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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: 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)DescriptionActionsGraphical viewLength
Active sitei146Nucleophile1
Active sitei427Proton acceptorPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri44 – 105UBP-typePROSITE-ProRule annotationAdd BLAST62

GO - Molecular functioni

  • protein complex scaffold Source: SGD
  • thiol-dependent ubiquitin-specific protease activity Source: SGD
  • zinc ion binding Source: InterPro

GO - Biological processi

  • histone deubiquitination Source: SGD
  • histone H3-K4 methylation Source: SGD
  • histone H3-K79 methylation Source: SGD
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • RNA splicing Source: SGD
  • transcription, DNA-templated Source: UniProtKB-KW
  • 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.
ReactomeiR-SCE-5689880. Ub-specific processing proteases.

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
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YMR223W.
SGDiS000004836. UBP8.

Subcellular locationi

GO - Cellular componenti

  • DUBm complex Source: SGD
  • SAGA complex Source: SGD
  • SLIK (SAGA-like) complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi46C → A: Lowers histone H2B deubiquitination activity; when associated with A-49. 1 Publication1
Mutagenesisi49C → A: Lowers histone H2B deubiquitination activity; when associated with A-46. 1 Publication1
Mutagenesisi77H → A: Lowers histone H2B deubiquitination activity. 1 Publication1
Mutagenesisi146C → S: Lowers histone H2B deubiquitination activity. 1 Publication1
Mutagenesisi419H → A: Lowers histone H2B deubiquitination activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000805931 – 471Ubiquitin carboxyl-terminal hydrolase 8Add BLAST471

Proteomic databases

MaxQBiP50102.
PRIDEiP50102.

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

GO - Molecular functioni

  • protein complex scaffold Source: SGD

Protein-protein interaction databases

BioGridi35401. 285 interactors.
DIPiDIP-1506N.
IntActiP50102. 164 interactors.
MINTiMINT-393758.

Structurei

Secondary structure

1471
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 10Combined sources6
Helixi14 – 32Combined sources19
Helixi36 – 43Combined sources8
Turni47 – 49Combined sources3
Beta strandi54 – 64Combined sources11
Beta strandi66 – 68Combined sources3
Turni69 – 72Combined sources4
Helixi73 – 81Combined sources9
Beta strandi85 – 88Combined sources4
Turni89 – 91Combined sources3
Beta strandi94 – 96Combined sources3
Turni97 – 100Combined sources4
Beta strandi101 – 103Combined sources3
Helixi107 – 110Combined sources4
Helixi112 – 117Combined sources6
Helixi118 – 124Combined sources7
Helixi130 – 132Combined sources3
Beta strandi142 – 144Combined sources3
Helixi146 – 156Combined sources11
Helixi159 – 166Combined sources8
Helixi169 – 173Combined sources5
Turni179 – 181Combined sources3
Helixi183 – 195Combined sources13
Helixi214 – 226Combined sources13
Helixi228 – 230Combined sources3
Beta strandi231 – 234Combined sources4
Helixi238 – 256Combined sources19
Helixi260 – 267Combined sources8
Helixi274 – 278Combined sources5
Beta strandi281 – 288Combined sources8
Turni290 – 292Combined sources3
Beta strandi297 – 304Combined sources8
Beta strandi306 – 308Combined sources3
Helixi316 – 324Combined sources9
Beta strandi327 – 329Combined sources3
Turni337 – 340Combined sources4
Beta strandi341 – 343Combined sources3
Beta strandi346 – 354Combined sources9
Beta strandi356 – 362Combined sources7
Beta strandi365 – 367Combined sources3
Beta strandi369 – 371Combined sources3
Beta strandi373 – 375Combined sources3
Beta strandi384 – 387Combined sources4
Helixi389 – 391Combined sources3
Beta strandi409 – 422Combined sources14
Beta strandi425 – 433Combined sources9
Turni435 – 437Combined sources3
Beta strandi439 – 443Combined sources5
Beta strandi446 – 450Combined sources5
Helixi452 – 455Combined sources4
Beta strandi460 – 470Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
4WA6X-ray2.36A/D1-471[»]
4ZUXX-ray3.82U/Z/e/j1-471[»]
ProteinModelPortaliP50102.
SMRiP50102.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50102.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini137 – 468USPAdd BLAST332

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)DescriptionActionsGraphical viewLength
Zinc fingeri44 – 105UBP-typePROSITE-ProRule annotationAdd BLAST62

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00860000133708.
HOGENOMiHOG000216626.
InParanoidiP50102.
KOiK11366.
OMAiYTRIEND.
OrthoDBiEOG092C5R71.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
Z49939 Genomic DNA. Translation: CAA90194.1.
BK006946 Genomic DNA. Translation: DAA10122.1.
PIRiS57591.
RefSeqiNP_013950.1. NM_001182730.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
4WA6X-ray2.36A/D1-471[»]
4ZUXX-ray3.82U/Z/e/j1-471[»]
ProteinModelPortaliP50102.
SMRiP50102.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35401. 285 interactors.
DIPiDIP-1506N.
IntActiP50102. 164 interactors.
MINTiMINT-393758.

Protein family/group databases

MEROPSiC19.087.

Proteomic databases

MaxQBiP50102.
PRIDEiP50102.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YMR223W.
SGDiS000004836. UBP8.

Phylogenomic databases

GeneTreeiENSGT00860000133708.
HOGENOMiHOG000216626.
InParanoidiP50102.
KOiK11366.
OMAiYTRIEND.
OrthoDBiEOG092C5R71.

Enzyme and pathway databases

BioCyciYEAST:G3O-32904-MONOMER.
ReactomeiR-SCE-5689880. Ub-specific processing proteases.

Miscellaneous databases

EvolutionaryTraceiP50102.
PROiP50102.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
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]
ProtoNetiSearch...

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: November 30, 2016
This is version 153 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

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.