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Branchpoint-bridging protein (Mud synthetic-lethal 5 protein) (Splicing factor 1) (Zinc finger protein BBP)

 BBP_YEAST               Reviewed;         476 AA.
Q12186; D6VYB4;
16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
27-SEP-2017, entry version 137.
RecName: Full=Branchpoint-bridging protein;
AltName: Full=Mud synthetic-lethal 5 protein;
AltName: Full=Splicing factor 1;
AltName: Full=Zinc finger protein BBP;
Name=MSL5; Synonyms=BBP, SF1; OrderedLocusNames=YLR116W;
ORFNames=L2949;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [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]
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).
[3]
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).
[4]
FUNCTION, INTERACTION WITH MUD2 AND PRP40, AND MUTAGENESIS OF GLY-230.
PubMed=9150140; DOI=10.1016/S0092-8674(00)80221-4;
Abovich N., Rosbash M.;
"Cross-intron bridging interactions in the yeast commitment complex
are conserved in mammals.";
Cell 89:403-412(1997).
[5]
FUNCTION, AND INTERACTION WITH MUD2.
PubMed=10376880; DOI=10.1017/S1355838299982286;
Rutz B., Seraphin B.;
"Transient interaction of BBP/ScSF1 and Mud2 with the splicing
machinery affects the kinetics of spliceosome assembly.";
RNA 5:819-831(1999).
[6]
FUNCTION, AND MUTAGENESIS OF ARG-60; ILE-72; PRO-155; VAL-195 AND
GLU-258.
PubMed=10775271; DOI=10.1093/emboj/19.8.1873;
Rutz B., Seraphin B.;
"A dual role for BBP/ScSF1 in nuclear pre-mRNA retention and
splicing.";
EMBO J. 19:1873-1886(2000).
[7]
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).
[8]
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).
[9]
INTERACTION WITH SMY2 AND SYH1.
PubMed=16120600; DOI=10.1074/mcp.M500129-MCP200;
Kofler M., Motzny K., Freund C.;
"GYF domain proteomics reveals interaction sites in known and novel
target proteins.";
Mol. Cell. Proteomics 4:1797-1811(2005).
[10]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-95, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-93; SER-95; TYR-100 AND
SER-382, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
-!- FUNCTION: Required for pre-spliceosome formation, which is the
first step of pre-mRNA splicing. 2 commitment complexes, CC1 and
CC2, have been defined. CC1 is a basal complex dependent only on
the 5'-splice site. CC2 is a complex of lower mobility and is
dependent on a branchpoint as well as a 5'-splice site region.
This protein is involved in CC2 formation where it binds to the
snRNP U1-associated protein PRP40, bridging the U1 snRNP-
associated 5'-splice site and the MSL5-associated branch point 3'
intron splice site. Involved in nuclear retention of pre-mRNA.
{ECO:0000269|PubMed:10376880, ECO:0000269|PubMed:10775271,
ECO:0000269|PubMed:9150140}.
-!- SUBUNIT: Interacts with MUD2 and PRP40. The proline-rich sequence
of this protein interacts with the GYF domains of SMY2 and SYH1.
{ECO:0000269|PubMed:10376880, ECO:0000269|PubMed:16120600,
ECO:0000269|PubMed:9150140}.
-!- INTERACTION:
P36084:MUD2; NbExp=7; IntAct=EBI-34012, EBI-11612;
Q02875:SYH1; NbExp=2; IntAct=EBI-34012, EBI-33176;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
-!- MISCELLANEOUS: Present with 4380 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the BBP/SF1 family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X89514; CAA61695.1; -; Genomic_DNA.
EMBL; U53877; AAB82363.1; -; Genomic_DNA.
EMBL; Z73288; CAA97683.1; -; Genomic_DNA.
EMBL; BK006945; DAA09430.1; -; Genomic_DNA.
PIR; S64953; S64953.
RefSeq; NP_013217.1; NM_001182003.1.
PDB; 3FMA; X-ray; 2.50 A; L/M/N/O/P=440-450.
PDB; 4WAL; X-ray; 2.20 A; A=144-271.
PDB; 4WAN; X-ray; 1.80 A; A/C/E/G=144-271.
PDBsum; 3FMA; -.
PDBsum; 4WAL; -.
PDBsum; 4WAN; -.
ProteinModelPortal; Q12186; -.
SMR; Q12186; -.
BioGrid; 31388; 258.
DIP; DIP-991N; -.
IntAct; Q12186; 13.
MINT; MINT-489287; -.
STRING; 4932.YLR116W; -.
iPTMnet; Q12186; -.
MaxQB; Q12186; -.
PRIDE; Q12186; -.
EnsemblFungi; YLR116W; YLR116W; YLR116W.
GeneID; 850807; -.
KEGG; sce:YLR116W; -.
EuPathDB; FungiDB:YLR116W; -.
SGD; S000004106; MSL5.
GeneTree; ENSGT00550000074434; -.
HOGENOM; HOG000197271; -.
InParanoid; Q12186; -.
KO; K13095; -.
OMA; QYFRIEE; -.
OrthoDB; EOG092C2J4N; -.
BioCyc; YEAST:G3O-32261-MONOMER; -.
