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Pre-mRNA-splicing factor CLF1 (Crooked neck-like factor 1) (PRP19-associated complex protein 77) (Synthetic lethal with CDC40 protein 3)

 CLF1_YEAST              Reviewed;         687 AA.
Q12309; D6VYB5;
30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
27-SEP-2017, entry version 135.
RecName: Full=Pre-mRNA-splicing factor CLF1;
AltName: Full=Crooked neck-like factor 1;
AltName: Full=PRP19-associated complex protein 77;
AltName: Full=Synthetic lethal with CDC40 protein 3;
Name=CLF1; Synonyms=NTC77, SYF3; OrderedLocusNames=YLR117C;
ORFNames=L2952;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 90840 / EAY235 / FY23;
PubMed=9090053;
DOI=10.1002/(SICI)1097-0061(19970315)13:3<241::AID-YEA61>3.0.CO;2-#;
Verhasselt P., Volckaert G.;
"Sequence analysis of a 37.6 kbp cosmid clone from the right arm of
Saccharomyces cerevisiae chromosome XII, carrying YAP3, HOG1, SNR6,
tRNA-Arg3 and 23 new open reading frames, among which several
homologies to proteins involved in cell division control and to
mammalian growth factors and other animal proteins are found.";
Yeast 13:241-250(1997).
[2]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169871;
Johnston M., Hillier L.W., Riles L., Albermann K., Andre B.,
Ansorge W., Benes V., Brueckner M., Delius H., Dubois E.,
Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U.,
Heumann K., Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K.,
Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T.,
Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E.,
Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M.,
Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C.,
Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M.,
Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H.,
Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A.,
Hani J., Hoheisel J.D.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
Nature 387:87-90(1997).
[4]
PROTEIN SEQUENCE OF 15-25, AND IDENTIFICATION IN THE PRP19-ASSOCIATED
COMPLEX.
PubMed=11842115; DOI=10.1093/nar/30.4.1029;
Chen C.-H., Yu W.-C., Tsao T.Y., Wang L.-Y., Chen H.-R., Lin J.-Y.,
Tsai W.-Y., Cheng S.-C.;
"Functional and physical interactions between components of the
Prp19p-associated complex.";
Nucleic Acids Res. 30:1029-1037(2002).
[5]
FUNCTION, AND INTERACTION WITH MUD2 AND PRP40.
PubMed=10445879; DOI=10.1017/S1355838299990635;
Chung S., McLean M.R., Rymond B.C.;
"Yeast ortholog of the Drosophila crooked neck protein promotes
spliceosome assembly through stable U4/U6.U5 snRNP addition.";
RNA 5:1042-1054(1999).
[6]
FUNCTION, AND INTERACTION WITH CEF1; ISY1; NTC20; PRP22 AND SYF2.
PubMed=11102353;
Ben-Yehuda S., Dix I., Russell C.S., McGarvey M., Beggs J.D.,
Kupiec M.;
"Genetic and physical interactions between factors involved in both
cell cycle progression and pre-mRNA splicing in Saccharomyces
cerevisiae.";
Genetics 156:1503-1517(2000).
[7]
FUNCTION, AND IDENTIFICATION IN THE SPLICEOSOME.
PubMed=11105756; DOI=10.1017/S1355838200000984;
Russell C.S., Ben-Yehuda S., Dix I., Kupiec M., Beggs J.D.;
"Functional analyses of interacting factors involved in both pre-mRNA
splicing and cell cycle progression in Saccharomyces cerevisiae.";
RNA 6:1565-1572(2000).
[8]
FUNCTION, AND INTERACTION WITH ORC2.
PubMed=11973290;
Zhu W., Rainville I.R., Ding M., Bolus M., Heintz N.H., Pederson D.S.;
"Evidence that the pre-mRNA splicing factor Clf1p plays a role in DNA
replication in Saccharomyces cerevisiae.";
Genetics 160:1319-1333(2002).
[9]
IDENTIFICATION IN THE CWC COMPLEX, AND IDENTIFICATION BY MASS
SPECTROMETRY.
PubMed=11884590; DOI=10.1128/MCB.22.7.2011-2024.2002;
Ohi M.D., Link A.J., Ren L., Jennings J.L., McDonald W.H., Gould K.L.;
"Proteomics analysis reveals stable multiprotein complexes in both
fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel
pre-mRNA splicing factors, and snRNAs.";
Mol. Cell. Biol. 22:2011-2024(2002).
[10]
INTERACTION WITH ISY1; NTC20; PRP46 AND SYF1.
