Reviewed, UniProtKB/Swiss-Prot P46963 (CTK3_YEAST)

Names and origin

Protein names

Recommended name:
    CTD kinase subunit gamma
      Short name=CTDK-I gamma subunit
Alternative name(s):
    CTD kinase subunit 3
    CTD kinase 32 kDa subunit

Gene names

Name:	CTK3
Ordered Locus Names:	YML112W
ORF Names:	YM8339.07

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	296 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Gamma subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. CTDK-I phosphorylates 'Ser-5' if the CTD substrate is not phosphorylated at 'Ser-5', but will phosphorylate 'Ser-2' of a CTD substrate if 'Ser-5' is already phosphorylated. CTDK-I is also more reactive toward substrates that are prephosphorylated at 'Ser-2' or 'Ser-5' compared with an unphosphorylated CTD substrate, therefore efficiently creating doubly phosphorylated CTD repeats. Involved in RNA polymerase I transcription and RNA polymerase II transcriptional elongation, and as part of the CTDK-I complex, pre-mRNA 3'-end processing and SET2 mediated H3K36 methylation. Together with CTK2, required for CTK1 CTD kinase activation. Required for DNA damage induced transcription. Involved in the adaptation to alternative carbon sources, including galactose, glycerol and ethanol, but not raffinose. Required for the integrity of the rDNA locus.
Subunit structure	CTDK-I consists of three subunits, CTK1, CTK2 and CTK3 (also called alpha, beta and gamma). Interacts with CTK1. Heterodimerization with CTK2 is required to protect this subunit from degradation.
Subcellular location	Nucleus › nucleolus. Cytoplasm.
Post-translational modification	Ubiquitinated. Ubiquitination leads to degradation by the 26S proteasome pathway.
Miscellaneous	Present with 2640 molecules/cell in log phase SD medium. Null mutants are viable, but grow more slowly than wild-type cells at 30 degrees Celsius. They are cold-sensitive, failing to grow at 12 degrees Celsius. They display flocculent growth in liquid media and they show abnormal cell morphologies, for example, a significant fraction of the cells are greatly enlarged. Deletion mutant is sensitive to the DNA synthesis inhibitor hydroxyurea (HU) and UV irradiation.
Sequence similarities	Belongs to the CTK3 family.

Ontologies

Keywords
Biological process	DNA damage Transcription mRNA processing
Cellular component	Cytoplasm Nucleus
PTM	Phosphoprotein Ubl conjugation
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	mRNA 3'-end processing Ref.6 Inferred by curator. Source: SGD positive regulation of RNA elongation Ref.5 Inferred from direct assay. Source: SGD protein amino acid phosphorylation Ref.1 Inferred from physical interaction. Source: SGD
Cellular component	carboxy-terminal domain protein kinase complex Ref.1 Inferred from physical interaction. Source: SGD
Molecular function	protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CTK1	Q03957	1	EBI-5241,EBI-5230

