CTK3_YEAST
ID CTK3_YEAST Reviewed; 296 AA.
AC P46963; D6W0H2; Q6LBS6;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 03-AUG-2022, entry version 178.
DE RecName: Full=CTD kinase subunit gamma;
DE Short=CTDK-I gamma subunit;
DE AltName: Full=CTD kinase 32 kDa subunit;
DE AltName: Full=CTD kinase subunit 3;
GN Name=CTK3; OrderedLocusNames=YML112W; ORFNames=YM8339.07;
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], PROTEIN SEQUENCE OF 146-173, CTD KINASE
RP ACTIVITY, SUBUNIT, AND DISRUPTION PHENOTYPE.
RX PubMed=7565723; DOI=10.1128/mcb.15.10.5716;
RA Sterner D.E., Lee J.M., Hardin S.E., Greenleaf A.L.;
RT "The yeast carboxyl-terminal repeat domain kinase CTDK-I is a divergent
RT cyclin-cyclin-dependent kinase complex.";
RL Mol. Cell. Biol. 15:5716-5724(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 46-262.
RX PubMed=2670564; DOI=10.1002/j.1460-2075.1989.tb03583.x;
RA Winter E., Varshavsky A.;
RT "A DNA binding protein that recognizes oligo(dA).oligo(dT) tracts.";
RL EMBO J. 8:1867-1877(1989).
RN [6]
RP FUNCTION IN RNA POLYMERASE II TRANSCRIPTION.
RX PubMed=9110987; DOI=10.1074/jbc.272.17.10990;
RA Lee J.M., Greenleaf A.L.;
RT "Modulation of RNA polymerase II elongation efficiency by C-terminal
RT heptapeptide repeat domain kinase I.";
RL J. Biol. Chem. 272:10990-10993(1997).
RN [7]
RP CTK1 ACTIVATION, INTERACTION WITH CTK1 AND CTK2, UBIQUITINATION, AND
RP MUTAGENESIS OF 247-TYR--TYR-296.
RX PubMed=11118453; DOI=10.1074/jbc.m010162200;
RA Hautbergue G., Goguel V.;
RT "Activation of the cyclin-dependent kinase CTDK-I requires the
RT heterodimerization of two unstable subunits.";
RL J. Biol. Chem. 276:8005-8013(2001).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12684377; DOI=10.1128/ec.2.2.274-283.2003;
RA Ostapenko D., Solomon M.J.;
RT "Budding yeast CTDK-I is required for DNA damage-induced transcription.";
RL Eukaryot. Cell 2:274-283(2003).
RN [9]
RP FUNCTION IN H3 METHYLATION.
RX PubMed=12629047; DOI=10.1101/gad.1055503;
RA Xiao T., Hall H., Kizer K.O., Shibata Y., Hall M.C., Borchers C.H.,
RA Strahl B.D.;
RT "Phosphorylation of RNA polymerase II CTD regulates H3 methylation in
RT yeast.";
RL Genes Dev. 17:654-663(2003).
RN [10]
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 [11]
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 [12]
RP FUNCTION OF THE CTDK-I COMPLEX.
RX PubMed=15047695; DOI=10.1074/jbc.m402218200;
RA Jones J.C., Phatnani H.P., Haystead T.A., MacDonald J.A., Alam S.M.,
RA Greenleaf A.L.;
RT "C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA
RT polymerase II C-terminal domain repeats.";
RL J. Biol. Chem. 279:24957-24964(2004).
RN [13]
RP FUNCTION IN RNA POLYMERASE I TRANSCRIPTION, AND SUBCELLULAR LOCATION.
RX PubMed=15520468; DOI=10.1093/nar/gkh927;
RA Bouchoux C., Hautbergue G., Grenetier S., Carles C., Riva M., Goguel V.;
RT "CTD kinase I is involved in RNA polymerase I transcription.";
RL Nucleic Acids Res. 32:5851-5860(2004).
RN [14]
RP FUNCTION IN ADAPTATION TO ALTERNATIVE CARBON SOURCES.
RX PubMed=16182287; DOI=10.1016/j.febslet.2005.08.057;
RA Van Driessche B., Coddens S., Van Mullem V., Vandenhaute J.;
RT "Glucose deprivation mediates interaction between CTDK-I and Snf1 in
RT Saccharomyces cerevisiae.";
RL FEBS Lett. 579:5318-5324(2005).
