ID   REF2_YEAST              Reviewed;         533 AA.
AC   P42073; D6VSH8;
DT   01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1996, sequence version 2.
DT   27-MAR-2024, entry version 174.
DE   RecName: Full=RNA end formation protein 2;
GN   Name=REF2; OrderedLocusNames=YDR195W; ORFNames=YD9346.06;
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].
RA   Russnak R.;
RL   Submitted (JAN-1995) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169867;
RA   Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA   Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA   Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA   Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA   Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA   Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA   Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA   Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA   Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA   Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA   Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA   Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA   Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA   Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA   Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA   Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA   Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA   Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA   Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA   Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA   Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA   Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA   Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA   Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA   Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA   Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA   Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA   Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA   Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA   Mewes H.-W., Zollner A., Zaccaria P.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL   Nature 387:75-78(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   PRELIMINARY NUCLEOTIDE SEQUENCE OF 1-429, AND FUNCTION.
RX   PubMed=7862160; DOI=10.1128/mcb.15.3.1689;
RA   Russnak R., Nehrke K.W., Platt T.;
RT   "REF2 encodes an RNA-binding protein directly involved in yeast mRNA 3'-end
RT   formation.";
RL   Mol. Cell. Biol. 15:1689-1697(1995).
RN   [5]
RP   FUNCTION, AND INTERACTION WITH FIR1.
RX   PubMed=9196079;
RA   Russnak R., Pereira S., Platt T.;
RT   "RNA binding analysis of yeast REF2 and its two-hybrid interaction with a
RT   new gene product, FIR1.";
RL   Gene Expr. 6:241-258(1996).
RN   [6]
RP   FUNCTION IN SNORNA 3-END FORMATION.
RX   PubMed=12773397; DOI=10.1093/emboj/cdg253;
RA   Dheur S., Vo le T.A., Voisinet-Hakil F., Minet M., Schmitter J.-M.,
RA   Lacroute F., Wyers F., Minvielle-Sebastia L.;
RT   "Pti1p and Ref2p found in association with the mRNA 3' end formation
RT   complex direct snoRNA maturation.";
RL   EMBO J. 22:2831-2840(2003).
RN   [7]
RP   IDENTIFICATION IN THE CPF COMPLEX, COMPOSITION OF THE APT COMPLEX,
RP   SUBCELLULAR LOCATION, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX   PubMed=12819204; DOI=10.1074/jbc.m304454200;
RA   Nedea E., He X., Kim M., Pootoolal J., Zhong G., Canadien V., Hughes T.,
RA   Buratowski S., Moore C.L., Greenblatt J.;
RT   "Organization and function of APT, a subcomplex of the yeast cleavage and
RT   polyadenylation factor involved in the formation of mRNA and small
RT   nucleolar RNA 3'-ends.";
RL   J. Biol. Chem. 278:33000-33010(2003).
RN   [8]
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   [9]
RP   FUNCTION.
RX   PubMed=15121841; DOI=10.1128/mcb.24.10.4196-4206.2004;
RA   Mangus D.A., Smith M.M., McSweeney J.M., Jacobson A.;
RT   "Identification of factors regulating poly(A) tail synthesis and
RT   maturation.";
RL   Mol. Cell. Biol. 24:4196-4206(2004).
RN   [10]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=ADR376;
RX   PubMed=17330950; DOI=10.1021/pr060559j;
RA   Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA   Elias J.E., Gygi S.P.;
RT   "Large-scale phosphorylation analysis of alpha-factor-arrested
RT   Saccharomyces cerevisiae.";
RL   J. Proteome Res. 6:1190-1197(2007).
RN   [11]
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).
CC   -!- FUNCTION: RNA-binding component of the cleavage and polyadenylation
CC       factor (CPF) complex, which plays a key role in polyadenylation-
CC       dependent pre-mRNA 3'-end formation and cooperates with cleavage
CC       factors including the CFIA complex and NAB4/CFIB. Negative regulator of
CC       poly(A) synthesis. Component of the APT complex, which may be involved
CC       in polyadenylation-independent transcript 3'-end formation. REF2 is
CC       required for 3'-end formation of snoRNAs. {ECO:0000269|PubMed:12773397,
CC       ECO:0000269|PubMed:15121841, ECO:0000269|PubMed:7862160,
CC       ECO:0000269|PubMed:9196079}.
CC   -!- SUBUNIT: Interacts with FIR1. Component of the cleavage and
CC       polyadenylation factor (CPF) complex, which is composed of PTI1, SYC1,
CC       SSU72, GLC7, MPE1, REF2, PFS2, PTA1, YSH1/BRR5, SWD2, CFT2/YDH1, YTH1,
CC       CFT1/YHH1, FIP1 and PAP1. Component of the APT complex, which is a
CC       subcomplex of CPF, and is composed of PTI1, SYC1, SSU72, GLC7, REF2,
CC       PTA1 and SWD2. {ECO:0000269|PubMed:12819204,
CC       ECO:0000269|PubMed:9196079}.
