ID CLP1_YEAST Reviewed; 445 AA.
AC Q08685; D6W2V1;
DT 24-JAN-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 27-MAR-2024, entry version 169.
DE RecName: Full=mRNA cleavage and polyadenylation factor CLP1 {ECO:0000255|HAMAP-Rule:MF_03035};
GN Name=CLP1 {ECO:0000255|HAMAP-Rule:MF_03035}; OrderedLocusNames=YOR250C;
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].
RX PubMed=9153759;
RX DOI=10.1002/(sici)1097-0061(199704)13:5<483::aid-yea105>3.0.co;2-u;
RA Poirey R., Jauniaux J.-C.;
RT "Sequencing analysis of a 36.8 kb fragment of yeast chromosome XV reveals
RT 26 open reading frames including SEC63, CDC31, SUG2, GCD1, RBL2, PNT1, PAC1
RT and VPH1.";
RL Yeast 13:483-487(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(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 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP COMPOSITION OF THE CFIA COMPLEX.
RX PubMed=8900210; DOI=10.1074/jbc.271.43.27167;
RA Kessler M.M., Zhao J., Moore C.L.;
RT "Purification of the Saccharomyces cerevisiae cleavage/polyadenylation
RT factor I. Separation into two components that are required for both
RT cleavage and polyadenylation of mRNA 3' ends.";
RL J. Biol. Chem. 271:27167-27175(1996).
RN [6]
RP IDENTIFICATION IN THE CFIA COMPLEX.
RX PubMed=9223284; DOI=10.1073/pnas.94.15.7897;
RA Minvielle-Sebastia L., Preker P.J., Wiederkehr T., Strahm Y., Keller W.;
RT "The major yeast poly(A)-binding protein is associated with cleavage factor
RT IA and functions in premessenger RNA 3'-end formation.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:7897-7902(1997).
RN [7]
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 [8]
RP LACK OF POLYNUCLEOTIDE KINASE ACTIVITY, AND MUTAGENESIS OF 136-LYS-THR-137
RP AND ASP-161.
RX PubMed=18648070; DOI=10.1261/rna.1142908;
RA Ramirez A., Shuman S., Schwer B.;
RT "Human RNA 5'-kinase (hClp1) can function as a tRNA splicing enzyme in
RT vivo.";
RL RNA 14:1737-1745(2008).
RN [9]
RP SUBUNIT.
RX PubMed=22026644; DOI=10.1021/bi200964p;
RA Gordon J.M., Shikov S., Kuehner J.N., Liriano M., Lee E., Stafford W.,
RA Poulsen M.B., Harrison C., Moore C., Bohm A.;
RT "Reconstitution of CF IA from overexpressed subunits reveals stoichiometry
RT and provides insights into molecular topology.";
RL Biochemistry 50:10203-10214(2011).
RN [10]
RP FUNCTION, SUBUNIT, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF LYS-136;
RP THR-137 AND ASP-161.
RX PubMed=22216186; DOI=10.1371/journal.pone.0029139;
RA Holbein S., Scola S., Loll B., Dichtl B.S., Hubner W., Meinhart A.,
RA Dichtl B.;
RT "The P-loop domain of yeast Clp1 mediates interactions between CF IA and
RT CPF factors in pre-mRNA 3' end formation.";
RL PLoS ONE 6:E29139-E29139(2011).
RN [11]
RP FUNCTION, AND INTERACTION WITH PCF11.
RX PubMed=21993299; DOI=10.1093/nar/gkr801;
RA Ghazy M.A., Gordon J.M., Lee S.D., Singh B.N., Bohm A., Hampsey M.,
RA Moore C.;
RT "The interaction of Pcf11 and Clp1 is needed for mRNA 3'-end formation and
RT is modulated by amino acids in the ATP-binding site.";
RL Nucleic Acids Res. 40:1214-1225(2012).
RN [12]
RP FUNCTION.
RX PubMed=21993300; DOI=10.1093/nar/gkr800;
RA Haddad R., Maurice F., Viphakone N., Voisinet-Hakil F., Fribourg S.,
RA Minvielle-Sebastia L.;
RT "An essential role for Clp1 in assembly of polyadenylation complex CF IA
RT and Pol II transcription termination.";
RL Nucleic Acids Res. 40:1226-1239(2012).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF 2-445 IN COMPLEX WITH ATP AND
RP PCF11.
RX PubMed=17151076; DOI=10.1093/nar/gkl1010;
RA Noble C.G., Beuth B., Taylor I.A.;
RT "Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor.";
RL Nucleic Acids Res. 35:87-99(2007).