RN [15]
RP FUNCTION IN THE INTEGRITY OF RDNA.
RX PubMed=16984969; DOI=10.1093/nar/gkl493;
RA Grenetier S., Bouchoux C., Goguel V.;
RT "CTD kinase I is required for the integrity of the rDNA tandem array.";
RL Nucleic Acids Res. 34:4996-5006(2006).
RN [16]
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 [17]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-35, AND IDENTIFICATION BY
RP 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).
CC -!- FUNCTION: Gamma subunit of the CTDK-I complex, which
CC hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of
CC the largest RNA polymerase II subunit. CTDK-I phosphorylates 'Ser-5' if
CC the CTD substrate is not phosphorylated at 'Ser-5', but will
CC phosphorylate 'Ser-2' of a CTD substrate if 'Ser-5' is already
CC phosphorylated. CTDK-I is also more reactive toward substrates that are
CC prephosphorylated at 'Ser-2' or 'Ser-5' compared with an
CC unphosphorylated CTD substrate, therefore efficiently creating doubly
CC phosphorylated CTD repeats. Involved in RNA polymerase I transcription
CC and RNA polymerase II transcriptional elongation, and as part of the
CC CTDK-I complex, pre-mRNA 3'-end processing and SET2 mediated H3K36
CC methylation. Together with CTK2, required for CTK1 CTD kinase
CC activation. Required for DNA damage induced transcription. Involved in
CC the adaptation to alternative carbon sources, including galactose,
CC glycerol and ethanol, but not raffinose. Required for the integrity of
CC the rDNA locus. {ECO:0000269|PubMed:12629047,
CC ECO:0000269|PubMed:12684377, ECO:0000269|PubMed:15047695,
CC ECO:0000269|PubMed:15520468, ECO:0000269|PubMed:16182287,
CC ECO:0000269|PubMed:16984969, ECO:0000269|PubMed:9110987}.
CC -!- SUBUNIT: CTDK-I consists of three subunits, CTK1, CTK2 and CTK3 (also
CC called alpha, beta and gamma). Interacts with CTK1. Heterodimerization
CC with CTK2 is required to protect this subunit from degradation.
CC {ECO:0000269|PubMed:11118453, ECO:0000269|PubMed:7565723}.
CC -!- INTERACTION:
CC P46963; Q03957: CTK1; NbExp=7; IntAct=EBI-5241, EBI-5230;
CC P46963; P46962: CTK2; NbExp=10; IntAct=EBI-5241, EBI-5236;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus. Cytoplasm.
CC -!- PTM: Ubiquitinated. Ubiquitination leads to degradation by the 26S
CC proteasome pathway. {ECO:0000269|PubMed:11118453}.
CC -!- DISRUPTION PHENOTYPE: Null mutants are viable, but grow more slowly
CC than wild-type cells at 30 degrees Celsius. They are cold-sensitive,
CC failing to grow at 12 degrees Celsius. They display flocculent growth
CC in liquid media and they show abnormal cell morphologies, for example,
CC a significant fraction of the cells are greatly enlarged. Deletion
CC mutant is sensitive to the DNA synthesis inhibitor hydroxyurea (HU) and
CC UV irradiation. {ECO:0000269|PubMed:12684377,
CC ECO:0000269|PubMed:7565723}.
CC -!- MISCELLANEOUS: Present with 2640 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the CTK3 family. {ECO:0000305}.
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DR EMBL; U30296; AAC49078.1; -; Genomic_DNA.
DR EMBL; Z49210; CAA89106.1; -; Genomic_DNA.
DR EMBL; AY557764; AAS56090.1; -; Genomic_DNA.
DR EMBL; X15478; CAE82078.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA09786.1; -; Genomic_DNA.
DR PIR; S53960; S53960.
DR RefSeq; NP_013595.1; NM_001182474.1.
DR PDB; 7JV7; X-ray; 1.85 A; C=1-296.
DR PDBsum; 7JV7; -.
DR AlphaFoldDB; P46963; -.
DR SMR; P46963; -.
DR BioGRID; 35092; 349.
DR ComplexPortal; CPX-1710; Carboxy-terminal domain protein kinase complex.
DR DIP; DIP-2106N; -.
DR IntAct; P46963; 12.
DR MINT; P46963; -.
