CLF1_YEAST
ID CLF1_YEAST Reviewed; 687 AA.
AC Q12309; D6VYB5;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 168.
DE RecName: Full=Pre-mRNA-splicing factor CLF1;
DE AltName: Full=Crooked neck-like factor 1;
DE AltName: Full=PRP19-associated complex protein 77;
DE AltName: Full=Synthetic lethal with CDC40 protein 3;
GN Name=CLF1; Synonyms=NTC77, SYF3; OrderedLocusNames=YLR117C; ORFNames=L2952;
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 90840 / EAY235 / FY23;
RX PubMed=9090053;
RX DOI=10.1002/(sici)1097-0061(19970315)13:3<241::aid-yea61>3.0.co;2-#;
RA Verhasselt P., Volckaert G.;
RT "Sequence analysis of a 37.6 kbp cosmid clone from the right arm of
RT Saccharomyces cerevisiae chromosome XII, carrying YAP3, HOG1, SNR6, tRNA-
RT Arg3 and 23 new open reading frames, among which several homologies to
RT proteins involved in cell division control and to mammalian growth factors
RT and other animal proteins are found.";
RL Yeast 13:241-250(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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [4]
RP PROTEIN SEQUENCE OF 15-25, AND IDENTIFICATION IN THE PRP19-ASSOCIATED
RP COMPLEX.
RX PubMed=11842115; DOI=10.1093/nar/30.4.1029;
RA Chen C.-H., Yu W.-C., Tsao T.Y., Wang L.-Y., Chen H.-R., Lin J.-Y.,
RA Tsai W.-Y., Cheng S.-C.;
RT "Functional and physical interactions between components of the Prp19p-
RT associated complex.";
RL Nucleic Acids Res. 30:1029-1037(2002).
RN [5]
RP FUNCTION, AND INTERACTION WITH MUD2 AND PRP40.
RX PubMed=10445879; DOI=10.1017/s1355838299990635;
RA Chung S., McLean M.R., Rymond B.C.;
RT "Yeast ortholog of the Drosophila crooked neck protein promotes spliceosome
RT assembly through stable U4/U6.U5 snRNP addition.";
RL RNA 5:1042-1054(1999).
RN [6]
RP FUNCTION, AND INTERACTION WITH CEF1; ISY1; NTC20; PRP22 AND SYF2.
RX PubMed=11102353; DOI=10.1093/genetics/156.4.1503;
RA Ben-Yehuda S., Dix I., Russell C.S., McGarvey M., Beggs J.D., Kupiec M.;
RT "Genetic and physical interactions between factors involved in both cell
RT cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae.";
RL Genetics 156:1503-1517(2000).
RN [7]
RP FUNCTION, AND IDENTIFICATION IN THE SPLICEOSOME.
RX PubMed=11105756; DOI=10.1017/s1355838200000984;
RA Russell C.S., Ben-Yehuda S., Dix I., Kupiec M., Beggs J.D.;
RT "Functional analyses of interacting factors involved in both pre-mRNA
RT splicing and cell cycle progression in Saccharomyces cerevisiae.";
RL RNA 6:1565-1572(2000).
RN [8]
RP FUNCTION, AND INTERACTION WITH ORC2.
RX PubMed=11973290; DOI=10.1093/genetics/160.4.1319;
RA Zhu W., Rainville I.R., Ding M., Bolus M., Heintz N.H., Pederson D.S.;
RT "Evidence that the pre-mRNA splicing factor Clf1p plays a role in DNA
RT replication in Saccharomyces cerevisiae.";
RL Genetics 160:1319-1333(2002).
RN [9]
RP IDENTIFICATION IN THE CWC COMPLEX, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=11884590; DOI=10.1128/mcb.22.7.2011-2024.2002;
RA Ohi M.D., Link A.J., Ren L., Jennings J.L., McDonald W.H., Gould K.L.;
RT "Proteomics analysis reveals stable multiprotein complexes in both fission
RT and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA
RT splicing factors, and snRNAs.";
RL Mol. Cell. Biol. 22:2011-2024(2002).
RN [10]
RP INTERACTION WITH ISY1; NTC20; PRP46 AND SYF1.
RX PubMed=12088152; DOI=10.1017/s1355838202025050;
RA Ohi M.D., Gould K.L.;
RT "Characterization of interactions among the Cef1p-Prp19p-associated
RT splicing complex.";
RL RNA 8:798-815(2002).
