YSH1_YEAST
ID YSH1_YEAST Reviewed; 779 AA.
AC Q06224; D6VYS4;
DT 10-JAN-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 177.
DE RecName: Full=Endoribonuclease YSH1;
DE EC=3.1.27.-;
DE AltName: Full=Yeast 73 kDa homolog 1;
DE AltName: Full=mRNA 3'-end-processing protein YSH1;
GN Name=YSH1; Synonyms=BRR5; OrderedLocusNames=YLR277C;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [2]
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 [3]
RP IDENTIFICATION IN THE CPF COMPLEX.
RX PubMed=8929409; DOI=10.1126/science.274.5292.1514;
RA Jenny A., Minvielle-Sebastia L., Preker P.J., Keller W.;
RT "Sequence similarity between the 73-kilodalton protein of mammalian CPSF
RT and a subunit of yeast polyadenylation factor I.";
RL Science 274:1514-1517(1996).
RN [4]
RP INTERACTION WITH FIP1; PFS2 AND RNA14.
RX PubMed=10619842; DOI=10.1093/emboj/19.1.37;
RA Ohnacker M., Barabino S.M.L., Preker P.J., Keller W.;
RT "The WD-repeat protein pfs2p bridges two essential factors within the yeast
RT pre-mRNA 3'-end-processing complex.";
RL EMBO J. 19:37-47(2000).
RN [5]
RP IDENTIFICATION IN THE CPF COMPLEX, SUBCELLULAR LOCATION, AND IDENTIFICATION
RP BY MASS SPECTROMETRY.
RX PubMed=12819204; DOI=10.1074/jbc.m304454200;
RA Nedea E., He X., Kim M., Pootoolal J., Zhong G., Canadien V., Hughes T.,
RA Buratowski S., Moore C.L., Greenblatt J.;
RT "Organization and function of APT, a subcomplex of the yeast cleavage and
RT polyadenylation factor involved in the formation of mRNA and small
RT nucleolar RNA 3'-ends.";
RL J. Biol. Chem. 278:33000-33010(2003).
RN [6]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [7]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [8]
RP INTERACTION WITH YTH1.
RX PubMed=12626716; DOI=10.1093/nar/gkg265;
RA Tacahashi Y., Helmling S., Moore C.L.;
RT "Functional dissection of the zinc finger and flanking domains of the Yth1
RT cleavage/polyadenylation factor.";
RL Nucleic Acids Res. 31:1744-1752(2003).
RN [9]
RP FUNCTION, ZINC-BINDING, AND MUTAGENESIS OF ASP-37; HIS-163; ASP-184;
RP GLU-209 AND HIS-408.
RX PubMed=15037765; DOI=10.1261/rna.5214404;
RA Ryan K., Calvo O., Manley J.L.;
RT "Evidence that polyadenylation factor CPSF-73 is the mRNA 3' processing
RT endonuclease.";
RL RNA 10:565-573(2004).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-517, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
CC -!- FUNCTION: Component of the cleavage and polyadenylation factor (CPF)
CC complex, which plays a key role in polyadenylation-dependent pre-mRNA
CC 3'-end formation and cooperates with cleavage factors including the
CC CFIA complex and NAB4/CFIB. Has endonuclease activity.
CC {ECO:0000269|PubMed:15037765}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000250};
CC -!- SUBUNIT: Component of the cleavage and polyadenylation factor (CPF)
CC complex, which is composed of at least PTI1, SYC1, SSU72, GLC7, MPE1,
CC REF2, PFS2, PTA1, YSH1/BRR5, SWD2, CFT2/YDH1, YTH1, CFT1/YHH1, FIP1 and
CC PAP1. Interacts with FIP1, PFS2, RNA14 and YTH1.
CC {ECO:0000269|PubMed:10619842, ECO:0000269|PubMed:12626716,
CC ECO:0000269|PubMed:12819204, ECO:0000269|PubMed:8929409}.
CC -!- INTERACTION:
CC Q06224; Q01329: PTA1; NbExp=4; IntAct=EBI-38345, EBI-14145;
CC Q06224; Q06102: YTH1; NbExp=4; IntAct=EBI-38345, EBI-38049;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12819204,
CC ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 17400 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the metallo-beta-lactamase superfamily. RNA-
CC metabolizing metallo-beta-lactamase-like family. CPSF2/YSH1 subfamily.
CC {ECO:0000305}.
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DR EMBL; U17245; AAB67367.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09590.1; -; Genomic_DNA.
DR PIR; S51413; S51413.
DR RefSeq; NP_013379.1; NM_001182164.1.
DR PDB; 6I1D; X-ray; 2.28 A; A=1-474.
DR PDBsum; 6I1D; -.
DR AlphaFoldDB; Q06224; -.
DR SMR; Q06224; -.
DR BioGRID; 31545; 38.
DR ComplexPortal; CPX-1053; Cleavage and polyadenylation specificity factor complex.
