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Protein

Ubiquitin carboxyl-terminal hydrolase 6

Gene

UBP6

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

Predominant proteasome-associated deubiquitinase which releases ubiquitin from the proteasome targeted ubiquitinated proteins. Ensures the regeneration of ubiquitin at the proteasome. Has proteasome-inhibitory activity and delays the degradation of ubiquitinated proteins to provide a time window allowing gradual deubiquitination of the substrate. Stabilizes the association of HUL5 with proteasomes and works in opposition to polyubiquitin elongation activity of HUL5.6 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).

Enzyme regulationi

Activated by it's association with the proteasome.1 Publication

pH dependencei

Optimum pH is 8.5-9.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei118NucleophilePROSITE-ProRule annotation1
Active sitei447Proton acceptorPROSITE-ProRule annotation1

GO - Molecular functioni

  • thiol-dependent ubiquitin-specific protease activity Source: SGD

GO - Biological processi

  • negative regulation of proteasomal protein catabolic process Source: SGD
  • protein deubiquitination Source: SGD
  • regulation of proteasomal ubiquitin-dependent protein catabolic process Source: CACAO
  • ubiquitin-dependent protein catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-30463-MONOMER.
ReactomeiR-SCE-5689880. Ub-specific processing proteases.

Protein family/group databases

MEROPSiC19.079.
MoonProtiP43593.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 6 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 6
Ubiquitin thioesterase 6
Ubiquitin-specific-processing protease 6
Gene namesi
Name:UBP6
Ordered Locus Names:YFR010W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VI

Organism-specific databases

EuPathDBiFungiDB:YFR010W.
SGDiS000001906. UBP6.

Subcellular locationi

GO - Cellular componenti

  • proteasome complex Source: SGD
  • proteasome regulatory particle Source: SGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000805911 – 499Ubiquitin carboxyl-terminal hydrolase 6Add BLAST499

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei389PhosphothreonineCombined sources1
Modified residuei470PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP43593.
PRIDEiP43593.

PTM databases

iPTMnetiP43593.

Interactioni

Subunit structurei

Associates with the regulatory particle (RP) of the proteasome.

Protein-protein interaction databases

BioGridi31160. 365 interactors.
DIPiDIP-6731N.
IntActiP43593. 25 interactors.
MINTiMINT-619095.

Structurei

Secondary structure

1499
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi118 – 129Combined sources12
Helixi131 – 138Combined sources8
Helixi142 – 144Combined sources3
Helixi154 – 172Combined sources19
Helixi182 – 191Combined sources10
Helixi193 – 196Combined sources4
Helixi210 – 225Combined sources16
Helixi227 – 230Combined sources4
Turni231 – 233Combined sources3
Beta strandi235 – 243Combined sources9
Beta strandi246 – 253Combined sources8
Beta strandi257 – 259Combined sources3
Beta strandi261 – 263Combined sources3
Helixi272 – 280Combined sources9
Beta strandi297 – 305Combined sources9
Beta strandi307 – 314Combined sources8
Beta strandi317 – 320Combined sources4
Turni321 – 324Combined sources4
Beta strandi325 – 328Combined sources4
Beta strandi337 – 340Combined sources4
Helixi342 – 344Combined sources3
Helixi347 – 369Combined sources23
Helixi390 – 413Combined sources24
Beta strandi426 – 442Combined sources17
Beta strandi445 – 453Combined sources9
Beta strandi461 – 465Combined sources5
Beta strandi468 – 472Combined sources5
Helixi474 – 478Combined sources5
Helixi479 – 481Combined sources3
Beta strandi488 – 496Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VJVX-ray1.74A97-499[»]
5A5Belectron microscopy9.50897-499[»]
ProteinModelPortaliP43593.
SMRiP43593.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP43593.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini6 – 80Ubiquitin-likeAdd BLAST75
Domaini109 – 497USPAdd BLAST389

Domaini

The N-terminal ubiquitin-like domain is required for proteasome association and UBP6 activation at the proteasome.2 Publications

