P42073 (REF2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
RNA end formation protein 2

Gene names

Name:	REF2
Ordered Locus Names:	YDR195W
ORF Names:	YD9346.06

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	533 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	RNA-binding component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. Negative regulator of poly(A) synthesis. Component of the APT complex, which may be involved in polyadenylation-independent transcript 3'-end formation. REF2 is required for 3'-end formation of snoRNAs. Ref.4 Ref.5 Ref.6 Ref.9
Subunit structure	Interacts with FIR1. Component of the cleavage and polyadenylation factor (CPF) complex, which is composed of PTI1, SYC1, SSU72, GLC7, MPE1, REF2, PFS2, PTA1, YSH1/BRR5, SWD2, CFT2/YDH1, YTH1, CFT1/YHH1, FIP1 and PAP1. Component of the APT complex, which is a subcomplex of CPF, and is composed of PTI1, SYC1, SSU72, GLC7, REF2, PTA1 and SWD2. Ref.5 Ref.7
Subcellular location	Nucleus Ref.7.
Miscellaneous	Present with 7450 molecules/cell in log phase SD medium.

Ontologies

Keywords
Biological process	mRNA processing
Cellular component	Nucleus
Ligand	RNA-binding
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	mRNA 3'-end processing Inferred from mutant phenotype Ref.4. Source: SGD negative regulation of mRNA polyadenylation Inferred from mutant phenotype Ref.9. Source: SGD snoRNA 3'-end processing Inferred from mutant phenotype Ref.6. Source: SGD termination of RNA polymerase II transcription, poly(A)-coupled Inferred from mutant phenotype Ref.7. Source: SGD
Cellular_component	mRNA cleavage and polyadenylation specificity factor complex Inferred from direct assay Ref.7. Source: SGD
Molecular_function	RNA binding Inferred from direct assay Ref.4. Source: SGD chromatin binding Inferred from direct assay Ref.7. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
GLC7	P32598	7	EBI-14915,EBI-13715

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 533	533	RNA end formation protein 2		PRO_0000097239
Regions
	Compositional bias	321 – 331	11	Ser/Thr-rich
Amino acid modifications
	Modified residue	396	1	Phosphoserine Ref.10

Sequences

	Sequence		Length	Mass (Da)
	P42073 [UniParc]. Last modified February 1, 1996. Version 2. Checksum: 36B0982B005697C4	FASTA	533	59,819
	10 20 30 40 50 60 MSAPVPQLVN ISHALQASTI QQIRLDMVDF NKDCKLSSIQ LARIDKYIDS LQAALNQFTK 70 80 90 100 110 120 DNLHIERKEK NVTEADIQLY SGLKSMYLDY LNQLIKLKHE KQHHSTPPIA NDVSLDFFVN 130 140 150 160 170 180 QLPKFSPEER KNYIDNLILN KNSHNRLSKM DGLVDAVINL CVLDTSVAEN VRSYMKLLDT 190 200 210 220 230 240 LGFQKGSNST GTKANLKKKL ASSKAKIKDS EKEKEKEKDK SKVKMKTKLK PSPLLNNDDK 250 260 270 280 290 300 NSSPSPTAST SSMKKLKSGL FNKNEAKSTE SLPTSSKKKL SFSKYLNKDD ADMTKLGTKR 310 320 330 340 350 360 SIDVDFKVNP EASTVASNII SSSTSGSSTT TVATPASSEE PLKKKTKISV QDSNVQSILR 370 380 390 400 410 420 NGKPKKARIS SIKFLDDSQL IKVYGDDLPN QGLQVSPTQL KKILKPFKEG EPKEIILFED 430 440 450 460 470 480 MSIKLKPLDL MFLKNTNSDD YMDISETKGG PIHCETRTPL IYRKNFNHFN PDLNKRPPRE 490 500 510 520 530 PIEFDLNGNT NSTPTIAKAF GKNSLLLRKD RGGLPYKHVP IVKRNKYPPR PVH

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	Russnak R. Submitted (JAN-1995) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"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 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"REF2 encodes an RNA-binding protein directly involved in yeast mRNA 3'-end formation." Russnak R., Nehrke K.W., Platt T. Mol. Cell. Biol. 15:1689-1697(1995) [PubMed] [Europe PMC] [Abstract] Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE OF 1-429, FUNCTION.
[5]	"RNA binding analysis of yeast REF2 and its two-hybrid interaction with a new gene product, FIR1." Russnak R., Pereira S., Platt T. Gene Expr. 6:241-258(1996) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH FIR1.
[6]	"Pti1p and Ref2p found in association with the mRNA 3' end formation complex direct snoRNA maturation." Dheur S., Vo le T.A., Voisinet-Hakil F., Minet M., Schmitter J.-M., Lacroute F., Wyers F., Minvielle-Sebastia L. EMBO J. 22:2831-2840(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN SNORNA 3-END FORMATION.
[7]	"Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends." Nedea E., He X., Kim M., Pootoolal J., Zhong G., Canadien V., Hughes T., Buratowski S., Moore C.L., Greenblatt J. J. Biol. Chem. 278:33000-33010(2003) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE CPF COMPLEX, COMPOSITION OF THE APT COMPLEX, SUBCELLULAR LOCATION, IDENTIFICATION BY MASS SPECTROMETRY.
[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]	"Identification of factors regulating poly(A) tail synthesis and maturation." Mangus D.A., Smith M.M., McSweeney J.M., Jacobson A. Mol. Cell. Biol. 24:4196-4206(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[10]	"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-396, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U20261 Genomic DNA. Translation: AAA85866.1. Z48784 Genomic DNA. Translation: CAA88708.1. BK006938 Genomic DNA. Translation: DAA12038.1.
PIR	S52702.
RefSeq	NP_010481.3. NM_001180503.3.
3D structure databases
ProteinModelPortal	P42073.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-871N.
IntAct	P42073. 31 interactions.
MINT	MINT-394246.
STRING	4932.YDR195W.
Proteomic databases
PaxDb	P42073.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YDR195W; YDR195W; YDR195W.
GeneID	851776.
KEGG	sce:YDR195W. sce:YDR200C.
Organism-specific databases
CYGD	YDR195w.
SGD	S000002603. REF2.
Phylogenomic databases
eggNOG	NOG46408.
KO	K15543.
OMA	DRGGLPY.
OrthoDB	EOG454D7W.
Gene expression databases
Genevestigator	P42073.
GermOnline	YDR195W. Saccharomyces cerevisiae.
Family and domain databases
ProtoNet	Search...
Other
NextBio	969576.

Entry information

Entry name

REF2_YEAST

Accession

Primary (citable) accession number: P42073
Secondary accession number(s): D6VSH8

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	February 1, 1996
Last modified:	April 3, 2013
This is version 106 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program