CC -!- FUNCTION: Component of the cleavage factor IA (CF IA) complex, which is
CC involved in the endonucleolytic cleavage during polyadenylation-
CC dependent pre-mRNA 3'-end formation. Associates with HRB1/CF IB to form
CC the cleavage factor I (CF I) complex. CF I is required for correct
CC positioning of a larger protein complex, the cleavage and
CC polyadenylation factor (CPF) complex, which contains the catalytic
CC subunits executing mRNA cleavage and polyadenylation. CLP1 mediates
CC interactions between CF IA and CPF factors. CLP1 is also involved in
CC maintaining the CF IA interaction with the C-terminal domain of RNA Pol
CC II largest subunit via PCF11, which links pre-mRNA 3'-end processing to
CC transcription termination. {ECO:0000255|HAMAP-Rule:MF_03035,
CC ECO:0000269|PubMed:11344258, ECO:0000269|PubMed:21993299,
CC ECO:0000269|PubMed:21993300, ECO:0000269|PubMed:22216186}.
CC -!- SUBUNIT: Component of the cleavage factor IA (CF IA) complex, which is
CC a heterohexameric complex with 2:2:1:1 stoichiometry of RNA14, RNA15,
CC PCF11 and CLP1. It contains 2 copies of an RNA14-RNA15 dimer and 1 copy
CC of CLP1-PCF11. The complex interacts with the cleavage factor HRB1/CF
CC IB to form the cleavage factor I (CF I) complex, and binds to RNA.
CC Interacts directly with PCF11. Interacts with the CPF components CFT1,
CC PTA1, PFS2, YSH1 and SSU72. {ECO:0000269|PubMed:17151076,
CC ECO:0000269|PubMed:21993299, ECO:0000269|PubMed:22026644,
CC ECO:0000269|PubMed:22216186, ECO:0000269|PubMed:9223284}.
CC -!- INTERACTION:
CC Q08685; P39081: PCF11; NbExp=13; IntAct=EBI-29732, EBI-12980;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03035}.
CC -!- DISRUPTION PHENOTYPE: Causes defective 3'-end formation and
CC transcriptional read-through. {ECO:0000269|PubMed:22216186}.
CC -!- SIMILARITY: Belongs to the Clp1 family. Clp1 subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_03035}.
CC -!- CAUTION: May lack the polyribonucleotide 5'-hydroxyl-kinase and
CC polynucleotide 5'-hydroxyl-kinase activities that are characteristic of
CC the human ortholog. {ECO:0000305}.
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DR EMBL; Z75158; CAA99472.1; -; Genomic_DNA.
DR EMBL; AY558048; AAS56374.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA11017.1; -; Genomic_DNA.
DR PIR; S67147; S67147.
DR RefSeq; NP_014893.1; NM_001183669.1.
DR PDB; 2NPI; X-ray; 2.95 A; A/B=2-445.
DR PDB; 4C0B; X-ray; 2.77 A; A/B=1-445.
DR PDB; 4C0H; X-ray; 2.70 A; A/B=1-445.
DR PDB; 4OI4; X-ray; 2.40 A; A/C=1-445.
DR PDBsum; 2NPI; -.
DR PDBsum; 4C0B; -.
DR PDBsum; 4C0H; -.
DR PDBsum; 4OI4; -.
DR AlphaFoldDB; Q08685; -.
DR SMR; Q08685; -.
DR BioGRID; 34640; 449.
DR ComplexPortal; CPX-1895; mRNA cleavage factor complex CFIA.
DR ComplexPortal; CPX-1896; mRNA cleavage factor complex CFI.
DR DIP; DIP-1487N; -.
DR IntAct; Q08685; 10.
DR MINT; Q08685; -.
DR STRING; 4932.YOR250C; -.
DR MaxQB; Q08685; -.
DR PaxDb; 4932-YOR250C; -.
DR PeptideAtlas; Q08685; -.
DR EnsemblFungi; YOR250C_mRNA; YOR250C; YOR250C.
DR GeneID; 854424; -.
DR KEGG; sce:YOR250C; -.
DR AGR; SGD:S000005776; -.
DR SGD; S000005776; CLP1.
DR VEuPathDB; FungiDB:YOR250C; -.
DR eggNOG; KOG2749; Eukaryota.
DR GeneTree; ENSGT00940000153668; -.
DR HOGENOM; CLU_018195_3_1_1; -.
DR InParanoid; Q08685; -.
DR OMA; VQYVNCH; -.
DR OrthoDB; 56092at2759; -.
DR BioCyc; YEAST:G3O-33742-MONOMER; -.
DR BioGRID-ORCS; 854424; 5 hits in 10 CRISPR screens.
DR EvolutionaryTrace; Q08685; -.
DR PRO; PR:Q08685; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q08685; Protein.
DR GO; GO:0005849; C:mRNA cleavage factor complex; IPI:SGD.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0051731; F:polynucleotide 5'-hydroxyl-kinase activity; IBA:GO_Central.