DR DIP; DIP-2470N; -.
DR IntAct; Q06224; 23.
DR MINT; Q06224; -.
DR STRING; 4932.YLR277C; -.
DR iPTMnet; Q06224; -.
DR MaxQB; Q06224; -.
DR PaxDb; Q06224; -.
DR PRIDE; Q06224; -.
DR EnsemblFungi; YLR277C_mRNA; YLR277C; YLR277C.
DR GeneID; 850983; -.
DR KEGG; sce:YLR277C; -.
DR SGD; S000004267; YSH1.
DR VEuPathDB; FungiDB:YLR277C; -.
DR eggNOG; KOG1137; Eukaryota.
DR GeneTree; ENSGT00940000155699; -.
DR HOGENOM; CLU_009673_2_3_1; -.
DR InParanoid; Q06224; -.
DR OMA; VMIPRRC; -.
DR BioCyc; YEAST:G3O-32376-MON; -.
DR Reactome; R-SCE-77595; Processing of Intronless Pre-mRNAs.
DR PRO; PR:Q06224; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; Q06224; protein.
DR GO; GO:0005847; C:mRNA cleavage and polyadenylation specificity factor complex; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IC:ComplexPortal.
DR GO; GO:0008409; F:5'-3' exonuclease activity; IBA:GO_Central.
DR GO; GO:0004521; F:endoribonuclease activity; IMP:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0006378; P:mRNA polyadenylation; IDA:ComplexPortal.
DR GO; GO:0098789; P:pre-mRNA cleavage required for polyadenylation; IDA:ComplexPortal.
DR GO; GO:0008380; P:RNA splicing; IMP:SGD.
DR GO; GO:0031126; P:sno(s)RNA 3'-end processing; IMP:SGD.
DR GO; GO:0034247; P:snoRNA splicing; IMP:SGD.
DR GO; GO:0006369; P:termination of RNA polymerase II transcription; IMP:SGD.
DR GO; GO:0030846; P:termination of RNA polymerase II transcription, poly(A)-coupled; IC:ComplexPortal.
DR Gene3D; 3.60.15.10; -; 1.
DR InterPro; IPR022712; Beta_Casp.
DR InterPro; IPR021718; CPSF73-100_C.
DR InterPro; IPR001279; Metallo-B-lactamas.
DR InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
DR InterPro; IPR011108; RMMBL.
DR Pfam; PF10996; Beta-Casp; 1.
DR Pfam; PF11718; CPSF73-100_C; 1.
DR Pfam; PF00753; Lactamase_B; 1.
DR Pfam; PF07521; RMMBL; 1.
DR SMART; SM01027; Beta-Casp; 1.
DR SMART; SM01098; CPSF73-100_C; 1.
DR SMART; SM00849; Lactamase_B; 1.
DR SUPFAM; SSF56281; SSF56281; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Endonuclease; Hydrolase; Metal-binding; mRNA processing;
KW Nuclease; Nucleus; Phosphoprotein; Reference proteome; Zinc.
FT CHAIN 1..779
FT /note="Endoribonuclease YSH1"
FT /id="PRO_0000076368"
FT ACT_SITE 408
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 70
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 72
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 73
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 163
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 184
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 184
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 430
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT MOD_RES 517
FT /note="Phosphoserine; by ATM or ATR"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MUTAGEN 37
FT /note="D->N: Loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:15037765"
FT MUTAGEN 163
FT /note="H->F: Loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:15037765"
FT MUTAGEN 184
FT /note="D->N: Loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:15037765"
FT MUTAGEN 209
FT /note="E->Q: Loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:15037765"
FT MUTAGEN 408
FT /note="H->F: Loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:15037765"
FT STRAND 7..15
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 17..22
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 24..29
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 32..36
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 46..49
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 53..55
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 58..60
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 63..65
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 71..74
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 77..83
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 88..93
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 94..111
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 133..136
FT /evidence="ECO:0007829|PDB:6I1D"
FT TURN 137..139
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 141..143
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 149..151
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 154..160
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 168..174
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 177..181
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 191..193
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 204..209
FT /evidence="ECO:0007829|PDB:6I1D"
FT TURN 211..214
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 220..236
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 241..244
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 247..250
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 251..264
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 266..269
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 276..279
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 283..290
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 294..296
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 299..307
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 308..310
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 316..322
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 334..338
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 345..354
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 361..364
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 373..377
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 382..385
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 392..395
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 398..402
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 411..421
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 424..431
FT /evidence="ECO:0007829|PDB:6I1D"
FT HELIX 433..446
FT /evidence="ECO:0007829|PDB:6I1D"
FT TURN 449..452
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 458..460
FT /evidence="ECO:0007829|PDB:6I1D"
FT STRAND 468..472
FT /evidence="ECO:0007829|PDB:6I1D"
SQ 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
