PCF11_YEAST
ID PCF11_YEAST Reviewed; 626 AA.
AC P39081; D6VSL0; Q04932;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1998, sequence version 2.
DT 03-AUG-2022, entry version 179.
DE RecName: Full=Protein PCF11;
DE AltName: Full=protein 1 of CF I;
GN Name=PCF11; OrderedLocusNames=YDR228C; ORFNames=YD9934.13C;
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 [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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 286-626.
RX PubMed=7885847; DOI=10.1093/nar/23.3.507;
RA Davies C.J., Hutchison C.A. III;
RT "Insertion site specificity of the transposon Tn3.";
RL Nucleic Acids Res. 23:507-514(1995).
RN [4]
RP IDENTIFICATION IN THE CFIA COMPLEX, AND INTERACTION WITH RNA14 AND RNA15.
RX PubMed=9032237; DOI=10.1128/mcb.17.3.1102;
RA Amrani N., Minet M., Wyers F., Dufour M.-E., Aggerbeck L.P., Lacroute F.;
RT "PCF11 encodes a third protein component of yeast cleavage and
RT polyadenylation factor I.";
RL Mol. Cell. Biol. 17:1102-1109(1997).
RN [5]
RP FUNCTION OF THE CFIA COMPLEX.
RX PubMed=11344258; DOI=10.1073/pnas.101046598;
RA Gross S., Moore C.;
RT "Five subunits are required for reconstitution of the cleavage and
RT polyadenylation activities of Saccharomyces cerevisiae cleavage factor I.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:6080-6085(2001).
RN [6]
RP INTERACTION WITH RBP1.
RX PubMed=11149954; DOI=10.1073/pnas.98.2.445;
RA Barilla D., Lee B.A., Proudfoot N.J.;
RT "Cleavage/polyadenylation factor IA associates with the carboxyl-terminal
RT domain of RNA polymerase II in Saccharomyces cerevisiae.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:445-450(2001).
RN [7]
RP INTERACTION WITH RBP1, AND MUTAGENESIS OF ALA-66 AND 68-ASP--ILE-70.
RX PubMed=12727883; DOI=10.1093/emboj/cdg200;
RA Sadowski M., Dichtl B., Huebner W., Keller W.;
RT "Independent functions of yeast Pcf11p in pre-mRNA 3' end processing and in
RT transcription termination.";
RL EMBO J. 22:2167-2177(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 INTERACTION WITH RTT103.
RX PubMed=15565157; DOI=10.1038/nature03041;
RA Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F.,
RA Buratowski S.;
RT "The yeast Rat1 exonuclease promotes transcription termination by RNA
RT polymerase II.";
RL Nature 432:517-522(2004).
RN [10]
RP FUNCTION, AND RNA-BINDING.
RX PubMed=15998810; DOI=10.1101/gad.1296305;
RA Zhang Z., Fu J., Gilmour D.S.;
RT "CTD-dependent dismantling of the RNA polymerase II elongation complex by
RT the pre-mRNA 3'-end processing factor, Pcf11.";
RL Genes Dev. 19:1572-1580(2005).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-140.
RX PubMed=15241417; DOI=10.1038/nature02679;
RA Meinhart A., Cramer P.;
RT "Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-
RT processing factors.";
RL Nature 430:223-226(2004).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-138.
RX PubMed=15665873; DOI=10.1038/nsmb887;
RA Noble C.G., Hollingworth D., Martin S.R., Ennis-Adeniran V., Smerdon S.J.,
RA Kelly G., Taylor I.A., Ramos A.;
RT "Key features of the interaction between Pcf11 CID and RNA polymerase II
RT CTD.";
RL Nat. Struct. Mol. Biol. 12:144-151(2005).
CC -!- FUNCTION: Component of the cleavage factor IA (CFIA) complex, which is
CC involved in the endonucleolytic cleavage during polyadenylation-
CC dependent pre-mRNA 3'-end formation and cooperates with cleavage factor
CC NAB4/CFIB and the cleavage and polyadenylation factor (CPF) complex.
CC Independently involved in RNA polymerase II transcript termination.
CC Binds RNA. Seems to bridge RNA polymerase II and the native transcript
CC and may be involved in dismantling the RNA polymerase II elongation
CC complex. {ECO:0000269|PubMed:11344258, ECO:0000269|PubMed:15998810}.
CC -!- SUBUNIT: Component of the CFIA complex, which is composed of RNA14,
CC RNA15, PCF11 and CLP1. Interacts with RNA14, RNA15 and RTT103.
CC Interacts directly with the phosphorylated CTD domain of RPB1/RNA
CC polymerase II. {ECO:0000269|PubMed:11149954,
CC ECO:0000269|PubMed:12727883, ECO:0000269|PubMed:15565157,
CC ECO:0000269|PubMed:9032237}.
