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P50102

- UBP8_YEAST

UniProt

P50102 - UBP8_YEAST

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Protein

Ubiquitin carboxyl-terminal hydrolase 8

Gene

UBP8

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

Functioni

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.3 Publications

Catalytic activityi

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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei146 – 1461Nucleophile
Active sitei427 – 4271Proton acceptorPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri44 – 10562UBP-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. protein complex scaffold Source: SGD
  2. ubiquitin-specific protease activity Source: SGD
  3. zinc ion binding Source: InterPro

GO - Biological processi

  1. histone deubiquitination Source: SGD
  2. histone H3-K4 methylation Source: SGD
  3. histone H3-K79 methylation Source: SGD
  4. regulation of transcription, DNA-templated Source: UniProtKB-KW
  5. RNA splicing Source: SGD
  6. transcription, DNA-templated Source: UniProtKB-KW
  7. ubiquitin-dependent protein catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Transcription, Transcription regulation, Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-32904-MONOMER.

Protein family/group databases

MEROPSiC19.087.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:UBP8
Ordered Locus Names:YMR223W
ORF Names:YM9959.05
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XIII

Organism-specific databases

CYGDiYMR223w.
SGDiS000004836. UBP8.

Subcellular locationi

Nucleus Curated

GO - Cellular componenti

  1. DUBm complex Source: SGD
  2. SAGA complex Source: SGD
  3. SLIK (SAGA-like) complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi46 – 461C → A: Lowers histone H2B deubiquitination activity; when associated with A-49. 1 Publication
Mutagenesisi49 – 491C → A: Lowers histone H2B deubiquitination activity; when associated with A-46. 1 Publication
Mutagenesisi77 – 771H → A: Lowers histone H2B deubiquitination activity. 1 Publication
Mutagenesisi146 – 1461C → S: Lowers histone H2B deubiquitination activity. 1 Publication
Mutagenesisi419 – 4191H → A: Lowers histone H2B deubiquitination activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 471471Ubiquitin carboxyl-terminal hydrolase 8PRO_0000080593Add
BLAST

Proteomic databases

MaxQBiP50102.
PaxDbiP50102.
PeptideAtlasiP50102.

Expressioni

Gene expression databases

GenevestigatoriP50102.

Interactioni

Subunit structurei

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 TAF9.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
HFI1Q120609EBI-19863,EBI-8287

Protein-protein interaction databases

BioGridi35401. 284 interactions.
DIPiDIP-1506N.
IntActiP50102. 164 interactions.
MINTiMINT-393758.
STRINGi4932.YMR223W.

Structurei

Secondary structure

1
471
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 106Combined sources
Helixi14 – 3219Combined sources
Helixi36 – 438Combined sources
Turni47 – 493Combined sources
Beta strandi54 – 6411Combined sources
Beta strandi66 – 683Combined sources
Turni69 – 724Combined sources
Helixi73 – 819Combined sources
Beta strandi85 – 884Combined sources
Turni89 – 913Combined sources
Beta strandi94 – 963Combined sources
Turni97 – 1004Combined sources
Beta strandi101 – 1033Combined sources
Helixi107 – 1104Combined sources
Helixi112 – 1176Combined sources
Helixi118 – 1247Combined sources
Helixi130 – 1323Combined sources
Beta strandi142 – 1443Combined sources
Helixi146 – 15611Combined sources
Helixi159 – 1668Combined sources
Helixi169 – 1735Combined sources
Turni179 – 1813Combined sources
Helixi183 – 19513Combined sources
Helixi214 – 22613Combined sources
Helixi228 – 2303Combined sources
Beta strandi231 – 2344Combined sources
Helixi238 – 25619Combined sources
Helixi260 – 2678Combined sources
Helixi274 – 2785Combined sources
Beta strandi281 – 2888Combined sources
Turni290 – 2923Combined sources
Beta strandi297 – 3048Combined sources
Beta strandi306 – 3083Combined sources
Helixi316 – 3249Combined sources
Beta strandi327 – 3293Combined sources
Turni337 – 3404Combined sources
Beta strandi341 – 3433Combined sources
Beta strandi346 – 3549Combined sources
Beta strandi356 – 3627Combined sources
Beta strandi365 – 3673Combined sources
Beta strandi369 – 3713Combined sources
Beta strandi373 – 3753Combined sources
Beta strandi384 – 3874Combined sources
Helixi389 – 3913Combined sources
Beta strandi409 – 42214Combined sources
Beta strandi425 – 4339Combined sources
Turni435 – 4373Combined sources
Beta strandi439 – 4435Combined sources
Beta strandi446 – 4505Combined sources
Helixi452 – 4554Combined sources
Beta strandi460 – 47011Combined sources