Reactome; R-SCE-8849468; PTK6 Regulates Proteins Involved in RNA Processing.
EvolutionaryTrace; Q12186; -.
PRO; PR:Q12186; -.
Proteomes; UP000002311; Chromosome XII.
GO; GO:0000243; C:commitment complex; IDA:SGD.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0045131; F:pre-mRNA branch point binding; IDA:SGD.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0000398; P:mRNA splicing, via spliceosome; IPI:SGD.
Gene3D; 3.30.1370.10; -; 1.
Gene3D; 4.10.60.10; -; 2.
InterPro; IPR031150; BBP/SF1.
InterPro; IPR013041; Coatomer/clathrin_app_Ig-like.
InterPro; IPR004087; KH_dom.
InterPro; IPR004088; KH_dom_type_1.
InterPro; IPR032570; SF1-HH.
InterPro; IPR001878; Znf_CCHC.
PANTHER; PTHR11208:SF62; PTHR11208:SF62; 1.
Pfam; PF00013; KH_1; 1.
Pfam; PF16275; SF1-HH; 1.
Pfam; PF00098; zf-CCHC; 1.
SMART; SM00322; KH; 1.
SMART; SM00343; ZnF_C2HC; 2.
SUPFAM; SSF49348; SSF49348; 1.
SUPFAM; SSF54791; SSF54791; 1.
SUPFAM; SSF57756; SSF57756; 1.
PROSITE; PS50158; ZF_CCHC; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Metal-binding; mRNA processing;
mRNA splicing; Nucleus; Phosphoprotein; Reference proteome; Repeat;
RNA-binding; Zinc; Zinc-finger.
CHAIN 1 476 Branchpoint-bridging protein.
/FTId=PRO_0000234564.
DOMAIN 153 219 KH.
ZN_FING 271 288 CCHC-type 1. {ECO:0000255|PROSITE-
ProRule:PRU00047}.
ZN_FING 297 314 CCHC-type 2. {ECO:0000255|PROSITE-
ProRule:PRU00047}.
COMPBIAS 363 474 Pro-rich.
MOD_RES 93 93 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 95 95 Phosphoserine.
{ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
MOD_RES 100 100 Phosphotyrosine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 382 382 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MUTAGEN 60 60 R->G: In MSL5-2; temperature-sensitive;
growth defect; when associated with N-72
and S-155. {ECO:0000269|PubMed:10775271}.
MUTAGEN 72 72 I->N: In MSL5-2; temperature-sensitive;
growth defect; when associated with G-60
and S-155. {ECO:0000269|PubMed:10775271}.
MUTAGEN 155 155 P->S: In MSL5-2; temperature-sensitive;
growth defect; when associated with G-60
and N-72. {ECO:0000269|PubMed:10775271}.
MUTAGEN 195 195 V->D: In MSL5-5; cold-sensitive; growth
defect; when associated with V-258.
{ECO:0000269|PubMed:10775271}.
MUTAGEN 230 230 G->S: In msl-5; loss of function.
{ECO:0000269|PubMed:9150140}.
MUTAGEN 258 258 E->V: In MSL5-5; cold-sensitive; growth
defect; when associated with D-195.
{ECO:0000269|PubMed:10775271}.
STRAND 148 153 {ECO:0000244|PDB:4WAN}.
TURN 156 158 {ECO:0000244|PDB:4WAN}.
HELIX 164 169 {ECO:0000244|PDB:4WAN}.
HELIX 171 173 {ECO:0000244|PDB:4WAN}.
HELIX 174 183 {ECO:0000244|PDB:4WAN}.
STRAND 186 192 {ECO:0000244|PDB:4WAN}.
HELIX 201 203 {ECO:0000244|PDB:4WAN}.
TURN 206 209 {ECO:0000244|PDB:4WAN}.
STRAND 212 223 {ECO:0000244|PDB:4WAN}.
HELIX 224 242 {ECO:0000244|PDB:4WAN}.
HELIX 250 262 {ECO:0000244|PDB:4WAN}.
SEQUENCE 476 AA; 53034 MW; F94FF7175345C47D CRC64;
MSFRRINSRY FENRKGSSME EKKAKVPPNV NLSLWRKNTV ESDVHRFNSL PSKISGALTR
EQIYSYQVMF RIQEITIKLR TNDFVPPSRK NRSPSPPPVY DAQGKRTNTR EQRYRKKLED
ERIKLVEIAL KTIPYFVPPD DYKRPTKFQD KYYIPVDQYP DVNFVGLLLG PRGRTLRKLQ
EDSNCKIAIR GRGSVKEGKN ASDLPPGAMN FEDPLHCLII ADSEDKIQKG IKVCQNIVIK
AVTSPEGQND LKRGQLRELA ELNGTLREDN RPCPICGLKD HKRYDCPNRK IPNIQGIVCK
ICGQTGHFSR DCNSSSQRMS RFDRNATVNN SAPIQSNDVH YNSNTHPIQA PKRSRYDNNS
TEPPLKFPAS SRYAPSPSPP ASHISRQAQN VTPTPPPGLT SSSFSSGVPG IAPPPLQSPP
ESEQPKFSLP PPPGMTTVQS SIAPPPGLSG PPGFSNNMGN DINKPTPPGL QGPPGL


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