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P50102 (UBP8_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 133. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ubiquitin carboxyl-terminal hydrolase 8

EC=3.4.19.12
Alternative name(s):
Deubiquitinating enzyme 8
Ubiquitin thioesterase 8
Ubiquitin-specific-processing protease 8
Gene names
Name:UBP8
Ordered Locus Names:YMR223W
ORF Names:YM9959.05
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length471 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Functions as histone deubiquitinating component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Together with SGF11, is required for histone H2B deubiquitination. Ref.3 Ref.6 Ref.7

Catalytic activity

Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

Subunit structure

Component of the 1.8 MDa SAGA complex, which consists of at least of TRA1, CHD1, SPT7, TAF5, ADA3, SGF73, SPT20/ADA5, SPT8, TAF12, TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and SUS1. TAF5, TAF6, TAF9, TAF19, TAF12 and ADA1 seem to be present in 2 copies. SAGA is built of 5 distinct domains with specialized functions. Domain I (containing TRA1) probably represents the activator interaction surface. Domain II (containing TAF5 and TAF6, and probably TAF9 and TAF10), domain III (containing GCN5, TAF10, SPT7, TAF5 and ADA1, and probably ADA2, ADA3 and TAF12), and domain IV (containing HFI1/ADA1 and TAF6, and probably TAF9) are believed to play primarily an architectural role. Domain III also harbors the HAT activity. Domain V (containing SPT3 and SPT20, and probably SPT8) represents the TBP-interacting module, which may be associated transiently with SAGA. UBP8 interacts with SGF11. Component of the SLIK complex, which consists of at least TRA1, CHD1, SPT7, TAF5, ADA3, SPT20, RTG2, TAF12, TAF6, HFI1, UBP8, GCN5, ADA2, SPT3, TAF10 and TAF9. Ref.4 Ref.6 Ref.7 Ref.8

Subcellular location

Nucleus Probable.

Domain

The UBP-type zinc finger domain is required for the interaction with the SAGA complex.

Miscellaneous

Present with 1030 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the peptidase C19 family. UBP8 subfamily.

Contains 1 UBP-type zinc finger.

Contains 1 USP domain.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
Ubl conjugation pathway
   Cellular componentNucleus
   DomainZinc-finger
   LigandMetal-binding
Zinc
   Molecular functionHydrolase
Protease
Thiol protease
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processRNA splicing

Inferred from mutant phenotype PubMed 23209445. Source: SGD

histone H3-K4 methylation

Inferred from mutant phenotype PubMed 16855026. Source: SGD

histone H3-K79 methylation

Inferred from mutant phenotype PubMed 16855026. Source: SGD

histone deubiquitination

Inferred from mutant phenotype PubMed 14563679. Source: SGD

regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

ubiquitin-dependent protein catabolic process

Inferred from electronic annotation. Source: InterPro

   Cellular_componentDUBm complex

Inferred from direct assay PubMed 20395473. Source: SGD

SAGA complex

Inferred from direct assay PubMed 12052880PubMed 14563679. Source: SGD

SLIK (SAGA-like) complex

Inferred from direct assay PubMed 14563679. Source: SGD

   Molecular_functionprotein binding

Inferred from physical interaction PubMed 16888622PubMed 21734642. Source: IntAct

protein complex scaffold

Inferred from direct assay PubMed 20434206. Source: SGD

ubiquitin-specific protease activity

Inferred from mutant phenotype PubMed 14563679. Source: SGD

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

HFI1Q120609EBI-19863,EBI-8287

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 471471Ubiquitin carboxyl-terminal hydrolase 8
PRO_0000080593

Regions

Domain137 – 468332USP
Zinc finger44 – 10562UBP-type

Sites

Active site1461Nucleophile
Active site4271Proton acceptor By similarity

Experimental info

Mutagenesis461C → A: Lowers histone H2B deubiquitination activity; when associated with A-49. Ref.7
Mutagenesis491C → A: Lowers histone H2B deubiquitination activity; when associated with A-46. Ref.7
Mutagenesis771H → A: Lowers histone H2B deubiquitination activity. Ref.7
Mutagenesis1461C → S: Lowers histone H2B deubiquitination activity. Ref.7
Mutagenesis4191H → A: Lowers histone H2B deubiquitination activity. Ref.7

Secondary structure

............................................................................................... 471
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P50102 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: BC632F12FBD0F73C

FASTA47153,623
        10         20         30         40         50         60 
MSICPHIQQV FQNEKSKDGV LKTCNAARYI LNHSVPKEKF LNTMKCGTCH EINSGATFMC 

        70         80         90        100        110        120 
LQCGFCGCWN HSHFLSHSKQ IGHIFGINSN NGLLFCFKCE DYIGNIDLIN DAILAKYWDD 

       130        140        150        160        170        180 
VCTKTMVPSM ERRDGLSGLI NMGSTCFMSS ILQCLIHNPY FIRHSMSQIH SNNCKVRSPD 