DR GO; GO:0031124; P:mRNA 3'-end processing; IDA:SGD.
DR GO; GO:0006378; P:mRNA polyadenylation; IDA:ComplexPortal.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IBA:GO_Central.
DR Gene3D; 2.60.120.1030; Clp1, DNA binding domain; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR Gene3D; 2.40.30.330; Pre-mRNA cleavage complex subunit Clp1, C-terminal domain; 1.
DR HAMAP; MF_03035; Clp1; 1.
DR InterPro; IPR028606; Clp1.
DR InterPro; IPR045116; Clp1/Grc3.
DR InterPro; IPR010655; Clp1_C.
DR InterPro; IPR038238; Clp1_C_sf.
DR InterPro; IPR032324; Clp1_N.
DR InterPro; IPR038239; Clp1_N_sf.
DR InterPro; IPR032319; CLP1_P.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR12755; CLEAVAGE/POLYADENYLATION FACTOR IA SUBUNIT CLP1P; 1.
DR PANTHER; PTHR12755:SF6; POLYRIBONUCLEOTIDE 5'-HYDROXYL-KINASE CLP1; 1.
DR Pfam; PF06807; Clp1; 1.
DR Pfam; PF16573; CLP1_N; 1.
DR Pfam; PF16575; CLP1_P; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; mRNA processing; Nucleotide-binding; Nucleus;
KW Reference proteome.
FT CHAIN 1..445
FT /note="mRNA cleavage and polyadenylation factor CLP1"
FT /id="PRO_0000076211"
FT BINDING 33
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03035,
FT ECO:0000269|PubMed:17151076"
FT BINDING 72
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03035,
FT ECO:0000269|PubMed:17151076"
FT BINDING 133..138
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03035,
FT ECO:0000269|PubMed:17151076"
FT MUTAGEN 136
FT /note="K->A: Completely abolishes interaction with PCF11.
FT No effect on growth; when associated with A-137."
FT /evidence="ECO:0000269|PubMed:22216186"
FT MUTAGEN 137
FT /note="T->A: Completely abolishes interaction with PCF11.
FT No effect on growth; when associated with A-136."
FT /evidence="ECO:0000269|PubMed:22216186"
FT MUTAGEN 161
FT /note="D->A: Compromises interaction with PCF11. No effect
FT on growth."
FT /evidence="ECO:0000269|PubMed:18648070,
FT ECO:0000269|PubMed:22216186"
FT STRAND 24..28
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 43..51
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 53..55
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 65..70
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 72..79
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 81..86
FT /evidence="ECO:0007829|PDB:4OI4"
FT TURN 92..94
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 103..119
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 120..122
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 125..131
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 136..147
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 148..151
FT /evidence="ECO:0007829|PDB:2NPI"
FT STRAND 156..159
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 172..177
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 194..196
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 212..214
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 215..217
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 219..239
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 241..246
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 248..251
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 255..257
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 263..271
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 276..281
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 286..299
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 304..307
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 318..334
FT /evidence="ECO:0007829|PDB:4OI4"
FT TURN 337..339
FT /evidence="ECO:0007829|PDB:2NPI"
FT STRAND 344..349
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 350..352
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 355..358
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 361..364
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 371..373
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 378..381
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 384..392
FT /evidence="ECO:0007829|PDB:4OI4"
FT HELIX 397..402
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 405..415
FT /evidence="ECO:0007829|PDB:4OI4"
FT TURN 416..419
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 420..430
FT /evidence="ECO:0007829|PDB:4OI4"
FT STRAND 434..442
FT /evidence="ECO:0007829|PDB:4OI4"
SQ SEQUENCE 445 AA; 50226 MW; B00F7659E83090DA CRC64;
MASLPGIDEH TTSEELITGD NEWHKLVIPK GSDWQIDLKA EGKLIVKVNS GIVEIFGTEL
AVDDEYTFQN WKFPIYAVEE TELLWKCPDL TTNTITVKPN HTMKYIYNLH FMLEKIRMSN
FEGPRVVIVG GSQTGKTSLS RTLCSYALKF NAYQPLYINL DPQQPIFTVP GCISATPISD
ILDAQLPTWG QSLTSGATLL HNKQPMVKNF GLERINENKD LYLECISQLG QVVGQRLHLD
PQVRRSGCIV DTPSISQLDE NLAELHHIIE KLNVNIMLVL CSETDPLWEK VKKTFGPELG
NNNIFFIPKL DGVSAVDDVY KRSLQRTSIR EYFYGSLDTA LSPYAIGVDY EDLTIWKPSN
VFDNEVGRVE LFPVTITPSN LQHAIIAITF AERRADQATV IKSPILGFAL ITEVNEKRRK
LRVLLPVPGR LPSKAMILTS YRYLE
//
