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}; GN 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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 //