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Endoribonuclease YSH1 (EC 3.1.27.-) (Yeast 73 kDa homolog 1) (mRNA 3'-end-processing protein YSH1)

 YSH1_YEAST              Reviewed;         779 AA.
Q06224; D6VYS4;
10-JAN-2006, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
05-DEC-2018, entry version 157.
RecName: Full=Endoribonuclease YSH1;
EC=3.1.27.-;
AltName: Full=Yeast 73 kDa homolog 1;
AltName: Full=mRNA 3'-end-processing protein YSH1;
Name=YSH1; Synonyms=BRR5; OrderedLocusNames=YLR277C;
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=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).
[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]
IDENTIFICATION IN THE CPF COMPLEX.
PubMed=8929409; DOI=10.1126/science.274.5292.1514;
Jenny A., Minvielle-Sebastia L., Preker P.J., Keller W.;
"Sequence similarity between the 73-kilodalton protein of mammalian
CPSF and a subunit of yeast polyadenylation factor I.";
Science 274:1514-1517(1996).
[4]
INTERACTION WITH FIP1; PFS2 AND RNA14.
PubMed=10619842; DOI=10.1093/emboj/19.1.37;
Ohnacker M., Barabino S.M.L., Preker P.J., Keller W.;
"The WD-repeat protein pfs2p bridges two essential factors within the
yeast pre-mRNA 3'-end-processing complex.";
EMBO J. 19:37-47(2000).
[5]
IDENTIFICATION IN THE CPF COMPLEX, SUBCELLULAR LOCATION, AND
IDENTIFICATION BY MASS SPECTROMETRY.
PubMed=12819204; DOI=10.1074/jbc.M304454200;
Nedea E., He X., Kim M., Pootoolal J., Zhong G., Canadien V.,
Hughes T., Buratowski S., Moore C.L., Greenblatt J.;
"Organization and function of APT, a subcomplex of the yeast cleavage
and polyadenylation factor involved in the formation of mRNA and small
nucleolar RNA 3'-ends.";
J. Biol. Chem. 278:33000-33010(2003).
[6]
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).
[7]
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).
[8]
INTERACTION WITH YTH1.
PubMed=12626716; DOI=10.1093/nar/gkg265;
Tacahashi Y., Helmling S., Moore C.L.;
"Functional dissection of the zinc finger and flanking domains of the
Yth1 cleavage/polyadenylation factor.";
Nucleic Acids Res. 31:1744-1752(2003).
[9]
FUNCTION, ZINC-BINDING, AND MUTAGENESIS OF ASP-37; HIS-163; ASP-184;
GLU-209 AND HIS-408.
PubMed=15037765; DOI=10.1261/rna.5214404;
Ryan K., Calvo O., Manley J.L.;
"Evidence that polyadenylation factor CPSF-73 is the mRNA 3'
processing endonuclease.";
RNA 10:565-573(2004).
[10]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-517, 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).
-!- FUNCTION: Component of the cleavage and polyadenylation factor
(CPF) complex, which plays a key role in polyadenylation-dependent
pre-mRNA 3'-end formation and cooperates with cleavage factors
including the CFIA complex and NAB4/CFIB. Has endonuclease
activity. {ECO:0000269|PubMed:15037765}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000250};
-!- SUBUNIT: Component of the cleavage and polyadenylation factor
(CPF) complex, which is composed of at least PTI1, SYC1, SSU72,
GLC7, MPE1, REF2, PFS2, PTA1, YSH1/BRR5, SWD2, CFT2/YDH1, YTH1,
CFT1/YHH1, FIP1 and PAP1. Interacts with FIP1, PFS2, RNA14 and
YTH1. {ECO:0000269|PubMed:10619842, ECO:0000269|PubMed:12626716,
ECO:0000269|PubMed:12819204, ECO:0000269|PubMed:8929409}.
-!- INTERACTION:
Q01329:PTA1; NbExp=4; IntAct=EBI-38345, EBI-14145;
Q06102:YTH1; NbExp=4; IntAct=EBI-38345, EBI-38049;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12819204,
ECO:0000269|PubMed:14562095}.
-!- MISCELLANEOUS: Present with 17400 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the metallo-beta-lactamase superfamily.
RNA-metabolizing metallo-beta-lactamase-like family. CPSF2/YSH1
subfamily. {ECO:0000305}.
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EMBL; U17245; AAB67367.1; -; Genomic_DNA.
EMBL; BK006945; DAA09590.1; -; Genomic_DNA.
PIR; S51413; S51413.
RefSeq; NP_013379.1; NM_001182164.1.
ProteinModelPortal; Q06224; -.
SMR; Q06224; -.
BioGrid; 31545; 34.
ComplexPortal; CPX-1053; Cleavage and polyadenylation specificity factor complex.
DIP; DIP-2470N; -.
IntAct; Q06224; 23.
MINT; Q06224; -.
STRING; 4932.YLR277C; -.
iPTMnet; Q06224; -.
MaxQB; Q06224; -.
PaxDb; Q06224; -.
PRIDE; Q06224; -.
EnsemblFungi; YLR277C_mRNA; YLR277C_mRNA; YLR277C.
GeneID; 850983; -.
KEGG; sce:YLR277C; -.
SGD; S000004267; YSH1.
GeneTree; ENSGT00940000155699; -.
HOGENOM; HOG000203394; -.
InParanoid; Q06224; -.
KO; K14403; -.
OMA; KAIYRWM; -.
OrthoDB; EOG092C11WH; -.
BioCyc; YEAST:G3O-32376-MONOMER; -.
