Q03290 (TFB3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
RNA polymerase II transcription factor B subunit 3

Alternative name(s):
RNA polymerase II transcription factor B 38 kDa subunit
RNA polymerase II transcription factor B p38 subunit

Gene names

Name:	TFB3
Synonyms:	RIG2
Ordered Locus Names:	YDR460W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	321 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Acts as component of the general transcription and DNA repair factor IIH (TFIIH or factor B), which is essential for both basal and activated transcription, and is involved in nucleotide excision repair (NER) of damaged DNA. TFIIH has CTD kinase and DNA-dependent ATPase activity, and is essential for polymerase II transcription in vitro. Ref.1 Ref.2
Subunit structure	Component of the transcription factor IIH (TFIIH) holo but not the TFIIH core complex. Component of a complex consisting of KIN28, CCL1 and TFB3; the KIN28-CCL1 dimer is known as the TFIIK complex. Ref.1 Ref.2 Ref.6 Ref.7
Subcellular location	Nucleus By similarity.
Miscellaneous	Present with 3050 molecules/cell in log phase SD medium.
Sequence similarities	Contains 1 RING-type zinc finger.
Sequence caution	The sequence AAB40629.1 differs from that shown. Reason: Frameshift at position 262.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Zinc-finger
Ligand	Metal-binding Zinc
PTM	Phosphoprotein
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	cell cycle Inferred from electronic annotation. Source: InterPro nucleotide-excision repair Inferred from mutant phenotype PubMed 10681587. Source: SGD phosphorylation of RNA polymerase II C-terminal domain Inferred from direct assay PubMed 19450536PubMed 19679665. Source: SGD transcription from RNA polymerase II promoter Inferred from direct assay PubMed 19818408. Source: SGD
Cellular_component	TFIIK complex Inferred from direct assay PubMed 19818408. Source: SGD
Molecular_function	zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CCL1	P37366	4	EBI-31406,EBI-4385
RAD3	P06839	2	EBI-31406,EBI-14762

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 321	321	RNA polymerase II transcription factor B subunit 3		PRO_0000055942
Regions
	Zinc finger	13 – 60	48	RING-type
Amino acid modifications
	Modified residue	157	1	Phosphoserine Ref.12
	Modified residue	258	1	Phosphothreonine Ref.9 Ref.10 Ref.11 Ref.12

Sequences

	Sequence		Length	Mass (Da)
	Q03290 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 528D61CF25ADFAF4	FASTA	321	38,128
	10 20 30 40 50 60 MLMDEYEENK DMCPICKTDR YLSPDVKFLV NPECYHRICE SCVDRIFSLG PAQCPYKGCD 70 80 90 100 110 120 KILRKNKFKT QIFDDVEVEK EVDIRKRVFN VFNKTIDDFN GDLVEYNKYL EEVEDIIYKL 130 140 150 160 170 180 DHGIDVAKTE EKLRTYEELN KQLIMNNLER SRTEIESFEQ RQKFEKEMKL KKRLLERQIE 190 200 210 220 230 240 EEERMNKEWT KKEIVNRLST TTQDINETIE GVKNTVKLKK SSARRKLEEL NRVLKNNPYF 250 260 270 280 290 300 NSNVNVQNSR LKDAVPFTPF NGDREAHPRF TLKGSVYNDP FIKDLEHRKE FIASGFNTNY 310 320 AYERVLTEAF MGLGCVISEE L

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 71-85 AND 236-250, FUNCTION, SUBUNIT, INTERACTION WITH KIN28. Strain: DBY2019.
[2]	"Rig2, a RING finger protein that interacts with the Kin28/Ccl1 CTD kinase in yeast." Faye G., Simon M., Valay J.G., Fesquet D., Facca C. Mol. Gen. Genet. 255:460-466(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, SUBUNIT.
[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]	Sethuraman A., Cherry J.M. Submitted (OCT-2003) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION. Strain: ATCC 204508 / S288c.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[6]	"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 KIN28 AND CCL1.
[7]	"Revised subunit structure of yeast transcription factor IIH (TFIIH) and reconciliation with human TFIIH." Takagi Y., Komori H., Chang W.-H., Hudmon A., Erdjument-Bromage H., Tempst P., Kornberg R.D. J. Biol. Chem. 278:43897-43900(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT.
[8]	"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] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[9]	"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-258, MASS SPECTROMETRY. Strain: YAL6B.
[10]	"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-258, MASS SPECTROMETRY. Strain: ADR376.
[11]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-258, MASS SPECTROMETRY.
[12]	"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-157 AND THR-258, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U62805 Genomic DNA. Translation: AAB40629.1. Frameshift. U33050 Genomic DNA. Translation: AAB64899.1. BK006938 Genomic DNA. Translation: DAA12294.1.
PIR	S69628.
RefSeq	NP_010748.3. NM_001180768.3.
3D structure databases
ProteinModelPortal	Q03290.
SMR	Q03290. Positions 13-75.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2398N.
IntAct	Q03290. 12 interactions.
MINT	MINT-528793.
Proteomic databases
PaxDb	Q03290.
PeptideAtlas	Q03290.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YDR460W; YDR460W; YDR460W.
GeneID	852071.
KEGG	sce:YDR460W. sce:YDR463W.
Organism-specific databases
CYGD	YDR460w.
SGD	S000002868. TFB3.
Phylogenomic databases
eggNOG	COG5220.
GeneTree	ENSGT00390000002319.
HOGENOM	HOG000189680.
KO	K10842.
OMA	CPICKTD.
OrthoDB	EOG4P5PK2.
Gene expression databases
Genevestigator	Q03290.
GermOnline	YDR460W. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	3.30.40.10. 1 hit.
InterPro	IPR015877. Cdk-activating_kinase_MAT1_cen. IPR004575. MAT1/Tfb3. IPR001841. Znf_RING. IPR013083. Znf_RING/FYVE/PHD. IPR017907. Znf_RING_CS. [Graphical view]
PANTHER	PTHR12683. PTHR12683. 1 hit.
Pfam	PF06391. MAT1. 1 hit. [Graphical view]
PIRSF	PIRSF003338. MAT1_metazoa. 1 hit.
SMART	SM00184. RING. 1 hit. [Graphical view]
TIGRFAMs	TIGR00570. cdk7. 1 hit.
PROSITE	PS00518. ZF_RING_1. 1 hit. PS50089. ZF_RING_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	970364.

Entry information

Entry name

TFB3_YEAST

Accession

Primary (citable) accession number: Q03290
Secondary accession number(s): D6VT84, P89104

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2005
Last sequence update:	November 1, 1996
Last modified:	May 1, 2013
This is version 117 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program