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Protein

Endoribonuclease YSH1

Gene

YSH1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.1 Publication

Cofactori

Zn2+By similarityNote: Binds 2 Zn2+ ions per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi68 – 681Zinc 1By similarity
Metal bindingi70 – 701Zinc 1By similarity
Metal bindingi72 – 721Zinc 2By similarity
Metal bindingi73 – 731Zinc 2By similarity
Metal bindingi163 – 1631Zinc 1By similarity
Metal bindingi184 – 1841Zinc 1By similarity
Metal bindingi184 – 1841Zinc 2By similarity
Active sitei408 – 4081Proton donorSequence analysis
Metal bindingi430 – 4301Zinc 2By similarity

GO - Molecular functioni

  • endoribonuclease activity Source: SGD
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • mRNA polyadenylation Source: SGD
  • pre-mRNA cleavage required for polyadenylation Source: SGD
  • RNA splicing Source: SGD
  • snoRNA 3'-end processing Source: SGD
  • snoRNA splicing Source: SGD
  • termination of RNA polymerase II transcription Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-32376-MONOMER.
ReactomeiR-SCE-77595. Processing of Intronless Pre-mRNAs.

Names & Taxonomyi

Protein namesi
Recommended name:
Endoribonuclease YSH1 (EC:3.1.27.-)
Alternative name(s):
Yeast 73 kDa homolog 1
mRNA 3'-end-processing protein YSH1
Gene namesi
Name:YSH1
Synonyms:BRR5
Ordered Locus Names:YLR277C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR277C.
SGDiS000004267. YSH1.

Subcellular locationi

GO - Cellular componenti

  • mRNA cleavage and polyadenylation specificity factor complex Source: SGD
  • mRNA cleavage factor complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi37 – 371D → N: Loss of endonuclease activity. 1 Publication
Mutagenesisi163 – 1631H → F: Loss of endonuclease activity. 1 Publication
Mutagenesisi184 – 1841D → N: Loss of endonuclease activity. 1 Publication
Mutagenesisi209 – 2091E → Q: Loss of endonuclease activity. 1 Publication
Mutagenesisi408 – 4081H → F: Loss of endonuclease activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 779779Endoribonuclease YSH1PRO_0000076368Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei517 – 5171Phosphoserine; by ATM or ATRCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ06224.

PTM databases

iPTMnetiQ06224.

Interactioni

Subunit structurei

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 YTH1.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
YTH1Q061026EBI-38345,EBI-38049

Protein-protein interaction databases

BioGridi31545. 32 interactions.
DIPiDIP-2470N.
IntActiQ06224. 23 interactions.
MINTiMINT-375457.

Structurei

3D structure databases

ProteinModelPortaliQ06224.
SMRiQ06224. Positions 14-473.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00840000129795.
HOGENOMiHOG000203394.
InParanoidiQ06224.
KOiK14403.
OMAiFMFLEAQ.
OrthoDBiEOG7TN01H.

Family and domain databases

Gene3Di3.60.15.10. 1 hit.
InterProiIPR022712. Beta_Casp.
IPR021718. CPSF73-100_C.
IPR001279. Metallo-B-lactamas.
IPR011108. RMMBL.
[Graphical view]
PfamiPF10996. Beta-Casp. 1 hit.
PF11718. CPSF73-100_C. 1 hit.
PF00753. Lactamase_B. 1 hit.
PF07521. RMMBL. 1 hit.
[Graphical view]
SMARTiSM01027. Beta-Casp. 1 hit.
SM01098. CPSF73-100_C. 1 hit.
SM00849. Lactamase_B. 1 hit.
[Graphical view]
SUPFAMiSSF56281. SSF56281. 1 hit.

Sequencei

Sequence statusi: Complete.

Q06224-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MERTNTTTFK FFSLGGSNEV GRSCHILQYK GKTVMLDAGI HPAYQGLASL
60 70 80 90 100
PFYDEFDLSK VDILLISHFH LDHAASLPYV MQRTNFQGRV FMTHPTKAIY
110 120 130 140 150
RWLLRDFVRV TSIGSSSSSM GTKDEGLFSD EDLVDSFDKI ETVDYHSTVD
160 170 180 190 200
VNGIKFTAFH AGHVLGAAMF QIEIAGLRVL FTGDYSREVD RHLNSAEVPP
210 220 230 240 250
LSSNVLIVES TFGTATHEPR LNRERKLTQL IHSTVMRGGR VLLPVFALGR
260 270 280 290 300
AQEIMLILDE YWSQHADELG GGQVPIFYAS NLAKKCMSVF QTYVNMMNDD
310 320 330 340 350
IRKKFRDSQT NPFIFKNISY LRNLEDFQDF GPSVMLASPG MLQSGLSRDL
360 370 380 390 400
LERWCPEDKN LVLITGYSIE GTMAKFIMLE PDTIPSINNP EITIPRRCQV
410 420 430 440 450
EEISFAAHVD FQENLEFIEK ISAPNIILVH GEANPMGRLK SALLSNFASL
460 470 480 490 500
KGTDNEVHVF NPRNCVEVDL EFQGVKVAKA VGNIVNEIYK EENVEIKEEI
510 520 530 540 550
AAKIEPIKEE NEDNLDSQAE KGLVDEEEHK DIVVSGILVS DDKNFELDFL
560 570 580 590 600
SLSDLREHHP DLSTTILRER QSVRVNCKKE LIYWHILQMF GEAEVLQDDD
610 620 630 640 650
RVTNQEPKVK EESKDNLTNT GKLILQIMGD IKLTIVNTLA VVEWTQDLMN
660 670 680 690 700
DTVADSIIAI LMNVDSAPAS VKLSSHSCDD HDHNNVQSNA QGKIDEVERV
710 720 730 740 750
KQISRLFKEQ FGDCFTLFLN KDEYASNKEE TITGVVTIGK STAKIDFNNM
760 770
KILECNSNPL KGRVESLLNI GGNLVTPLC
Length:779
Mass (Da):87,674
Last modified:November 1, 1996 - v1
Checksum:i901582F0C33AD6F7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U17245 Genomic DNA. Translation: AAB67367.1.
BK006945 Genomic DNA. Translation: DAA09590.1.
PIRiS51413.
RefSeqiNP_013379.1. NM_001182164.1.