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP50102.
SMRiP50102. Positions 1-471.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50102.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini137 – 468332USPAdd
BLAST

Domaini

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

Sequence similaritiesi

Belongs to the peptidase C19 family. UBP8 subfamily.Curated
Contains 1 UBP-type zinc finger.PROSITE-ProRule annotation
Contains 1 USP domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri44 – 10562UBP-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG5533.
GeneTreeiENSGT00760000119203.
HOGENOMiHOG000216626.
InParanoidiP50102.
KOiK11366.
OMAiNCKSHES.
OrthoDBiEOG7R2BSX.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view]
SMARTiSM00290. ZnF_UBP. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P50102-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSICPHIQQV FQNEKSKDGV LKTCNAARYI LNHSVPKEKF LNTMKCGTCH
60 70 80 90 100
EINSGATFMC LQCGFCGCWN HSHFLSHSKQ IGHIFGINSN NGLLFCFKCE
110 120 130 140 150
DYIGNIDLIN DAILAKYWDD VCTKTMVPSM ERRDGLSGLI NMGSTCFMSS
160 170 180 190 200
ILQCLIHNPY FIRHSMSQIH SNNCKVRSPD KCFSCALDKI VHELYGALNT
210 220 230 240 250
KQASSSSTST NRQTGFIYLL TCAWKINQNL AGYSQQDAHE FWQFIINQIH
260 270 280 290 300
QSYVLDLPNA KEVSRANNKQ CECIVHTVFE GSLESSIVCP GCQNNSKTTI
310 320 330 340 350
DPFLDLSLDI KDKKKLYECL DSFHKKEQLK DFNYHCGECN STQDAIKQLG
360 370 380 390 400
IHKLPSVLVL QLKRFEHLLN GSNRKLDDFI EFPTYLNMKN YCSTKEKDKH
410 420 430 440 450
SENGKVPDII YELIGIVSHK GTVNEGHYIA FCKISGGQWF KFNDSMVSSI
460 470
SQEEVLKEQA YLLFYTIRQV N
Length:471
Mass (Da):53,623
Last modified:October 1, 1996 - v1
Checksum:iBC632F12FBD0F73C
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z49939 Genomic DNA. Translation: CAA90194.1.
BK006946 Genomic DNA. Translation: DAA10122.1.
PIRiS57591.
RefSeqiNP_013950.1. NM_001182730.1.

Genome annotation databases

EnsemblFungiiYMR223W; YMR223W; YMR223W.
GeneIDi855263.
KEGGisce:YMR223W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z49939 Genomic DNA. Translation: CAA90194.1 .
BK006946 Genomic DNA. Translation: DAA10122.1 .
PIRi S57591.
RefSeqi NP_013950.1. NM_001182730.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3M99 X-ray 2.70 A 1-471 [» ]
3MHH X-ray 2.45 A 1-471 [» ]
3MHS X-ray 1.89 A 1-471 [» ]
4FIP X-ray 2.69 A/E 1-471 [» ]
4FJC X-ray 2.83 A/E 1-471 [» ]
4FK5 X-ray 2.03 A 1-471 [» ]
ProteinModelPortali P50102.
SMRi P50102. Positions 1-471.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 35401. 284 interactions.
DIPi DIP-1506N.
IntActi P50102. 164 interactions.
MINTi MINT-393758.
STRINGi 4932.YMR223W.

Protein family/group databases

MEROPSi C19.087.

Proteomic databases

MaxQBi P50102.
PaxDbi P50102.
PeptideAtlasi P50102.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YMR223W ; YMR223W ; YMR223W .
GeneIDi 855263.
KEGGi sce:YMR223W.

Organism-specific databases

CYGDi YMR223w.
SGDi S000004836. UBP8.

Phylogenomic databases

eggNOGi COG5533.
GeneTreei ENSGT00760000119203.
HOGENOMi HOG000216626.
InParanoidi P50102.
KOi K11366.
OMAi NCKSHES.
OrthoDBi EOG7R2BSX.

Enzyme and pathway databases

BioCyci YEAST:G3O-32904-MONOMER.

Miscellaneous databases

EvolutionaryTracei P50102.
NextBioi 978861.

Gene expression databases

Genevestigatori P50102.

Family and domain databases

Gene3Di 3.30.40.10. 1 hit.
InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view ]
Pfami PF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view ]
SMARTi SM00290. ZnF_UBP. 1 hit.
[Graphical view ]
PROSITEi PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. 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. 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.

Entry informationi

Entry nameiUBP8_YEAST
AccessioniPrimary (citable) accession number: P50102
Secondary accession number(s): D6W048
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: October 29, 2014
This is version 135 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 1030 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

External Data

Dasty 3