CC -!- INTERACTION:
CC P39081; Q08685: CLP1; NbExp=13; IntAct=EBI-12980, EBI-29732;
CC P39081; P25298: RNA14; NbExp=10; IntAct=EBI-12980, EBI-15632;
CC P39081; P25299: RNA15; NbExp=8; IntAct=EBI-12980, EBI-15640;
CC P39081; P40073: SHO1; NbExp=2; IntAct=EBI-12980, EBI-18140;
CC P39081; Q12159: YRA1; NbExp=2; IntAct=EBI-12980, EBI-29516;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- MISCELLANEOUS: Present with 2800 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
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DR EMBL; Z48612; CAA88508.1; -; Genomic_DNA.
DR EMBL; U13239; AAC33145.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12070.1; -; Genomic_DNA.
DR PIR; S59435; S59435.
DR RefSeq; NP_010514.3; NM_001180536.3.
DR PDB; 1SZ9; X-ray; 2.10 A; A/B/C=1-140.
DR PDB; 1SZA; X-ray; 2.20 A; A/B/C=1-140.
DR PDB; 2BF0; X-ray; 2.30 A; X=1-138.
DR PDB; 2NAX; NMR; -; A=538-608.
DR PDB; 2NPI; X-ray; 2.95 A; C/D=454-563.
DR PDB; 4C0B; X-ray; 2.77 A; C/D=454-563.
DR PDB; 4C0H; X-ray; 2.70 A; C/D=454-563.
DR PDB; 4OI4; X-ray; 2.40 A; B/D/U=454-563.
DR PDB; 5M9Z; NMR; -; A=530-626.
DR PDBsum; 1SZ9; -.
DR PDBsum; 1SZA; -.
DR PDBsum; 2BF0; -.
DR PDBsum; 2NAX; -.
DR PDBsum; 2NPI; -.
DR PDBsum; 4C0B; -.
DR PDBsum; 4C0H; -.
DR PDBsum; 4OI4; -.
DR PDBsum; 5M9Z; -.
DR AlphaFoldDB; P39081; -.
DR BMRB; P39081; -.
DR SMR; P39081; -.
DR BioGRID; 32280; 381.
DR ComplexPortal; CPX-1895; mRNA cleavage factor complex CFIA.
DR ComplexPortal; CPX-1896; mRNA cleavage factor complex CFI.
DR DIP; DIP-944N; -.
DR IntAct; P39081; 85.
DR MINT; P39081; -.
DR STRING; 4932.YDR228C; -.
DR iPTMnet; P39081; -.
DR MaxQB; P39081; -.
DR PaxDb; P39081; -.
DR PRIDE; P39081; -.
DR EnsemblFungi; YDR228C_mRNA; YDR228C; YDR228C.
DR GeneID; 851814; -.
DR KEGG; sce:YDR228C; -.
DR SGD; S000002636; PCF11.
DR VEuPathDB; FungiDB:YDR228C; -.
DR eggNOG; KOG2071; Eukaryota.
DR GeneTree; ENSGT00440000034259; -.
DR HOGENOM; CLU_015606_1_0_1; -.
DR InParanoid; P39081; -.
DR OMA; IEKCVPK; -.
DR BioCyc; YEAST:G3O-29807-MON; -.
DR EvolutionaryTrace; P39081; -.
DR PRO; PR:P39081; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P39081; protein.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0005849; C:mRNA cleavage factor complex; IPI:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0003729; F:mRNA binding; IDA:SGD.
DR GO; GO:0000993; F:RNA polymerase II complex binding; IDA:SGD.
DR GO; GO:0006378; P:mRNA polyadenylation; IDA:SGD.
DR GO; GO:0098789; P:pre-mRNA cleavage required for polyadenylation; IDA:SGD.
DR GO; GO:0006369; P:termination of RNA polymerase II transcription; IDA:SGD.
DR GO; GO:0030847; P:termination of RNA polymerase II transcription, exosome-dependent; IMP:SGD.
DR GO; GO:0030846; P:termination of RNA polymerase II transcription, poly(A)-coupled; IMP:SGD.
DR Gene3D; 1.25.40.90; -; 1.
DR InterPro; IPR021605; CFIA_Pcf11_C.
DR InterPro; IPR006569; CID_dom.
DR InterPro; IPR008942; ENTH_VHS.
DR InterPro; IPR045154; PCF11-like.
DR PANTHER; PTHR15921; PTHR15921; 2.
DR Pfam; PF11526; CFIA_Pcf11; 1.
DR Pfam; PF04818; CID; 1.
DR SMART; SM00582; RPR; 1.