DR STRING; 4932.YML112W; -.
DR iPTMnet; P46963; -.
DR MaxQB; P46963; -.
DR PaxDb; P46963; -.
DR PRIDE; P46963; -.
DR EnsemblFungi; YML112W_mRNA; YML112W; YML112W.
DR GeneID; 854928; -.
DR KEGG; sce:YML112W; -.
DR SGD; S000004580; CTK3.
DR VEuPathDB; FungiDB:YML112W; -.
DR eggNOG; ENOG502RZM5; Eukaryota.
DR HOGENOM; CLU_056411_0_0_1; -.
DR InParanoid; P46963; -.
DR OMA; HYEDFHQ; -.
DR BioCyc; YEAST:G3O-32694-MON; -.
DR PRO; PR:P46963; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; P46963; protein.
DR GO; GO:0032806; C:carboxy-terminal domain protein kinase complex; IPI:ComplexPortal.
DR GO; GO:0070692; C:CTDK-1 complex; IDA:SGD.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; IDA:SGD.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IEA:UniProtKB-KW.
DR GO; GO:0031124; P:mRNA 3'-end processing; IDA:ComplexPortal.
DR GO; GO:0070816; P:phosphorylation of RNA polymerase II C-terminal domain; IDA:ComplexPortal.
DR GO; GO:0032786; P:positive regulation of DNA-templated transcription, elongation; IDA:SGD.
DR GO; GO:0045943; P:positive regulation of transcription by RNA polymerase I; IDA:ComplexPortal.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IC:ComplexPortal.
DR GO; GO:0045903; P:positive regulation of translational fidelity; IPI:SGD.
DR GO; GO:0006468; P:protein phosphorylation; IPI:SGD.
DR InterPro; IPR042326; Ctk3.
DR InterPro; IPR024637; Ctk3_C.
DR PANTHER; PTHR28291; PTHR28291; 1.
DR Pfam; PF12350; CTK3_C; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; DNA damage;
KW mRNA processing; Nucleus; Phosphoprotein; Reference proteome;
KW Transcription; Ubl conjugation.
FT CHAIN 1..296
FT /note="CTD kinase subunit gamma"
FT /id="PRO_0000079495"
FT REGION 25..44
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 35
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MUTAGEN 274..296
FT /note="Missing: No interaction with CTK2. Still interacts
FT with CTK1."
FT CONFLICT 101
FT /note="N -> T (in Ref. 1; AAC49078)"
FT /evidence="ECO:0000305"
FT CONFLICT 112
FT /note="M -> MLM (in Ref. 5; CAE82078)"
FT /evidence="ECO:0000305"
FT CONFLICT 163
FT /note="L -> V (in Ref. 5; CAE82078)"
FT /evidence="ECO:0000305"
FT CONFLICT 174
FT /note="T -> I (in Ref. 5; CAE82078)"
FT /evidence="ECO:0000305"
FT CONFLICT 295
FT /note="I -> M (in Ref. 1; AAC49078)"
FT /evidence="ECO:0000305"
FT HELIX 6..15
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 17..20
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 48..72
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 75..92
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 104..108
FT /evidence="ECO:0007829|PDB:7JV7"
FT TURN 109..113
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 114..121
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 128..132
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 133..146
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 152..155
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 181..206
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 224..243
FT /evidence="ECO:0007829|PDB:7JV7"
FT TURN 244..246
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 258..270
FT /evidence="ECO:0007829|PDB:7JV7"
FT HELIX 277..294
FT /evidence="ECO:0007829|PDB:7JV7"
SQ SEQUENCE 296 AA; 34809 MW; 12F6D3F7181547ED CRC64;
MDSLEARLQF IQVLKNLQKT LHKTRDSITS SSTTTPPSSQ QKLNNDPIQF YLRNYRHHYE
DFHQCLFDTT MKMDPLDRLD VVIYYVRIIR NLYPHSHSNT NVTKVLNEVL LMDIDLVFEL
CLPCQDWKSL TNQATCKELF LDLSKLIHYD ATSVTHTPSD TTLIDATTWY SVKTERTTKD
YKESLQRTES LLKDRDLKKL AFFQQFNSDT TAINPDLQTQ PTNANILLHR MEADRELHKR
SKETSWYIER PSNDILDESE FKSLWTHFET TDSGFDKDDY KNIKALNDIA KASYIY