PubMed=12088152; DOI=10.1017/S1355838202025050;
Ohi M.D., Gould K.L.;
"Characterization of interactions among the Cef1p-Prp19p-associated
splicing complex.";
RNA 8:798-815(2002).
[11]
FUNCTION, AND IDENTIFICATION IN THE SPLICEOSOME.
PubMed=12509417; DOI=10.1074/jbc.M210839200;
Wang Q., Hobbs K., Lynn B., Rymond B.C.;
"The Clf1p splicing factor promotes spliceosome assembly through N-
terminal tetratricopeptide repeat contacts.";
J. Biol. Chem. 278:7875-7883(2003).
[12]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[13]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
-!- FUNCTION: Involved in pre-mRNA splicing and cell cycle
progression. Required for the spliceosome assembly by promoting
the functional integration of the U4/U6.U5 tri-snRNP particle into
the U1-, U2-dependent pre-spliceosome. Also recruits PRP19 to the
spliceosome, as a component of the NTC complex (or PRP19-
associated complex). The association of the NTC complex to the
spliceosome mediates conformational rearrangement or stabilizes
the structure of the spliceosome after U4 snRNA dissociation,
which leads to spliceosome maturation. Required for initiation of
the DNA replication by binding the RNA replication origins,
probably through its interaction with the origin recognition
complex (ORC). {ECO:0000269|PubMed:10445879,
ECO:0000269|PubMed:11102353, ECO:0000269|PubMed:11105756,
ECO:0000269|PubMed:11973290, ECO:0000269|PubMed:12509417}.
-!- SUBUNIT: Belongs to the NTC complex (or PRP19-associated complex),
composed of at least CEF1, CLF1, ISY1, NTC20, SNT309, SYF1, SYF2,
and PRP19. The NTC complex associates with the spliceosome after
the release of the U1 and U4 snRNAs and forms the CWC spliceosome
subcomplex (or CEF1-associated complex) reminiscent of a late-
stage spliceosome composed also of the U2, U5 and U6 snRNAs and at
least BUD13, BUD31, BRR2, CDC40, CUS1, CWC2, CWC15, CWC21, CWC22,
CWC23, CWC24, CWC25, CWC27, ECM2, HSH155, IST3, LEA1, MSL1, PRP8,
PRP9, PRP11, PRP21, PRP22, PRP45, PRP46, SLU7, SMB1, SMD1, SMD2,
SMD3, SMX2, SMX3, SNU114, SPP2, RSE1 and YJU2. Interacts with
CEF1, ISY1, MUD2, NTC20, PRP22, PRP40, PRP46, SYF1, SYF2, and the
ORC2 subunit of the origin recognition complex.
{ECO:0000269|PubMed:10445879, ECO:0000269|PubMed:11102353,
ECO:0000269|PubMed:11105756, ECO:0000269|PubMed:11842115,
ECO:0000269|PubMed:11884590, ECO:0000269|PubMed:11973290,
ECO:0000269|PubMed:12088152, ECO:0000269|PubMed:12509417}.
-!- INTERACTION:
Q03654:CEF1; NbExp=9; IntAct=EBI-484, EBI-476;
P53333:CWC22; NbExp=2; IntAct=EBI-484, EBI-565;
P21374:ISY1; NbExp=5; IntAct=EBI-484, EBI-9382;
P38302:NTC20; NbExp=7; IntAct=EBI-484, EBI-20921;
P32523:PRP19; NbExp=10; IntAct=EBI-484, EBI-493;
Q12417:PRP46; NbExp=3; IntAct=EBI-484, EBI-710;
Q06091:SNT309; NbExp=7; IntAct=EBI-484, EBI-818;
Q04048:SYF1; NbExp=9; IntAct=EBI-484, EBI-540;
P53277:SYF2; NbExp=4; IntAct=EBI-484, EBI-23308;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
-!- MISCELLANEOUS: Present with 2140 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the crooked-neck family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X89514; CAA61696.1; -; Genomic_DNA.
EMBL; U53877; AAB82364.1; -; Genomic_DNA.
EMBL; Z73289; CAA97685.1; -; Genomic_DNA.
EMBL; BK006945; DAA09431.1; -; Genomic_DNA.
PIR; S64954; S64954.
RefSeq; NP_013218.1; NM_001182004.1.
PDB; 5GM6; EM; 3.50 A; d=1-275.
PDB; 5GMK; EM; 3.40 A; d=1-275.
PDB; 5LJ3; EM; 3.80 A; S=1-687.
PDB; 5LJ5; EM; 3.80 A; S=1-687.
PDB; 5LQW; EM; 5.80 A; R=1-687.
PDB; 5MPS; EM; 3.85 A; S=1-687.
PDB; 5MQ0; EM; 4.17 A; S=1-687.