RN [11]
RP FUNCTION, AND IDENTIFICATION IN THE SPLICEOSOME.
RX PubMed=12509417; DOI=10.1074/jbc.m210839200;
RA Wang Q., Hobbs K., Lynn B., Rymond B.C.;
RT "The Clf1p splicing factor promotes spliceosome assembly through N-terminal
RT tetratricopeptide repeat contacts.";
RL J. Biol. Chem. 278:7875-7883(2003).
RN [12]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=14690591; DOI=10.1016/s1097-2765(03)00476-3;
RA Hazbun T.R., Malmstroem L., Anderson S., Graczyk B.J., Fox B., Riffle M.,
RA Sundin B.A., Aranda J.D., McDonald W.H., Chiu C.-H., Snydsman B.E.,
RA Bradley P., Muller E.G.D., Fields S., Baker D., Yates J.R. III, Davis T.N.;
RT "Assigning function to yeast proteins by integration of technologies.";
RL Mol. Cell 12:1353-1365(2003).
RN [13]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [14]
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).
CC -!- FUNCTION: Involved in pre-mRNA splicing and cell cycle progression.
CC Required for the spliceosome assembly by promoting the functional
CC integration of the U4/U6.U5 tri-snRNP particle into the U1-, U2-
CC dependent pre-spliceosome. Also recruits PRP19 to the spliceosome, as a
CC component of the NTC complex (or PRP19-associated complex). The
CC association of the NTC complex to the spliceosome mediates
CC conformational rearrangement or stabilizes the structure of the
CC spliceosome after U4 snRNA dissociation, which leads to spliceosome
CC maturation. Required for initiation of the DNA replication by binding
CC the RNA replication origins, probably through its interaction with the
CC origin recognition complex (ORC). {ECO:0000269|PubMed:10445879,
CC ECO:0000269|PubMed:11102353, ECO:0000269|PubMed:11105756,
CC ECO:0000269|PubMed:11973290, ECO:0000269|PubMed:12509417}.
CC -!- SUBUNIT: Belongs to the NTC complex (or PRP19-associated complex),
CC composed of at least CEF1, CLF1, ISY1, NTC20, SNT309, SYF1, SYF2, and
CC PRP19. The NTC complex associates with the spliceosome after the
CC release of the U1 and U4 snRNAs and forms the CWC spliceosome
CC subcomplex (or CEF1-associated complex) reminiscent of a late-stage
CC spliceosome composed also of the U2, U5 and U6 snRNAs and at least
CC BUD13, BUD31, BRR2, CDC40, CUS1, CWC2, CWC15, CWC21, CWC22, CWC23,
CC CWC24, CWC25, CWC27, ECM2, HSH155, IST3, LEA1, MSL1, PRP8, PRP9, PRP11,
CC PRP21, PRP22, PRP45, PRP46, SLU7, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3,
CC SNU114, SPP2, RSE1 and YJU2. Interacts with CEF1, ISY1, MUD2, NTC20,
CC PRP22, PRP40, PRP46, SYF1, SYF2, and the ORC2 subunit of the origin
CC recognition complex. {ECO:0000269|PubMed:10445879,
CC ECO:0000269|PubMed:11102353, ECO:0000269|PubMed:11105756,
CC ECO:0000269|PubMed:11842115, ECO:0000269|PubMed:11884590,
CC ECO:0000269|PubMed:11973290, ECO:0000269|PubMed:12088152,
CC ECO:0000269|PubMed:12509417}.
CC -!- INTERACTION:
CC Q12309; Q03654: CEF1; NbExp=8; IntAct=EBI-484, EBI-476;
CC Q12309; P21374: ISY1; NbExp=4; IntAct=EBI-484, EBI-9382;
CC Q12309; P38302: NTC20; NbExp=6; IntAct=EBI-484, EBI-20921;
CC Q12309; P32523: PRP19; NbExp=9; IntAct=EBI-484, EBI-493;
CC Q12309; Q06091: SNT309; NbExp=4; IntAct=EBI-484, EBI-818;
CC Q12309; Q04048: SYF1; NbExp=4; IntAct=EBI-484, EBI-540;
CC Q12309; P53277: SYF2; NbExp=2; IntAct=EBI-484, EBI-23308;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 2140 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the crooked-neck family. {ECO:0000305}.
