PRP40_YEAST
ID PRP40_YEAST Reviewed; 583 AA.
AC P33203; D6VXS4;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 1.
DT 03-AUG-2022, entry version 191.
DE RecName: Full=Pre-mRNA-processing protein PRP40;
GN Name=PRP40; OrderedLocusNames=YKL012W; ORFNames=YKL165;
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=1481574; DOI=10.1002/yea.320081109;
RA Pascolo S., Ghazvini M., Boyer J., Colleaux L., Thierry A., Dujon B.;
RT "The sequence of a 9.3 kb segment located on the left arm of the yeast
RT chromosome XI reveals five open reading frames including the CCE1 gene and
RT putative products related to MYO2 and to the ribosomal protein L10.";
RL Yeast 8:987-995(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8196765; DOI=10.1038/369371a0;
RA Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V.,
RA Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P.,
RA Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L.,
RA Daignan-Fornier B., del Rey F., Dion C., Domdey H., Duesterhoeft A.,
RA Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H.,
RA Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L.,
RA Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M.,
RA Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H.,
RA Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J.,
RA Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H.,
RA Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J.,
RA Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S.,
RA Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F.,
RA Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R.,
RA Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W.,
RA Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M.,
RA Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C.,
RA Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H.,
RA Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L.,
RA van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S.,
RA von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M.,
RA Becker I., Mewes H.-W.;
RT "Complete DNA sequence of yeast chromosome XI.";
RL Nature 369:371-378(1994).
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 PARTIAL PROTEIN SEQUENCE.
RX PubMed=9012791; DOI=10.1073/pnas.94.2.385;
RA Neubauer G., Gottschalk A., Fabrizio P., Seraphin B., Luehrmann R.,
RA Mann M.;
RT "Identification of the proteins of the yeast U1 small nuclear
RT ribonucleoprotein complex by mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:385-390(1997).
RN [5]
RP IDENTIFICATION, AND MUTAGENESIS OF SER-240.
RX PubMed=8622699; DOI=10.1128/mcb.16.3.960;
RA Kao H.-Y., Siliciano P.G.;
RT "Identification of Prp40, a novel essential yeast splicing factor
RT associated with the U1 small nuclear ribonucleoprotein particle.";
RL Mol. Cell. Biol. 16:960-967(1996).
RN [6]
RP FUNCTION, AND INTERACTION WITH MSL5; MUD2 AND PRP8.
RX PubMed=9150140; DOI=10.1016/s0092-8674(00)80221-4;
RA Abovich N., Rosbash M.;
RT "Cross-intron bridging interactions in the yeast commitment complex are
RT conserved in mammals.";
RL Cell 89:403-412(1997).
RN [7]
RP FUNCTION, AND INTERACTION WITH RPB1.
RX PubMed=10978320; DOI=10.1074/jbc.m004118200;
RA Morris D.P., Greenleaf A.L.;
RT "The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal
RT domain of RNA polymerase II.";
RL J. Biol. Chem. 275:39935-39943(2000).
RN [8]
RP FUNCTION, INTERACTION WITH CRM1, SUBCELLULAR LOCATION, AND MUTAGENESIS OF
RP LEU-274; LEU-277; LEU-281; LEU-340; LEU-344 AND LEU-347.
RX PubMed=15020406; DOI=10.1534/genetics.166.1.53;
RA Murphy M.W., Olson B.L., Siliciano P.G.;
RT "The yeast splicing factor Prp40p contains functional leucine-rich nuclear
RT export signals that are essential for splicing.";
RL Genetics 166:53-65(2004).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-576, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [10]
RP STRUCTURE BY NMR OF 1-75.
RX PubMed=12460579; DOI=10.1016/s0022-2836(02)01145-2;
RA Wiesner S., Stier G., Sattler M., Macias M.J.;
RT "Solution structure and ligand recognition of the WW domain pair of the
RT yeast splicing factor Prp40.";
RL J. Mol. Biol. 324:807-822(2002).
CC -!- FUNCTION: Required for pre-spliceosome formation, which is the first
CC step of pre-mRNA splicing. This protein is associated with snRNP U1.
CC Two commitment complexes, CC1 and CC2, have been defined in yeast. CC1
CC is a basal complex dependent only on the 5' splice site. CC2 is a
CC complex of lower mobility and is dependent on a branchpoint as well as
CC a 5' splice site region. This protein is involved in CC2 formation
CC where it binds to the branchpoint binding protein MSL5, bridging the U1
CC snRNP-associated 5' splice site and the MSL5-associated branch point 3'
CC intron splice site. {ECO:0000269|PubMed:10978320,
CC ECO:0000269|PubMed:15020406, ECO:0000269|PubMed:9150140}.
CC -!- SUBUNIT: Interacts with CRM1, MSL5, PRP8, and the RNA polymerase II
CC largest subunit (RPB1). MSL5, MUD2 and PRP40 interact to form the
CC commitment complex 2 (CC2), a precursor of mature spliceosomes.
CC {ECO:0000269|PubMed:10978320, ECO:0000269|PubMed:15020406,
CC ECO:0000269|PubMed:9150140}.