       190        200        210        220        230        240 
KCFSCALDKI VHELYGALNT KQASSSSTST NRQTGFIYLL TCAWKINQNL AGYSQQDAHE 

       250        260        270        280        290        300 
FWQFIINQIH QSYVLDLPNA KEVSRANNKQ CECIVHTVFE GSLESSIVCP GCQNNSKTTI 

       310        320        330        340        350        360 
DPFLDLSLDI KDKKKLYECL DSFHKKEQLK DFNYHCGECN STQDAIKQLG IHKLPSVLVL 

       370        380        390        400        410        420 
QLKRFEHLLN GSNRKLDDFI EFPTYLNMKN YCSTKEKDKH SENGKVPDII YELIGIVSHK 

       430        440        450        460        470 
GTVNEGHYIA FCKISGGQWF KFNDSMVSSI SQEEVLKEQA YLLFYTIRQV N 

« Hide

References

« Hide 'large scale' references
[1]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII."
Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T., Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P. expand/collapse author list , Skelton J., Walsh S.V., Whitehead S., Barrell B.G.
Nature 387:90-93(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[2]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
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.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[3]"Expanded lysine acetylation specificity of Gcn5 in native complexes."
Grant P.A., Eberharter A., John S., Cook R.G., Turner B.M., Workman J.L.
J. Biol. Chem. 274:5895-5900(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN HISTONE ACETYLATION AT THE SAGA COMPLEX.
[4]"The novel SLIK histone acetyltransferase complex functions in the yeast retrograde response pathway."
Pray-Grant M.G., Schieltz D., McMahon S.J., Wood J.M., Kennedy E.L., Cook R.G., Workman J.L., Yates J.R. III, Grant P.A.
Mol. Cell. Biol. 22:8774-8786(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE SLIK COMPLEX.
[5]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[6]"Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription."
Daniel J.A., Torok M.S., Sun Z.W., Schieltz D., Allis C.D., Yates J.R. III, Grant P.A.
J. Biol. Chem. 279:1867-1871(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN HISTONE DEUBIQUITINATION ACTIVITY OF THE SAGA COMPLEX, IDENTIFICATION IN THE SAGA COMPLEX, IDENTIFICATION IN THE SLIK COMPLEX.
[7]"H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex."
Ingvarsdottir K., Krogan N.J., Emre N.C.T., Wyce A., Thompson N.J., Emili A., Hughes T.R., Greenblatt J.F., Berger S.L.
Mol. Cell. Biol. 25:1162-1172(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN HISTONE DEUBIQUITINATION ACTIVITY OF THE SAGA COMPLEX, IDENTIFICATION IN THE SAGA COMPLEX, INTERACTION WITH SGF11, MUTAGENESIS OF CYS-46; CYS-49; HIS-77; CYS-146 AND HIS-419.
[8]"Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation."
Pray-Grant M.G., Daniel J.A., Schieltz D., Yates J.R. III, Grant P.A.
Nature 433:434-438(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE SLIK COMPLEX.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z49939 Genomic DNA. Translation: CAA90194.1.
BK006946 Genomic DNA. Translation: DAA10122.1.
PIRS57591.
RefSeqNP_013950.1. NM_001182730.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3M99X-ray2.70A1-471[»]
3MHHX-ray2.45A1-471[»]
3MHSX-ray1.89A1-471[»]
4FIPX-ray2.69A/E1-471[»]
4FJCX-ray2.83A/E1-471[»]
4FK5X-ray2.03A1-471[»]
ProteinModelPortalP50102.
SMRP50102. Positions 1-471.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid35401. 284 interactions.
DIPDIP-1506N.
IntActP50102. 164 interactions.
MINTMINT-393758.
STRING4932.YMR223W.

Protein family/group databases

MEROPSC19.087.

Proteomic databases

MaxQBP50102.
PaxDbP50102.
PeptideAtlasP50102.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYMR223W; YMR223W; YMR223W.
GeneID855263.
KEGGsce:YMR223W.

Organism-specific databases

CYGDYMR223w.
SGDS000004836. UBP8.

Phylogenomic databases

eggNOGCOG5533.
GeneTreeENSGT00750000117288.
HOGENOMHOG000216626.
KOK11366.
OMANCKSHES.
OrthoDBEOG7R2BSX.

Enzyme and pathway databases

BioCycYEAST:G3O-32904-MONOMER.

Gene expression databases

GenevestigatorP50102.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
InterProIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view]
PfamPF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view]
SMARTSM00290. ZnF_UBP. 1 hit.
[Graphical view]
PROSITEPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP50102.
NextBio978861.

Entry information

Entry nameUBP8_YEAST
AccessionPrimary (citable) accession number: P50102
Secondary accession number(s): D6W048
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: June 11, 2014
This is version 133 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XIII

Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references