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DR EMBL; X89514; CAA61696.1; -; Genomic_DNA.
DR EMBL; U53877; AAB82364.1; -; Genomic_DNA.
DR EMBL; Z73289; CAA97685.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09431.1; -; Genomic_DNA.
DR PIR; S64954; S64954.
DR RefSeq; NP_013218.1; NM_001182004.1.
DR PDB; 5GM6; EM; 3.50 A; d=1-275.
DR PDB; 5GMK; EM; 3.40 A; d=1-275.
DR PDB; 5LJ3; EM; 3.80 A; S=1-687.
DR PDB; 5LJ5; EM; 3.80 A; S=1-687.
DR PDB; 5LQW; EM; 5.80 A; R=1-687.
DR PDB; 5MPS; EM; 3.85 A; S=1-687.
DR PDB; 5MQ0; EM; 4.17 A; S=1-687.
DR PDB; 5WSG; EM; 4.00 A; d=36-275.
DR PDB; 5Y88; EM; 3.70 A; I=1-687.
DR PDB; 5YLZ; EM; 3.60 A; I=1-687.
DR PDB; 6BK8; EM; 3.30 A; T=1-687.
DR PDB; 6EXN; EM; 3.70 A; S=1-687.
DR PDB; 6J6G; EM; 3.20 A; d=1-687.
DR PDB; 6J6H; EM; 3.60 A; d=1-687.
DR PDB; 6J6N; EM; 3.86 A; d=1-687.
DR PDB; 6J6Q; EM; 3.70 A; d=1-687.
DR PDBsum; 5GM6; -.
DR PDBsum; 5GMK; -.
DR PDBsum; 5LJ3; -.
DR PDBsum; 5LJ5; -.
DR PDBsum; 5LQW; -.
DR PDBsum; 5MPS; -.
DR PDBsum; 5MQ0; -.
DR PDBsum; 5WSG; -.
DR PDBsum; 5Y88; -.
DR PDBsum; 5YLZ; -.
DR PDBsum; 6BK8; -.
DR PDBsum; 6EXN; -.
DR PDBsum; 6J6G; -.
DR PDBsum; 6J6H; -.
DR PDBsum; 6J6N; -.
DR PDBsum; 6J6Q; -.
DR AlphaFoldDB; Q12309; -.
DR SMR; Q12309; -.
DR BioGRID; 31389; 285.
DR ComplexPortal; CPX-1651; PRP19-associated complex.
DR ComplexPortal; CPX-1885; NineTeen complex.
DR DIP; DIP-1685N; -.
DR IntAct; Q12309; 36.
DR MINT; Q12309; -.
DR STRING; 4932.YLR117C; -.
DR MoonProt; Q12309; -.
DR MaxQB; Q12309; -.
DR PaxDb; Q12309; -.
DR PRIDE; Q12309; -.
DR EnsemblFungi; YLR117C_mRNA; YLR117C; YLR117C.
DR GeneID; 850808; -.
DR KEGG; sce:YLR117C; -.
DR SGD; S000004107; CLF1.
DR VEuPathDB; FungiDB:YLR117C; -.
DR eggNOG; KOG1915; Eukaryota.
DR GeneTree; ENSGT00550000074931; -.
DR HOGENOM; CLU_011554_1_0_1; -.
DR InParanoid; Q12309; -.
DR OMA; HIKVWIS; -.
DR BioCyc; YEAST:G3O-32262-MON; -.
DR PRO; PR:Q12309; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; Q12309; protein.
DR GO; GO:0000785; C:chromatin; IDA:SGD.
DR GO; GO:0071014; C:post-mRNA release spliceosomal complex; IBA:GO_Central.
DR GO; GO:0000974; C:Prp19 complex; IDA:SGD.
DR GO; GO:0071006; C:U2-type catalytic step 1 spliceosome; IDA:SGD.
DR GO; GO:0071007; C:U2-type catalytic step 2 spliceosome; IDA:SGD.
DR GO; GO:0071008; C:U2-type post-mRNA release spliceosomal complex; IDA:SGD.
DR GO; GO:0071004; C:U2-type prespliceosome; IDA:SGD.