CC   -!- INTERACTION:
CC       P42073; P32598: GLC7; NbExp=8; IntAct=EBI-14915, EBI-13715;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12819204}.
CC   -!- MISCELLANEOUS: Present with 7450 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
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DR   EMBL; U20261; AAA85866.1; -; Genomic_DNA.
DR   EMBL; Z48784; CAA88708.1; -; Genomic_DNA.
DR   EMBL; BK006938; DAA12038.1; -; Genomic_DNA.
DR   PIR; S52702; S52702.
DR   RefSeq; NP_010481.3; NM_001180503.3.
DR   PDB; 8A8F; X-ray; 1.85 A; B=348-406.
DR   PDBsum; 8A8F; -.
DR   AlphaFoldDB; P42073; -.
DR   BioGRID; 32247; 302.
DR   ComplexPortal; CPX-1053; Cleavage and polyadenylation specificity factor complex.
DR   DIP; DIP-871N; -.
DR   IntAct; P42073; 31.
DR   MINT; P42073; -.
DR   STRING; 4932.YDR195W; -.
DR   CarbonylDB; P42073; -.
DR   GlyGen; P42073; 5 sites, 1 O-linked glycan (5 sites).
DR   iPTMnet; P42073; -.
DR   MaxQB; P42073; -.
DR   PaxDb; 4932-YDR195W; -.
DR   PeptideAtlas; P42073; -.
DR   EnsemblFungi; YDR195W_mRNA; YDR195W; YDR195W.
DR   GeneID; 851776; -.
DR   KEGG; sce:YDR195W; -.
DR   AGR; SGD:S000002603; -.
DR   SGD; S000002603; REF2.
DR   VEuPathDB; FungiDB:YDR195W; -.
DR   eggNOG; ENOG502QR0S; Eukaryota.
DR   HOGENOM; CLU_025953_0_0_1; -.
DR   InParanoid; P42073; -.
DR   OMA; CKDNEHV; -.
DR   OrthoDB; 2039765at2759; -.
DR   BioCyc; YEAST:G3O-29782-MONOMER; -.
DR   BioGRID-ORCS; 851776; 2 hits in 10 CRISPR screens.
DR   PRO; PR:P42073; -.
DR   Proteomes; UP000002311; Chromosome IV.
DR   RNAct; P42073; Protein.
DR   GO; GO:0005829; C:cytosol; IDA:SGD.
DR   GO; GO:0005847; C:mRNA cleavage and polyadenylation specificity factor complex; IDA:SGD.
DR   GO; GO:0005634; C:nucleus; IDA:SGD.
DR   GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR   GO; GO:0003723; F:RNA binding; IDA:SGD.
DR   GO; GO:0031124; P:mRNA 3'-end processing; IMP:SGD.
DR   GO; GO:0006378; P:mRNA polyadenylation; IDA:ComplexPortal.
DR   GO; GO:1903501; P:positive regulation of mitotic actomyosin contractile ring assembly; IMP:SGD.
DR   GO; GO:1901901; P:regulation of protein localization to cell division site involved in cytokinesis; IMP:SGD.
DR   GO; GO:0031126; P:sno(s)RNA 3'-end processing; IMP:SGD.
DR   GO; GO:0030846; P:termination of RNA polymerase II transcription, poly(A)-coupled; IMP:SGD.
PE   1: Evidence at protein level;
KW   3D-structure; mRNA processing; Nucleus; Reference proteome; RNA-binding.
FT   CHAIN           1..533
FT                   /note="RNA end formation protein 2"
FT                   /id="PRO_0000097239"
FT   REGION          187..254
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          260..279
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          321..344
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        202..226
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        234..254
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        321..337
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   533 AA;  59819 MW;  36B0982B005697C4 CRC64;
     MSAPVPQLVN ISHALQASTI QQIRLDMVDF NKDCKLSSIQ LARIDKYIDS LQAALNQFTK
     DNLHIERKEK NVTEADIQLY SGLKSMYLDY LNQLIKLKHE KQHHSTPPIA NDVSLDFFVN
     QLPKFSPEER KNYIDNLILN KNSHNRLSKM DGLVDAVINL CVLDTSVAEN VRSYMKLLDT
     LGFQKGSNST GTKANLKKKL ASSKAKIKDS EKEKEKEKDK SKVKMKTKLK PSPLLNNDDK
     NSSPSPTAST SSMKKLKSGL FNKNEAKSTE SLPTSSKKKL SFSKYLNKDD ADMTKLGTKR
     SIDVDFKVNP EASTVASNII SSSTSGSSTT TVATPASSEE PLKKKTKISV QDSNVQSILR
     NGKPKKARIS SIKFLDDSQL IKVYGDDLPN QGLQVSPTQL KKILKPFKEG EPKEIILFED
     MSIKLKPLDL MFLKNTNSDD YMDISETKGG PIHCETRTPL IYRKNFNHFN PDLNKRPPRE
     PIEFDLNGNT NSTPTIAKAF GKNSLLLRKD RGGLPYKHVP IVKRNKYPPR PVH
//