DR SUPFAM; SSF48464; SSF48464; 1.
DR PROSITE; PS51391; CID; 1.
PE 1: Evidence at protein level;
KW 3D-structure; mRNA processing; Nucleus; Reference proteome; RNA-binding;
KW Transcription; Transcription regulation; Transcription termination.
FT CHAIN 1..626
FT /note="Protein PCF11"
FT /id="PRO_0000058247"
FT DOMAIN 4..139
FT /note="CID"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00724"
FT REGION 1..130
FT /note="Interaction with RBP1 CTD (CID)"
FT REGION 263..286
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 66
FT /note="A->D: Loss of interaction with RBP1 CTD."
FT /evidence="ECO:0000269|PubMed:12727883"
FT MUTAGEN 68..70
FT /note="DSI->AAA: Loss of interaction with RBP1 CTD."
FT /evidence="ECO:0000269|PubMed:12727883"
FT CONFLICT 286..288
FT /note="NSL -> ILS (in Ref. 3; AAC33145)"
FT /evidence="ECO:0000305"
FT CONFLICT 515
FT /note="I -> V (in Ref. 3; AAC33145)"
FT /evidence="ECO:0000305"
FT HELIX 3..16
FT /evidence="ECO:0007829|PDB:1SZ9"
FT HELIX 24..36
FT /evidence="ECO:0007829|PDB:1SZ9"
FT HELIX 38..40
FT /evidence="ECO:0007829|PDB:1SZ9"
FT HELIX 41..54
FT /evidence="ECO:0007829|PDB:1SZ9"
FT HELIX 57..73
FT /evidence="ECO:0007829|PDB:1SZ9"
FT HELIX 78..83
FT /evidence="ECO:0007829|PDB:1SZ9"
FT HELIX 86..95
FT /evidence="ECO:0007829|PDB:1SZ9"
FT HELIX 99..112
FT /evidence="ECO:0007829|PDB:1SZ9"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:1SZ9"
FT HELIX 125..137
FT /evidence="ECO:0007829|PDB:1SZ9"
FT HELIX 486..490
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 495..498
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 543..547
FT /evidence="ECO:0007829|PDB:2NAX"
FT STRAND 550..553
FT /evidence="ECO:0007829|PDB:2NAX"
FT TURN 555..557
FT /evidence="ECO:0007829|PDB:5M9Z"
FT STRAND 561..564
FT /evidence="ECO:0007829|PDB:2NAX"
FT TURN 565..568
FT /evidence="ECO:0007829|PDB:2NAX"
FT STRAND 569..576
FT /evidence="ECO:0007829|PDB:2NAX"
FT TURN 577..580
FT /evidence="ECO:0007829|PDB:2NAX"
FT STRAND 581..585
FT /evidence="ECO:0007829|PDB:2NAX"
FT STRAND 587..590
FT /evidence="ECO:0007829|PDB:2NAX"
FT STRAND 593..596
FT /evidence="ECO:0007829|PDB:2NAX"
FT HELIX 597..603
FT /evidence="ECO:0007829|PDB:2NAX"
SQ SEQUENCE 626 AA; 71898 MW; 66F91BA9577E82F1 CRC64;
MDHDTEVIVK DFNSILEELT FNSRPIITTL TKLAEENISC AQYFVDAIES RIEKCMPKQK
LYAFYALDSI CKNVGSPYTI YFSRNLFNLY KRTYLLVDNT TRTKLINMFK LWLNPNDTGL
PLFEGSALEK IEQFLIKASA LHQKNLQAML PTPTVPLLLR DIDKLTCLTS ERLKNQPNDE
KLKMKLLVLS QLKQELKREK LTLNALKQVQ MQLRQVFSQD QQVLQERMRY HELQQQQQQQ
QQQQQQQQQQ QQQYHETKDM VGSYTQNSNS AIPLFGNNSD TTNQQNSLSS SLFGNISGVE
SFQEIEKKKS LNKINNLYAS LKAEGLIYTP PKESIVTLYK KLNGHSNYSL DSHEKQLMKN
LPKIPLLNDI LSDCKAYFAT VNIDVLNNPS LQLSEQTLLQ ENPIVQNNLI HLLYRSKPNK
CSVCGKRFGN SESEKLLQNE HLDWHFRINT RIKGSQNTAN TGISNSNLNT TTTRKNIQSR
NWYLSDSQWA AFKDDEITST KHKNDYTDPH ANKNIDKSAL NIHADENDEG SVDNTLGSDR
SNELEIRGKY VVVPETSQDM AFKCPICKET VTGVYDEESG EWVWKNTIEV NGKYFHSTCY
HETSQNSSKS NSGKVGLDDL KKLVTK