Genome annotation databases

EnsemblFungiiYLR277C; YLR277C; YLR277C.
GeneIDi850983.
KEGGisce:YLR277C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U17245 Genomic DNA. Translation: AAB67367.1.
BK006945 Genomic DNA. Translation: DAA09590.1.
PIRiS51413.
RefSeqiNP_013379.1. NM_001182164.1.

3D structure databases

ProteinModelPortaliQ06224.
SMRiQ06224. Positions 14-473.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31545. 32 interactions.
DIPiDIP-2470N.
IntActiQ06224. 23 interactions.
MINTiMINT-375457.

PTM databases

iPTMnetiQ06224.

Proteomic databases

MaxQBiQ06224.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR277C; YLR277C; YLR277C.
GeneIDi850983.
KEGGisce:YLR277C.

Organism-specific databases

EuPathDBiFungiDB:YLR277C.
SGDiS000004267. YSH1.

Phylogenomic databases

GeneTreeiENSGT00840000129795.
HOGENOMiHOG000203394.
InParanoidiQ06224.
KOiK14403.
OMAiFMFLEAQ.
OrthoDBiEOG7TN01H.

Enzyme and pathway databases

BioCyciYEAST:G3O-32376-MONOMER.
ReactomeiR-SCE-77595. Processing of Intronless Pre-mRNAs.

Miscellaneous databases

PROiQ06224.

Family and domain databases

Gene3Di3.60.15.10. 1 hit.
InterProiIPR022712. Beta_Casp.
IPR021718. CPSF73-100_C.
IPR001279. Metallo-B-lactamas.
IPR011108. RMMBL.
[Graphical view]
PfamiPF10996. Beta-Casp. 1 hit.
PF11718. CPSF73-100_C. 1 hit.
PF00753. Lactamase_B. 1 hit.
PF07521. RMMBL. 1 hit.
[Graphical view]
SMARTiSM01027. Beta-Casp. 1 hit.
SM01098. CPSF73-100_C. 1 hit.
SM00849. Lactamase_B. 1 hit.
[Graphical view]
SUPFAMiSSF56281. SSF56281. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    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.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Sequence similarity between the 73-kilodalton protein of mammalian CPSF and a subunit of yeast polyadenylation factor I."
    Jenny A., Minvielle-Sebastia L., Preker P.J., Keller W.
    Science 274:1514-1517(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE CPF COMPLEX.
  4. "The WD-repeat protein pfs2p bridges two essential factors within the yeast pre-mRNA 3'-end-processing complex."
    Ohnacker M., Barabino S.M.L., Preker P.J., Keller W.
    EMBO J. 19:37-47(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH FIP1; PFS2 AND RNA14.
  5. "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."
    Nedea E., He X., Kim M., Pootoolal J., Zhong G., Canadien V., Hughes T., Buratowski S., Moore C.L., Greenblatt J.
    J. Biol. Chem. 278:33000-33010(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE CPF COMPLEX, SUBCELLULAR LOCATION, IDENTIFICATION BY MASS SPECTROMETRY.
  6. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. "Functional dissection of the zinc finger and flanking domains of the Yth1 cleavage/polyadenylation factor."
    Tacahashi Y., Helmling S., Moore C.L.
    Nucleic Acids Res. 31:1744-1752(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH YTH1.
  9. "Evidence that polyadenylation factor CPSF-73 is the mRNA 3' processing endonuclease."
    Ryan K., Calvo O., Manley J.L.
    RNA 10:565-573(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ZINC-BINDING, MUTAGENESIS OF ASP-37; HIS-163; ASP-184; GLU-209 AND HIS-408.
  10. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-517, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiYSH1_YEAST
AccessioniPrimary (citable) accession number: Q06224
Secondary accession number(s): D6VYS4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: November 1, 1996
Last modified: July 6, 2016
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 17400 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.