdk2-associated events at S phase entry.
R-SCE-72086. mRNA Capping.
R-SCE-73776. RNA Polymerase II Promoter Escape.
R-SCE-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SCE-75953. RNA Polymerase II Transcription Initiation.
R-SCE-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SCE-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine/threonine-protein kinase KIN28 (EC:2.7.11.23)
Gene namesi
Name:KIN28
Ordered Locus Names:YDL108W
ORF Names:D2330
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL108W.
SGDiS000002266. KIN28.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • holo TFIIH complex Source: SGD
  • nucleus Source: SGD
  • TFIIK complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi17 – 182TY → AF: No effect on phosphorylation; no effect on kinase activity. 1 Publication
Mutagenesisi17 – 171T → D: Slow growth. 1 Publication
Mutagenesisi17 – 171T → E, Q or V: Normal growth. 1 Publication
Mutagenesisi36 – 361K → A: Slow growth. 1 Publication
Mutagenesisi54 – 541E → Q: Non-viable. 1 Publication
Mutagenesisi147 – 1471D → N: Abolishes kinase activity. 2 Publications
Mutagenesisi162 – 1621T → A: Diminishes phosphorylation; 75-80% loss in kinase activity; no effect on survival. 3 Publications
Mutagenesisi162 – 1621T → S, D or E: No effect on kinase activity. 3 Publications
Mutagenesisi163 – 1631S → A: Normal growth. 1 Publication

Chemistry

ChEMBLiCHEMBL5370.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 306306Serine/threonine-protein kinase KIN28PRO_0000086132Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei162 – 1621Phosphothreonine; by CAK3 Publications

Post-translational modificationi

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.3 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP06242.

PTM databases

iPTMnetiP06242.

Interactioni

Subunit structurei

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 HOG1.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CCL1P373666EBI-9691,EBI-4385

Protein-protein interaction databases

BioGridi31954. 82 interactions.
DIPiDIP-2259N.
IntActiP06242. 9 interactions.
MINTiMINT-526112.

Chemistry

BindingDBiP06242.

Structurei

3D structure databases

ProteinModelPortaliP06242.
SMRiP06242. Positions 13-297.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini7 – 290284Protein kinasePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 protein kinase domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00830000128262.
HOGENOMiHOG000233024.
InParanoidiP06242.
KOiK02202.
OMAiQMEVTFR.
OrthoDBiEOG7K3TWD.

Family and domain databases

InterProiIPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR008271. Ser/Thr_kinase_AS.
[Graphical view]
PfamiPF00069. Pkinase. 1 hit.
[Graphical view]
SMARTiSM00220. S_TKc. 1 hit.
[Graphical view]
SUPFAMiSSF56112. SSF56112. 1 hit.
PROSITEiPS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P06242-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVNMEYTKE KKVGEGTYAV VYLGCQHSTG RKIAIKEIKT SEFKDGLDMS
60 70 80 90 100
AIREVKYLQE MQHPNVIELI DIFMAYDNLN LVLEFLPTDL EVVIKDKSIL
110 120 130 140 150
FTPADIKAWM LMTLRGVYHC HRNFILHRDL KPNNLLFSPD GQIKVADFGL
160 170 180 190 200
ARAIPAPHEI LTSNVVTRWY RAPELLFGAK HYTSAIDIWS VGVIFAELML
210 220 230 240 250
RIPYLPGQND VDQMEVTFRA LGTPTDRDWP EVSSFMTYNK LQIYPPPSRD
260 270 280 290 300
ELRKRFIAAS EYALDFMCGM LTMNPQKRWT AVQCLESDYF KELPPPSDPS

SIKIRN
Length:306
Mass (Da):35,247
Last modified:January 1, 1988 - v1
Checksum:i763A5720A1D9ACF3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04423 Genomic DNA. Translation: CAA28019.1.
X95644 Genomic DNA. Translation: CAA64904.1.
Z74156 Genomic DNA. Translation: CAA98675.1.
BK006938 Genomic DNA. Translation: DAA11752.1.
PIRiA25698.
RefSeqiNP_010175.1. NM_001180167.1.

Genome annotation databases

EnsemblFungiiYDL108W; YDL108W; YDL108W.
GeneIDi851450.
KEGGisce:YDL108W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04423 Genomic DNA. Translation: CAA28019.1.
X95644 Genomic DNA. Translation: CAA64904.1.
Z74156 Genomic DNA. Translation: CAA98675.1.
BK006938 Genomic DNA. Translation: DAA11752.1.
PIRiA25698.
RefSeqiNP_010175.1. NM_001180167.1.

3D structure databases

ProteinModelPortaliP06242.
SMRiP06242. Positions 13-297.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31954. 82 interactions.
DIPiDIP-2259N.
IntActiP06242. 9 interactions.
MINTiMINT-526112.

Chemistry

BindingDBiP06242.
ChEMBLiCHEMBL5370.