PDB; 5WSG; EM; 4.00 A; d=36-275.
PDBsum; 5GM6; -.
PDBsum; 5GMK; -.
PDBsum; 5LJ3; -.
PDBsum; 5LJ5; -.
PDBsum; 5LQW; -.
PDBsum; 5MPS; -.
PDBsum; 5MQ0; -.
PDBsum; 5WSG; -.
ProteinModelPortal; Q12309; -.
SMR; Q12309; -.
BioGrid; 31389; 279.
DIP; DIP-1685N; -.
IntAct; Q12309; 38.
MINT; MINT-385873; -.
STRING; 4932.YLR117C; -.
MaxQB; Q12309; -.
PRIDE; Q12309; -.
EnsemblFungi; YLR117C; YLR117C; YLR117C.
GeneID; 850808; -.
KEGG; sce:YLR117C; -.
EuPathDB; FungiDB:YLR117C; -.
SGD; S000004107; CLF1.
GeneTree; ENSGT00550000074931; -.
HOGENOM; HOG000207972; -.
InParanoid; Q12309; -.
KO; K12869; -.
OMA; FTFSKIW; -.
OrthoDB; EOG092C0UBN; -.
BioCyc; YEAST:G3O-32262-MONOMER; -.
PRO; PR:Q12309; -.
Proteomes; UP000002311; Chromosome XII.
GO; GO:0000785; C:chromatin; IDA:SGD.
GO; GO:0071011; C:precatalytic spliceosome; IBA:GO_Central.
GO; GO:0000974; C:Prp19 complex; IDA:SGD.
GO; GO:0071006; C:U2-type catalytic step 1 spliceosome; IDA:SGD.
GO; GO:0071007; C:U2-type catalytic step 2 spliceosome; IDA:SGD.
GO; GO:0071008; C:U2-type post-mRNA release spliceosomal complex; IDA:SGD.
GO; GO:0071004; C:U2-type prespliceosome; IDA:SGD.
GO; GO:0003682; F:chromatin binding; IDA:SGD.
GO; GO:0003688; F:DNA replication origin binding; IDA:SGD.
GO; GO:0000354; P:cis assembly of pre-catalytic spliceosome; IMP:SGD.
GO; GO:0006270; P:DNA replication initiation; IMP:SGD.
Gene3D; 1.25.40.10; -; 5.
InterPro; IPR003107; HAT.
InterPro; IPR013026; TPR-contain_dom.
InterPro; IPR011990; TPR-like_helical_dom.
Pfam; PF02184; HAT; 1.
SMART; SM00386; HAT; 12.
SUPFAM; SSF48452; SSF48452; 2.
1: Evidence at protein level;
3D-structure; Complete proteome; Direct protein sequencing;
mRNA processing; mRNA splicing; Nucleus; Reference proteome; Repeat;
Spliceosome.
CHAIN 1 687 Pre-mRNA-splicing factor CLF1.
/FTId=PRO_0000205753.
REPEAT 45 77 HAT 1.
REPEAT 79 111 HAT 2.
REPEAT 113 145 HAT 3.
REPEAT 147 178 HAT 4.
REPEAT 180 211 HAT 5.
REPEAT 213 247 HAT 6.
REPEAT 251 283 HAT 7.
REPEAT 300 332 HAT 8.
REPEAT 337 369 HAT 9.
REPEAT 383 416 HAT 10.
REPEAT 451 483 HAT 11.
REPEAT 525 557 HAT 12.
REPEAT 629 661 HAT 13.
HELIX 40 60 {ECO:0000244|PDB:5GMK}.
HELIX 65 77 {ECO:0000244|PDB:5GMK}.
HELIX 81 94 {ECO:0000244|PDB:5GMK}.
HELIX 99 111 {ECO:0000244|PDB:5GMK}.
HELIX 115 128 {ECO:0000244|PDB:5GMK}.
HELIX 133 144 {ECO:0000244|PDB:5GMK}.
TURN 145 147 {ECO:0000244|PDB:5GMK}.
HELIX 149 161 {ECO:0000244|PDB:5GMK}.
HELIX 166 178 {ECO:0000244|PDB:5GMK}.
HELIX 182 195 {ECO:0000244|PDB:5GMK}.
HELIX 199 212 {ECO:0000244|PDB:5GMK}.
HELIX 215 232 {ECO:0000244|PDB:5GMK}.
HELIX 233 235 {ECO:0000244|PDB:5GMK}.
HELIX 240 256 {ECO:0000244|PDB:5GMK}.
HELIX 260 273 {ECO:0000244|PDB:5GMK}.
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


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