DR GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR GO; GO:0003688; F:DNA replication origin binding; IDA:SGD.
DR GO; GO:0000354; P:cis assembly of pre-catalytic spliceosome; IMP:SGD.
DR GO; GO:0006270; P:DNA replication initiation; IMP:SGD.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
DR GO; GO:0000245; P:spliceosomal complex assembly; IBA:GO_Central.
DR Gene3D; 1.25.40.10; -; 2.
DR InterPro; IPR003107; HAT.
DR InterPro; IPR045075; Syf1-like.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR PANTHER; PTHR11246; PTHR11246; 1.
DR Pfam; PF02184; HAT; 1.
DR SMART; SM00386; HAT; 12.
DR SUPFAM; SSF48452; SSF48452; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; mRNA processing; mRNA splicing;
KW Nucleus; Reference proteome; Repeat; Spliceosome.
FT CHAIN 1..687
FT /note="Pre-mRNA-splicing factor CLF1"
FT /id="PRO_0000205753"
FT REPEAT 45..77
FT /note="HAT 1"
FT REPEAT 79..111
FT /note="HAT 2"
FT REPEAT 113..145
FT /note="HAT 3"
FT REPEAT 147..178
FT /note="HAT 4"
FT REPEAT 180..211
FT /note="HAT 5"
FT REPEAT 213..247
FT /note="HAT 6"
FT REPEAT 251..283
FT /note="HAT 7"
FT REPEAT 300..332
FT /note="HAT 8"
FT REPEAT 337..369
FT /note="HAT 9"
FT REPEAT 383..416
FT /note="HAT 10"
FT REPEAT 451..483
FT /note="HAT 11"
FT REPEAT 525..557
FT /note="HAT 12"
FT REPEAT 629..661
FT /note="HAT 13"
FT HELIX 15..27
FT /evidence="ECO:0007829|PDB:6BK8"
FT HELIX 40..60
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 65..77
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 81..94
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 99..111
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 115..128
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 133..145
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 149..159
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 166..179
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 182..195
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 199..212
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 215..231
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 232..234
FT /evidence="ECO:0007829|PDB:6BK8"
FT HELIX 240..256
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 260..273
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 278..291
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 294..315
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 320..333
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 337..349
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 354..369
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 375..382
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 383..385
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 389..395
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 398..400
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 406..417
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 425..438
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 447..459
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 463..474
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 481..493
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 498..511
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 515..522
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 532..547
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 557..570
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 576..589
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 597..614
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 621..635
FT /evidence="ECO:0007829|PDB:6J6G"
SQ SEQUENCE 687 AA; 82445 MW; AE7D5EC5B3979E00 CRC64;
MDTLEPTAVD THVSAEQILR DVYKKGQKAR GSTNIDILDL EELREYQRRK RTEYEGYLKR
NRLDMGQWIR YAQFEIEQHD MRRARSIFER ALLVDSSFIP LWIRYIDAEL KVKCINHARN
LMNRAISTLP RVDKLWYKYL IVEESLNNVE IVRSLYTKWC SLEPGVNAWN SFVDFEIRQK
NWNGVREIYS KYVMAHPQMQ TWLKWVRFEN RHGNTEFTRS VYSLAIDTVA NLQNLQIWSD
MEVAKLVNSF AHWEAAQQEY ERSSALYQIA IEKWPSNQLL KAGLLDFEKQ FGDINSIEET
ISYKRKMEYE TILSNNAYDY DTWWLYLDLI SESFPKQIMQ TFEKAIVDSR PKELSKNVQW
KRYIYLWMRY ICYVELELEN SLLEEELFQR LIDDIIPHKH FTFSKIWLMY AKFLIRHDDV
PKARKILGKA IGLCPKAKTF KGYIELEVKL KEFDRVRKIY EKFIEFQPSD LQIWSQYGEL
EENLGDWDRV RGIYTIALDE NSDFLTKEAK IVLLQKYITF ETESQEFEKA RKLYRRYLEL
NQYSPQSWIE FAMYQTSTPT EQQLLDLAKL QSENVDEDIE FEITDENKLE ARKVFEEAIV
FFKEKDDKQG RLSILEALKD YEETYGTELD QETVKKRFPK VIKKVRLQNG VEEEFVDYIF
PDDIDDDKPK PSKFLELAKK WKQEQAL