CC -!- INTERACTION:
CC P33203; P80210: ADE12; NbExp=2; IntAct=EBI-701, EBI-14267;
CC P33203; P15274: AMD1; NbExp=2; IntAct=EBI-701, EBI-2548;
CC P33203; Q08968: FMP40; NbExp=2; IntAct=EBI-701, EBI-29375;
CC P33203; P06738: GPH1; NbExp=2; IntAct=EBI-701, EBI-13389;
CC P33203; P33399: LHP1; NbExp=2; IntAct=EBI-701, EBI-10046;
CC P33203; P30952: MLS1; NbExp=2; IntAct=EBI-701, EBI-10428;
CC P33203; P39683: NPT1; NbExp=2; IntAct=EBI-701, EBI-12218;
CC P33203; P10963: PCK1; NbExp=2; IntAct=EBI-701, EBI-13770;
CC P33203; P39015: STM1; NbExp=2; IntAct=EBI-701, EBI-11238;
CC P33203; Q07505: YDL086W; NbExp=2; IntAct=EBI-701, EBI-5951;
CC P33203; P47137: YJR096W; NbExp=2; IntAct=EBI-701, EBI-25572;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15020406}.
CC -!- DOMAIN: The WW and FF domains bind to the phosphorylated carboxy-
CC terminal domain of RPB1.
CC -!- SIMILARITY: Belongs to the PRPF40 family. {ECO:0000305}.
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DR EMBL; S53418; AAB24902.1; -; Genomic_DNA.
DR EMBL; Z28012; CAA81847.1; -; Genomic_DNA.
DR EMBL; BK006944; DAA09144.1; -; Genomic_DNA.
DR PIR; S30014; S30014.
DR RefSeq; NP_012913.3; NM_001179578.3.
DR PDB; 1O6W; NMR; -; A=1-75.
DR PDB; 2B7E; NMR; -; A=134-189.
DR PDB; 2KFD; NMR; -; A=488-552.
DR PDB; 6N7P; EM; 3.60 A; J=1-583.
DR PDB; 7OQE; EM; 5.90 A; K=1-583.
DR PDBsum; 1O6W; -.
DR PDBsum; 2B7E; -.
DR PDBsum; 2KFD; -.
DR PDBsum; 6N7P; -.
DR PDBsum; 7OQE; -.
DR AlphaFoldDB; P33203; -.
DR BMRB; P33203; -.
DR SMR; P33203; -.
DR BioGRID; 34120; 244.
DR ComplexPortal; CPX-23; U1 small nuclear ribonucleoprotein complex.
DR DIP; DIP-1620N; -.
DR IntAct; P33203; 119.
DR MINT; P33203; -.
DR STRING; 4932.YKL012W; -.
DR iPTMnet; P33203; -.
DR MaxQB; P33203; -.
DR PaxDb; P33203; -.
DR PRIDE; P33203; -.
DR EnsemblFungi; YKL012W_mRNA; YKL012W; YKL012W.
DR GeneID; 853857; -.
DR KEGG; sce:YKL012W; -.
DR SGD; S000001495; PRP40.
DR VEuPathDB; FungiDB:YKL012W; -.
DR eggNOG; KOG0152; Eukaryota.
DR GeneTree; ENSGT00930000150980; -.
DR HOGENOM; CLU_005825_1_1_1; -.
DR InParanoid; P33203; -.
DR OMA; NEPIYKH; -.
DR BioCyc; YEAST:G3O-31821-MON; -.
DR EvolutionaryTrace; P33203; -.
DR PRO; PR:P33203; -.
DR Proteomes; UP000002311; Chromosome XI.
DR RNAct; P33203; protein.
DR GO; GO:0000243; C:commitment complex; IC:ComplexPortal.
DR GO; GO:0005634; C:nucleus; IMP:SGD.
DR GO; GO:0005681; C:spliceosomal complex; IC:ComplexPortal.
DR GO; GO:0005685; C:U1 snRNP; IDA:SGD.
DR GO; GO:0071004; C:U2-type prespliceosome; IDA:SGD.
DR GO; GO:0003723; F:RNA binding; IDA:SGD.
DR GO; GO:0000395; P:mRNA 5'-splice site recognition; IC:ComplexPortal.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IDA:SGD.
DR CDD; cd00201; WW; 2.
DR Gene3D; 1.10.10.440; -; 4.
DR InterPro; IPR002713; FF_domain.
DR InterPro; IPR036517; FF_domain_sf.
DR InterPro; IPR039726; Prp40-like.
DR InterPro; IPR001202; WW_dom.
DR InterPro; IPR036020; WW_dom_sf.
DR PANTHER; PTHR11864; PTHR11864; 1.
DR Pfam; PF01846; FF; 4.
DR Pfam; PF00397; WW; 2.
DR SMART; SM00441; FF; 4.
DR SMART; SM00456; WW; 2.
DR SUPFAM; SSF51045; SSF51045; 2.
DR SUPFAM; SSF81698; SSF81698; 3.