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view
Molecule processing
	Chain	1 – 296	296	CTD kinase subunit gamma
Amino acid modifications
	Modified residue	31	1	Phosphoserine
	Modified residue	32	1	Phosphoserine
	Modified residue	34	1	Phosphothreonine
	Modified residue	35	1	Phosphothreonine
Experimental info
	Mutagenesis	274 – 296	23	Missing: No interaction with CTK2. Still interacts with CTK1
	Sequence conflict	101	1	N → T in AAC49078. Ref.1
	Sequence conflict	112	1	M → MLM in CAE82078. Ref.4
	Sequence conflict	163	1	L → V in CAE82078. Ref.4
	Sequence conflict	174	1	T → I in CAE82078. Ref.4
	Sequence conflict	295	1	I → M in AAC49078. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P46963-1 [UniParc]. Last modified October 1, 1996. Version 2. Checksum: 12F6D3F7181547ED	FASTA	296	34,809
	10 20 30 40 50 60 MDSLEARLQF IQVLKNLQKT LHKTRDSITS SSTTTPPSSQ QKLNNDPIQF YLRNYRHHYE 70 80 90 100 110 120 DFHQCLFDTT MKMDPLDRLD VVIYYVRIIR NLYPHSHSNT NVTKVLNEVL LMDIDLVFEL 130 140 150 160 170 180 CLPCQDWKSL TNQATCKELF LDLSKLIHYD ATSVTHTPSD TTLIDATTWY SVKTERTTKD 190 200 210 220 230 240 YKESLQRTES LLKDRDLKKL AFFQQFNSDT TAINPDLQTQ PTNANILLHR MEADRELHKR 250 260 270 280 290 SKETSWYIER PSNDILDESE FKSLWTHFET TDSGFDKDDY KNIKALNDIA KASYIY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The yeast carboxyl-terminal repeat domain kinase CTDK-I is a divergent cyclin-cyclin-dependent kinase complex." Sterner D.E., Lee J.M., Hardin S.E., Greenleaf A.L. Mol. Cell. Biol. 15:5716-5724(1995) [PubMed: 7565723] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 146-173, CTD KINASE ACTIVITY, SUBUNIT, NULL MUTANT.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII." Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T., Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P. , Skelton J., Walsh S.V., Whitehead S., Barrell B.G. Nature 387:90-93(1997) [PubMed: 9169872] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"A DNA binding protein that recognizes oligo(dA).oligo(dT) tracts." Winter E., Varshavsky A. EMBO J. 8:1867-1877(1989) [PubMed: 2670564] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 46-262.
[5]	"Modulation of RNA polymerase II elongation efficiency by C-terminal heptapeptide repeat domain kinase I." Lee J.M., Greenleaf A.L. J. Biol. Chem. 272:10990-10993(1997) [PubMed: 9110987] [Abstract] Cited for: FUNCTION IN RNA POLYMERASE II TRANSCRIPTION.
[6]	"Activation of the cyclin-dependent kinase CTDK-I requires the heterodimerization of two unstable subunits." Hautbergue G., Goguel V. J. Biol. Chem. 276:8005-8013(2001) [PubMed: 11118453] [Abstract] Cited for: CTK1 ACTIVATION, INTERACTION WITH CTK1 AND CTK2, UBIQUITINATION, DELETION MUTANT OF 247-TYR--TYR-296.
[7]	"Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae." Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Nat. Biotechnol. 20:301-305(2002) [PubMed: 11875433] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-31 AND THR-34, MASS SPECTROMETRY.
[8]	"Budding yeast CTDK-I is required for DNA damage-induced transcription." Ostapenko D., Solomon M.J. Eukaryot. Cell 2:274-283(2003) [PubMed: 12684377] [Abstract] Cited for: FUNCTION, DELETION MUTANT.
[9]	"Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast." Xiao T., Hall H., Kizer K.O., Shibata Y., Hall M.C., Borchers C.H., Strahl B.D. Genes Dev. 17:654-663(2003) [PubMed: 12629047] [Abstract] Cited for: FUNCTION IN H3 METHYLATION.
[10]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[11]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[12]	"C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats." Jones J.C., Phatnani H.P., Haystead T.A., MacDonald J.A., Alam S.M., Greenleaf A.L. J. Biol. Chem. 279:24957-24964(2004) [PubMed: 15047695] [Abstract] Cited for: FUNCTION OF THE CTDK-I COMPLEX.
[13]	"CTD kinase I is involved in RNA polymerase I transcription." Bouchoux C., Hautbergue G., Grenetier S., Carles C., Riva M., Goguel V. Nucleic Acids Res. 32:5851-5860(2004) [PubMed: 15520468] [Abstract] Cited for: FUNCTION IN RNA POLYMERASE I TRANSCRIPTION, SUBCELLULAR LOCATION.
[14]	"Glucose deprivation mediates interaction between CTDK-I and Snf1 in Saccharomyces cerevisiae." Van Driessche B., Coddens S., Van Mullem V., Vandenhaute J. FEBS Lett. 579:5318-5324(2005) [PubMed: 16182287] [Abstract] Cited for: FUNCTION IN ADAPTATION TO ALTERNATIVE CARBON SOURCES.
[15]	"CTD kinase I is required for the integrity of the rDNA tandem array." Grenetier S., Bouchoux C., Goguel V. Nucleic Acids Res. 34:4996-5006(2006) [PubMed: 16984969] [Abstract] Cited for: FUNCTION IN THE INTEGRITY OF RDNA.
[16]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-32; THR-34 AND THR-35, MASS SPECTROMETRY.
[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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-32 AND THR-35, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	U30296 Genomic DNA. Translation: AAC49078.1. Z49210 Genomic DNA. Translation: CAA89106.1. AY557764 Genomic DNA. Translation: AAS56090.1. X15478 Genomic DNA. Translation: CAE82078.1.
PIR	S53960.
RefSeq	NP_013595.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:2106N.
IntAct	P46963.
Proteomic databases
PeptideAtlas	P46963.
Genome annotation databases
Ensembl	YML112W. Saccharomyces cerevisiae. [Contig view]
GeneID	854928.
GenomeReviews	Gene locus YML112W in contig Z71257_GR.
KEGG	sce:YML112W.
NMPDR	fig|4932.3.peg.4631.
Organism-specific databases
CYGD	YML112w.
SGD	S000004580. CTK3.
Yeast-GFP	Search...
Phylogenomic databases
HOGENOM	P46963.
Gene expression databases
GermOnline	YML112W. Saccharomyces cerevisiae.
Family and domain databases
ProDom	P46963. [Graphical view] [Entries sharing at least one domain]
BLOCKS	Search...
Other Resources
LinkHub	P46963.
ProtoNet	Search...

Entry information

Entry name

CTK3_YEAST

Accession

Primary (citable) accession number: P46963
Secondary accession number(s): Q6LBS6

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	October 1, 1996
Last modified:	September 2, 2008
This is version 69 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)