Reactome; R-SCE-77595; Processing of Intronless Pre-mRNAs.
PRO; PR:Q06224; -.
Proteomes; UP000002311; Chromosome XII.
GO; GO:0005847; C:mRNA cleavage and polyadenylation specificity factor complex; IDA:SGD.
GO; GO:0005849; C:mRNA cleavage factor complex; IPI:SGD.
GO; GO:0008409; F:5'-3' exonuclease activity; IBA:GO_Central.
GO; GO:0004521; F:endoribonuclease activity; IMP:SGD.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0003723; F:RNA binding; IBA:GO_Central.
GO; GO:0006398; P:mRNA 3'-end processing by stem-loop binding and cleavage; IBA:GO_Central.
GO; GO:0006378; P:mRNA polyadenylation; IMP:SGD.
GO; GO:0098789; P:pre-mRNA cleavage required for polyadenylation; IMP:SGD.
GO; GO:0008380; P:RNA splicing; IMP:SGD.
GO; GO:0031126; P:snoRNA 3'-end processing; IMP:SGD.
GO; GO:0034247; P:snoRNA splicing; IMP:SGD.
GO; GO:0006369; P:termination of RNA polymerase II transcription; IMP:SGD.
Gene3D; 3.60.15.10; -; 1.
InterPro; IPR022712; Beta_Casp.
InterPro; IPR021718; CPSF73-100_C.
InterPro; IPR001279; Metallo-B-lactamas.
InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
InterPro; IPR011108; RMMBL.
Pfam; PF10996; Beta-Casp; 1.
Pfam; PF11718; CPSF73-100_C; 1.
Pfam; PF00753; Lactamase_B; 1.
Pfam; PF07521; RMMBL; 1.
SMART; SM01027; Beta-Casp; 1.
SMART; SM01098; CPSF73-100_C; 1.
SMART; SM00849; Lactamase_B; 1.
SUPFAM; SSF56281; SSF56281; 1.
1: Evidence at protein level;
Complete proteome; Endonuclease; Hydrolase; Metal-binding;
mRNA processing; Nuclease; Nucleus; Phosphoprotein;
Reference proteome; Zinc.
CHAIN 1 779 Endoribonuclease YSH1.
/FTId=PRO_0000076368.
ACT_SITE 408 408 Proton donor. {ECO:0000255}.
METAL 68 68 Zinc 1. {ECO:0000250}.
METAL 70 70 Zinc 1. {ECO:0000250}.
METAL 72 72 Zinc 2. {ECO:0000250}.
METAL 73 73 Zinc 2. {ECO:0000250}.
METAL 163 163 Zinc 1. {ECO:0000250}.
METAL 184 184 Zinc 1. {ECO:0000250}.
METAL 184 184 Zinc 2. {ECO:0000250}.
METAL 430 430 Zinc 2. {ECO:0000250}.
MOD_RES 517 517 Phosphoserine; by ATM or ATR.
{ECO:0000244|PubMed:18407956}.
MUTAGEN 37 37 D->N: Loss of endonuclease activity.
{ECO:0000269|PubMed:15037765}.
MUTAGEN 163 163 H->F: Loss of endonuclease activity.
{ECO:0000269|PubMed:15037765}.
MUTAGEN 184 184 D->N: Loss of endonuclease activity.
{ECO:0000269|PubMed:15037765}.
MUTAGEN 209 209 E->Q: Loss of endonuclease activity.
{ECO:0000269|PubMed:15037765}.
MUTAGEN 408 408 H->F: Loss of endonuclease activity.
{ECO:0000269|PubMed:15037765}.
SEQUENCE 779 AA; 87674 MW; 901582F0C33AD6F7 CRC64;
MERTNTTTFK FFSLGGSNEV GRSCHILQYK GKTVMLDAGI HPAYQGLASL PFYDEFDLSK
VDILLISHFH LDHAASLPYV MQRTNFQGRV FMTHPTKAIY RWLLRDFVRV TSIGSSSSSM
GTKDEGLFSD EDLVDSFDKI ETVDYHSTVD VNGIKFTAFH AGHVLGAAMF QIEIAGLRVL
FTGDYSREVD RHLNSAEVPP LSSNVLIVES TFGTATHEPR LNRERKLTQL IHSTVMRGGR
VLLPVFALGR AQEIMLILDE YWSQHADELG GGQVPIFYAS NLAKKCMSVF QTYVNMMNDD
IRKKFRDSQT NPFIFKNISY LRNLEDFQDF GPSVMLASPG MLQSGLSRDL LERWCPEDKN
LVLITGYSIE GTMAKFIMLE PDTIPSINNP EITIPRRCQV EEISFAAHVD FQENLEFIEK
ISAPNIILVH GEANPMGRLK SALLSNFASL KGTDNEVHVF NPRNCVEVDL EFQGVKVAKA
VGNIVNEIYK EENVEIKEEI AAKIEPIKEE NEDNLDSQAE KGLVDEEEHK DIVVSGILVS
DDKNFELDFL SLSDLREHHP DLSTTILRER QSVRVNCKKE LIYWHILQMF GEAEVLQDDD
RVTNQEPKVK EESKDNLTNT GKLILQIMGD IKLTIVNTLA VVEWTQDLMN DTVADSIIAI
LMNVDSAPAS VKLSSHSCDD HDHNNVQSNA QGKIDEVERV KQISRLFKEQ FGDCFTLFLN
KDEYASNKEE TITGVVTIGK STAKIDFNNM KILECNSNPL KGRVESLLNI GGNLVTPLC


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