DR PROSITE; PS51676; FF; 6.
DR PROSITE; PS01159; WW_DOMAIN_1; 2.
DR PROSITE; PS50020; WW_DOMAIN_2; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; mRNA processing; mRNA splicing;
KW Nucleus; Phosphoprotein; Reference proteome; Repeat; Ribonucleoprotein.
FT CHAIN 1..583
FT /note="Pre-mRNA-processing protein PRP40"
FT /id="PRO_0000076084"
FT DOMAIN 1..31
FT /note="WW 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00224"
FT DOMAIN 42..72
FT /note="WW 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00224"
FT DOMAIN 132..188
FT /note="FF 1"
FT DOMAIN 201..257
FT /note="FF 2"
FT DOMAIN 262..332
FT /note="FF 3"
FT DOMAIN 354..413
FT /note="FF 4"
FT DOMAIN 427..488
FT /note="FF 5"
FT DOMAIN 491..552
FT /note="FF 6"
FT MOD_RES 576
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MUTAGEN 240
FT /note="S->P: In PRP40-1 suppressor; affects SAR1 mRNA
FT accumulation in U1-U4 mutant at 18 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:8622699"
FT MUTAGEN 274
FT /note="L->A: Temperature sensitive growth at 36 degrees
FT Celsius."
FT /evidence="ECO:0000269|PubMed:15020406"
FT MUTAGEN 277
FT /note="L->A: Temperature sensitive growth at 36 degrees
FT Celsius."
FT /evidence="ECO:0000269|PubMed:15020406"
FT MUTAGEN 281
FT /note="L->A: Temperature sensitive growth at 36 degrees
FT Celsius."
FT /evidence="ECO:0000269|PubMed:15020406"
FT MUTAGEN 340
FT /note="L->A: Wild-type growth at 36 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:15020406"
FT MUTAGEN 344
FT /note="L->A: Wild-type growth at 36 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:15020406"
FT MUTAGEN 347
FT /note="L->I: Wild-type growth at 36 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:15020406"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:1O6W"
FT STRAND 14..18
FT /evidence="ECO:0007829|PDB:1O6W"
FT TURN 19..22
FT /evidence="ECO:0007829|PDB:1O6W"
FT STRAND 23..27
FT /evidence="ECO:0007829|PDB:1O6W"
FT HELIX 30..43
FT /evidence="ECO:0007829|PDB:1O6W"
FT STRAND 46..49
FT /evidence="ECO:0007829|PDB:1O6W"
FT STRAND 55..59
FT /evidence="ECO:0007829|PDB:1O6W"
FT TURN 60..63
FT /evidence="ECO:0007829|PDB:1O6W"
FT STRAND 64..68
FT /evidence="ECO:0007829|PDB:1O6W"
FT HELIX 134..145
FT /evidence="ECO:0007829|PDB:2B7E"
FT HELIX 154..164
FT /evidence="ECO:0007829|PDB:2B7E"
FT HELIX 167..170
FT /evidence="ECO:0007829|PDB:2B7E"
FT HELIX 175..187
FT /evidence="ECO:0007829|PDB:2B7E"
FT HELIX 489..507
FT /evidence="ECO:0007829|PDB:2KFD"
FT STRAND 510..513
FT /evidence="ECO:0007829|PDB:2KFD"
FT HELIX 519..526
FT /evidence="ECO:0007829|PDB:2KFD"
FT HELIX 533..535
FT /evidence="ECO:0007829|PDB:2KFD"
FT HELIX 539..549
FT /evidence="ECO:0007829|PDB:2KFD"
SQ SEQUENCE 583 AA; 69065 MW; BA1C1C91D532524C CRC64;
MSIWKEAKDA SGRIYYYNTL TKKSTWEKPK ELISQEELLL RENGWKAAKT ADGKVYYYNP
TTRETSWTIP AFEKKVEPIA EQKHDTVSHA QVNGNRIALT AGEKQEPGRT INEEESQYAN
NSKLLNVRRR TKEEAEKEFI TMLKENQVDS TWSFSRIISE LGTRDPRYWM VDDDPLWKKE
MFEKYLSNRS ADQLLKEHNE TSKFKEAFQK MLQNNSHIKY YTRWPTAKRL IADEPIYKHS
VVNEKTKRQT FQDYIDTLID TQKESKKKLK TQALKELREY LNGIITTSSS ETFITWQQLL
NHYVFDKSKR YMANRHFKVL THEDVLNEYL KIVNTIENDL QNKLNELRLR NYTRDRIARD
NFKSLLREVP IKIKANTRWS DIYPHIKSDP RFLHMLGRNG SSCLDLFLDF VDEQRMYIFA
QRSIAQQTLI DQNFEWNDAD SDEITKQNIE KVLENDRKFD KVDKEDISLI VDGLIKQRNE
KIQQKLQNER RILEQKKHYF WLLLQRTYTK TGKPKPSTWD LASKELGESL EYKALGDEDN
IRRQIFEDFK PESSAPTAES ATANLTLTAS KKRHLTPAVE LDY