Sequence similaritiesi

Contains 1 ubiquitin-like domain.Curated
Contains 1 USP domain.Curated

Phylogenomic databases

GeneTreeiENSGT00390000009615.
HOGENOMiHOG000202292.
InParanoidiP43593.
KOiK11843.
OMAiSGHYQSF.
OrthoDBiEOG092C3DT5.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR029071. Ubiquitin-rel_dom.
IPR000626. Ubiquitin_dom.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
[Graphical view]
SMARTiSM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P43593-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGETFEFNI RHSGKVYPIT LSTDATSADL KSKAEELTQV PSARQKYMVK
60 70 80 90 100
GGLSGEESIK IYPLIKPGST VMLLGTPDAN LISKPAKKNN FIEDLAPEQQ
110 120 130 140 150
VQQFAQLPVG FKNMGNTCYL NATLQALYRV NDLRDMILNY NPSQGVSNSG
160 170 180 190 200
AQDEEIHKQI VIEMKRCFEN LQNKSFKSVL PIVLLNTLRK CYPQFAERDS
210 220 230 240 250
QGGFYKQQDA EELFTQLFHS MSIVFGDKFS EDFRIQFKTT IKDTANDNDI
260 270 280 290 300
TVKENESDSK LQCHISGTTN FMRNGLLEGL NEKIEKRSDL TGANSIYSVE
310 320 330 340 350
KKISRLPKFL TVQYVRFFWK RSTNKKSKIL RKVVFPFQLD VADMLTPEYA
360 370 380 390 400
AEKVKVRDEL RKVEKEKNEK EREIKRRKFD PSSSENVMTP REQYETQVAL
410 420 430 440 450
NESEKDQWLE EYKKHFPPNL EKGENPSCVY NLIGVITHQG ANSESGHYQA
460 470 480 490
FIRDELDENK WYKFNDDKVS VVEKEKIESL AGGGESDSAL ILMYKGFGL
Length:499
Mass (Da):57,111
Last modified:November 1, 1995 - v1
Checksum:iDAE54D1F8AC9960C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D50617 Genomic DNA. Translation: BAA09249.1.
BK006940 Genomic DNA. Translation: DAA12450.1.
PIRiS56265.
RefSeqiNP_116665.1. NM_001179975.1.

Genome annotation databases

EnsemblFungiiBAA09249; BAA09249; BAA09249.
YFR010W; YFR010W; YFR010W.
GeneIDi850562.
KEGGisce:YFR010W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D50617 Genomic DNA. Translation: BAA09249.1.
BK006940 Genomic DNA. Translation: DAA12450.1.
PIRiS56265.
RefSeqiNP_116665.1. NM_001179975.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VJVX-ray1.74A97-499[»]
5A5Belectron microscopy9.50897-499[»]
ProteinModelPortaliP43593.
SMRiP43593.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31160. 365 interactors.
DIPiDIP-6731N.
IntActiP43593. 25 interactors.
MINTiMINT-619095.

Protein family/group databases

MEROPSiC19.079.
MoonProtiP43593.

PTM databases

iPTMnetiP43593.

Proteomic databases

MaxQBiP43593.
PRIDEiP43593.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiBAA09249; BAA09249; BAA09249.
YFR010W; YFR010W; YFR010W.
GeneIDi850562.
KEGGisce:YFR010W.

Organism-specific databases

EuPathDBiFungiDB:YFR010W.
SGDiS000001906. UBP6.

Phylogenomic databases

GeneTreeiENSGT00390000009615.
HOGENOMiHOG000202292.
InParanoidiP43593.
KOiK11843.
OMAiSGHYQSF.
OrthoDBiEOG092C3DT5.

Enzyme and pathway databases

BioCyciYEAST:G3O-30463-MONOMER.
ReactomeiR-SCE-5689880. Ub-specific processing proteases.

Miscellaneous databases

EvolutionaryTraceiP43593.
PROiP43593.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR029071. Ubiquitin-rel_dom.
IPR000626. Ubiquitin_dom.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
[Graphical view]
SMARTiSM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiUBP6_YEAST
AccessioniPrimary (citable) accession number: P43593
Secondary accession number(s): D6VTP0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: November 2, 2016
This is version 158 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 6770 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 VI
    Yeast (Saccharomyces cerevisiae) chromosome VI: 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.