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Pre-mRNA-splicing factor SYF1 (PRP19-associated complex protein 90) (Synthetic lethal with CDC40 protein 1)

 SYF1_YEAST              Reviewed;         859 AA.
Q04048; D6VT47;
30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
25-OCT-2017, entry version 140.
RecName: Full=Pre-mRNA-splicing factor SYF1;
AltName: Full=PRP19-associated complex protein 90;
AltName: Full=Synthetic lethal with CDC40 protein 1;
Name=SYF1; Synonyms=NTC90; OrderedLocusNames=YDR416W;
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 204508 / S288c;
PubMed=9169867;
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N.,
Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M.,
Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L.,
Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M.,
Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S.,
Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M.,
Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S.,
Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K.,
Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D.,
Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C.,
Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T.,
Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E.,
Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W.,
Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K.,
Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S.,
Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A.,
Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S.,
Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M.,
Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y.,
Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M.,
Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E.,
Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R.,
Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
Mewes H.-W., Zollner A., Zaccaria P.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
Nature 387:75-78(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]
PROTEIN SEQUENCE OF 6-23, 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).
[4]
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).
[5]
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).
[6]
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).
[7]
INTERACTION WITH CEF1; CLF1; ISY1; NTC20 AND PRP46.
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).
[8]
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).
[9]
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).
[10]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22814378; DOI=10.1073/pnas.1210303109;
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E.,
Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K.,
Aldabe R.;
"N-terminal acetylome analyses and functional insights of the N-
terminal acetyltransferase NatB.";
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
-!- FUNCTION: Involved in pre-mRNA splicing and cell cycle control. As
a component of the NTC complex (or PRP19-associated complex),
associates to the spliceosome to mediate conformational
rearrangement or to stabilize the structure of the spliceosome
after U4 snRNA dissociation, which leads to spliceosome
maturation. {ECO:0000269|PubMed:11102353,
ECO:0000269|PubMed:11105756}.
-!- 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, CLF1, ISY1, NTC20, PRP22, PRP46 and SYF2.
{ECO:0000269|PubMed:11102353, ECO:0000269|PubMed:11105756,
ECO:0000269|PubMed:11842115, ECO:0000269|PubMed:11884590,
ECO:0000269|PubMed:12088152}.
-!- INTERACTION:
Q03654:CEF1; NbExp=5; IntAct=EBI-540, EBI-476;
Q12309:CLF1; NbExp=4; IntAct=EBI-540, EBI-484;
P21374:ISY1; NbExp=4; IntAct=EBI-540, EBI-9382;
P38302:NTC20; NbExp=6; IntAct=EBI-540, EBI-20921;
P32523:PRP19; NbExp=6; IntAct=EBI-540, EBI-493;
P28004:PRP45; NbExp=3; IntAct=EBI-540, EBI-20640;
P53277:SYF2; NbExp=3; IntAct=EBI-540, EBI-23308;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
-!- MISCELLANEOUS: Present with 2170 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; U33007; AAB64862.1; -; Genomic_DNA.
EMBL; BK006938; DAA12257.1; -; Genomic_DNA.
PIR; S69700; S69700.
RefSeq; NP_010704.1; NM_001180724.1.
PDB; 5GM6; EM; 3.50 A; v=569-734.
PDB; 5GMK; EM; 3.40 A; v=569-734.
PDB; 5LJ3; EM; 3.80 A; T=1-859.
PDB; 5LJ5; EM; 3.80 A; T=1-859.
PDB; 5LQW; EM; 5.80 A; P=1-859.
PDB; 5MPS; EM; 3.85 A; T=1-859.
PDB; 5MQ0; EM; 4.17 A; T=1-859.
PDB; 5WSG; EM; 4.00 A; v=569-734.
PDBsum; 5GM6; -.
PDBsum; 5GMK; -.
PDBsum; 5LJ3; -.
PDBsum; 5LJ5; -.
PDBsum; 5LQW; -.
PDBsum; 5MPS; -.
PDBsum; 5MQ0; -.
PDBsum; 5WSG; -.
ProteinModelPortal; Q04048; -.
SMR; Q04048; -.
BioGrid; 32475; 245.
DIP; DIP-1681N; -.
IntAct; Q04048; 27.
MINT; MINT-385933; -.
STRING; 4932.YDR416W; -.
MaxQB; Q04048; -.
PRIDE; Q04048; -.
EnsemblFungi; YDR416W; YDR416W; YDR416W.
GeneID; 852025; -.
KEGG; sce:YDR416W; -.
EuPathDB; FungiDB:YDR416W; -.