PTM databases

iPTMnetiP06242.

Proteomic databases

MaxQBiP06242.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL108W; YDL108W; YDL108W.
GeneIDi851450.
KEGGisce:YDL108W.

Organism-specific databases

EuPathDBiFungiDB:YDL108W.
SGDiS000002266. KIN28.

Phylogenomic databases

GeneTreeiENSGT00830000128262.
HOGENOMiHOG000233024.
InParanoidiP06242.
KOiK02202.
OMAiQMEVTFR.
OrthoDBiEOG7K3TWD.

Enzyme and pathway databases

BioCyciYEAST:G3O-29509-MONOMER.
BRENDAi2.7.11.22. 984.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-5696395. Formation of Incision Complex in GG-NER.
R-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-SCE-69202. Cyclin E associated events during G1/S transition.
R-SCE-69273. Cyclin A/B1 associated events during G2/M transition.
R-SCE-69656. Cyclin A:Cdk2-associated events at S phase entry.
R-SCE-72086. mRNA Capping.
R-SCE-73776. RNA Polymerase II Promoter Escape.
R-SCE-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SCE-75953. RNA Polymerase II Transcription Initiation.
R-SCE-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SCE-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

PROiP06242.

Family and domain databases

InterProiIPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR008271. Ser/Thr_kinase_AS.
[Graphical view]
PfamiPF00069. Pkinase. 1 hit.
[Graphical view]
SMARTiSM00220. S_TKc. 1 hit.
[Graphical view]
SUPFAMiSSF56112. SSF56112. 1 hit.
PROSITEiPS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "KIN28, a yeast split gene coding for a putative protein kinase homologous to CDC28."
    Simon M., Seraphin B., Faye G.
    EMBO J. 5:2697-2701(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "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."
    Saiz J.E., Buitrago M.J., Garcia R., Revuelta J.L., del Rey F.
    Yeast 12:1077-1084(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    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.
    Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "The kin28 protein kinase is associated with a cyclin in Saccharomyces cerevisiae."
    Valay J.G., Simon M., Faye G.
    J. Mol. Biol. 234:307-310(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH CCL1.
  6. "Genes for Tfb2, Tfb3, and Tfb4 subunits of yeast transcription/repair factor IIH. Homology to human cyclin-dependent kinase activating kinase and IIH subunits."
    Feaver W.J., Henry N.L., Wang Z., Wu X., Svejstrup J.Q., Bushnell D.A., Friedberg E.C., Kornberg R.D.
    J. Biol. Chem. 272:19319-19327(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, INTERACTION WITH TFB3.
    Strain: DBY2019.
  7. "Cak1 is required for Kin28 phosphorylation and activation in vivo."
    Espinoza F.H., Farrell A., Nourse J.L., Chamberlin H.M., Gileadi O., Morgan D.O.
    Mol. Cell. Biol. 18:6365-6373(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT THR-162, MUTAGENESIS OF THR-162.
  8. "Activating phosphorylation of the Kin28p subunit of yeast TFIIH by Cak1p."
    Kimmelman J., Kaldis P., Hengartner C.J., Laff G.M., Koh S.S., Young R.A., Solomon M.J.
    Mol. Cell. Biol. 19:4774-4787(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT THR-162, MUTAGENESIS OF ASP-147; 17-THR-TYR-18 AND THR-162.
  9. "Interactions of Cdk7 and Kin28 with Hint/PKCI-1 and Hnt1 histidine triad proteins."
    Korsisaari N., Makela T.P.
    J. Biol. Chem. 275:34837-34840(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HNT1.
  10. "Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II."
    Rodriguez C.R., Cho E.-J., Keogh M.-C., Moore C.L., Greenleaf A.L., Buratowski S.
    Mol. Cell. Biol. 20:104-112(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  11. "Kin28 is found within TFIIH and a Kin28-Ccl1-Tfb3 trimer complex with differential sensitivities to T-loop phosphorylation."
    Keogh M.-C., Cho E.-J., Podolny V., Buratowski S.
    Mol. Cell. Biol. 22:1288-1297(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A COMPLEX WITH CCL1 AND TFB3, PHOSPHORYLATION AT THR-162, MUTAGENESIS OF THR-17; LYS-36; GLU-54; ASP-147; THR-162 AND SER-163.
  12. "Osmostress-induced transcription by Hot1 depends on a Hog1-mediated recruitment of the RNA Pol II."
    Alepuz P.M., de Nadal E., Zapater M., Ammerer G., Posas F.
    EMBO J. 22:2433-2442(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HOG1.
  13. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  14. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  15. "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway."
    Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N.
    Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: YAL6B.
  16. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  17. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiKIN28_YEAST
AccessioniPrimary (citable) accession number: P06242
Secondary accession number(s): D6VRP2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 1, 1988
Last modified: July 6, 2016
This is version 175 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 4400 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.