SGD; S000002824; SYF1.
GeneTree; ENSGT00550000075140; -.
HOGENOM; HOG000065931; -.
InParanoid; Q04048; -.
KO; K12867; -.
OMA; CAVYDRM; -.
OrthoDB; EOG092C1YSM; -.
BioCyc; YEAST:G3O-29958-MONOMER; -.
Reactome; R-SCE-6781823; Formation of TC-NER Pre-Incision Complex.
Reactome; R-SCE-6782135; Dual incision in TC-NER.
Reactome; R-SCE-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
PRO; PR:Q04048; -.
Proteomes; UP000002311; Chromosome IV.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
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:0000349; P:generation of catalytic spliceosome for first transesterification step; IDA:SGD.
Gene3D; 1.25.40.10; -; 4.
InterPro; IPR003107; HAT.
InterPro; IPR011990; TPR-like_helical_dom.
SMART; SM00386; HAT; 8.
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 1 859 Pre-mRNA-splicing factor SYF1.
/FTId=PRO_0000205737.
REPEAT 17 49 HAT 1.
REPEAT 52 84 HAT 2.
REPEAT 88 108 HAT 3.
REPEAT 123 157 HAT 4.
REPEAT 177 219 HAT 5.
REPEAT 238 271 HAT 6.
REPEAT 427 459 HAT 7.
REPEAT 461 482 HAT 8.
REPEAT 520 554 HAT 9.
REPEAT 599 633 HAT 10.
REPEAT 639 675 HAT 11.
REPEAT 685 718 HAT 12.
REPEAT 720 754 HAT 13.
REPEAT 756 790 HAT 14.
HELIX 570 578 {ECO:0000244|PDB:5GMK}.
HELIX 585 597 {ECO:0000244|PDB:5GMK}.
HELIX 602 611 {ECO:0000244|PDB:5GMK}.
TURN 612 614 {ECO:0000244|PDB:5GMK}.
HELIX 616 635 {ECO:0000244|PDB:5GMK}.
HELIX 641 652 {ECO:0000244|PDB:5GMK}.
HELIX 664 675 {ECO:0000244|PDB:5GMK}.
HELIX 680 688 {ECO:0000244|PDB:5GMK}.
HELIX 707 719 {ECO:0000244|PDB:5GMK}.
HELIX 723 733 {ECO:0000244|PDB:5GMK}.
SEQUENCE 859 AA; 100229 MW; ED4368A624A40E7C CRC64;
MSAYIAMKGV ITNVDENIRN DEDVAFEYEI QKTPQNILTW KRYIEYWKEE GRTDKQIRWL
YERFCSQFVT DTSIWEDYIR WESTKEVVET SRIFWLFQRC LKSCVRDCDR ICLSYLELAI
EQYDLAMIRH ALASSLMKME REMHRKVWDP VIKFVEEKVL PLTQLDSTQE DEEESTDEAE
LINVLLVKGF TKGGFISEEI SENGSRGDIW SSHILERYLK VAPQQKRNES LATLALTRDN
ITIKSVYEKY LPQDENSGKY LPSSELPFEL NFNYLASLEK LGLDNQYEEF MRQMNGIYPD
KWLFLILSLA KYYISRGRLD SCGDLLKKSL QQTLRYSDFD RIYNFYLLFE QECSQFILGK
LKENDSKFFN QKDWTEKLQA HMATFESLIN LYDIYLNDVA LRQDSNLVET WMKRVSLQKS
AAEKCNVYSE AILKIDPRKV GTPGSFGRLW CSYGDLYWRS NAISTARELW TQSLKVPYPY
IEDLEEIYLN WADRELDKEG VERAFSILED ALHVPTNPEI LLEKYKNGHR KIPAQTVLFN
SLRIWSKYID YLEAYCPKDA NSSDKIFNKT KMAYNTVIDL RLITPAMAEN FALFLQNHYE
VMESFQVYEK TIPLFPPEIQ YELWIEYLEV ATSHQLSSLS PEHIRFLFEK ALKNLCSNGI
DCKTIFIAYS VFEERISGLI SKSIEILRRG AVIGTVSVST HLESRLQLWR MCISKAESTL
GPSVTRELYQ ECIQILPNSK AVEFVIKFSD FESSIGETIR AREILAYGAK LLPPSRNTEL
WDSFEIFELK HGDKETYKDM LKMKKVLESN MLIDSASVSH EEGNINFVAA ATSHAPNSHT
LTQSTSSYSI NPDEIELDI


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