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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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei118 – 1181NucleophilePROSITE-ProRule annotation
Active sitei447 – 4471Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

  1. ubiquitin-specific protease activity Source: SGD

GO - Biological processi

  1. negative regulation of proteasomal protein catabolic process Source: SGD
  2. protein deubiquitination Source: SGD
  3. 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.

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
ProteomesiUP000002311 Componenti: Chromosome VI

Organism-specific databases

CYGDiYFR010w.
SGDiS000001906. UBP6.

Subcellular locationi

GO - Cellular componenti

  1. proteasome complex Source: SGD
  2. proteasome regulatory particle Source: SGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 499499Ubiquitin carboxyl-terminal hydrolase 6PRO_0000080591Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei389 – 3891Phosphothreonine3 Publications
Modified residuei470 – 4701Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP43593.
PaxDbiP43593.
PeptideAtlasiP43593.

Expressioni

Gene expression databases

GenevestigatoriP43593.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi31160. 364 interactions.
DIPiDIP-6731N.
IntActiP43593. 25 interactions.
MINTiMINT-619095.
STRINGi4932.YFR010W.

Structurei

Secondary structure

1
499
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi118 – 12912Combined sources
Helixi131 – 1388Combined sources
Helixi142 – 1443Combined sources
Helixi154 – 17219Combined sources
Helixi182 – 19110Combined sources
Helixi193 – 1964Combined sources
Helixi210 – 22516Combined sources
Helixi227 – 2304Combined sources
Turni231 – 2333Combined sources
Beta strandi235 – 2439Combined sources
Beta strandi246 – 2538Combined sources
Beta strandi257 – 2593Combined sources
Beta strandi261 – 2633Combined sources
Helixi272 – 2809Combined sources
Beta strandi297 – 3059Combined sources
Beta strandi307 – 3148Combined sources
Beta strandi317 – 3204Combined sources
Turni321 – 3244Combined sources
Beta strandi325 – 3284Combined sources
Beta strandi337 – 3404Combined sources
Helixi342 – 3443Combined sources
Helixi347 – 36923Combined sources
Helixi390 – 41324Combined sources
Beta strandi426 – 44217Combined sources
Beta strandi445 – 4539Combined sources
Beta strandi461 – 4655Combined sources
Beta strandi468 – 4725Combined sources
Helixi474 – 4785Combined sources
Helixi479 – 4813Combined sources
Beta strandi488 – 4969Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VJVX-ray1.74A97-499[»]
ProteinModelPortaliP43593.
SMRiP43593. Positions 103-499.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP43593.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 8075Ubiquitin-likeAdd
BLAST
Domaini109 – 497389USPAdd
BLAST

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

eggNOGiNOG286607.
GeneTreeiENSGT00390000009615.
HOGENOMiHOG000202292.
InParanoidiP43593.
KOiK11843.
OMAiELCTTEL.
OrthoDBiEOG789CMF.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_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:October 31, 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

EnsemblFungiiYFR010W; 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
EntryMethodResolution (Å)ChainPositionsPDBsum
1VJVX-ray1.74A97-499[»]
ProteinModelPortaliP43593.
SMRiP43593. Positions 103-499.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31160. 364 interactions.
DIPiDIP-6731N.
IntActiP43593. 25 interactions.
MINTiMINT-619095.
STRINGi4932.YFR010W.

Protein family/group databases

MEROPSiC19.079.
MoonProtiP43593.

Proteomic databases

MaxQBiP43593.
PaxDbiP43593.
PeptideAtlasiP43593.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYFR010W; YFR010W; YFR010W.
GeneIDi850562.
KEGGisce:YFR010W.

Organism-specific databases

CYGDiYFR010w.
SGDiS000001906. UBP6.

Phylogenomic databases

eggNOGiNOG286607.
GeneTreeiENSGT00390000009615.
HOGENOMiHOG000202292.
InParanoidiP43593.
KOiK11843.
OMAiELCTTEL.
OrthoDBiEOG789CMF.

Enzyme and pathway databases

BioCyciYEAST:G3O-30463-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP43593.
NextBioi966361.
PROiP43593.

Gene expression databases

GenevestigatoriP43593.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_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...

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. "Purification and characterization of UBP6, a new ubiquitin-specific protease in Saccharomyces cerevisiae."
    Park K.C., Woo S.K., Yoo Y.J., Wyndham A.M., Baker R.T., Chung C.H.
    Arch. Biochem. Biophys. 347:78-84(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
  4. "Chemically synthesized ubiquitin extension proteins detect distinct catalytic capacities of deubiquitinating enzymes."
    Layfield R., Franklin K., Landon M., Walker G., Wang P., Ramage R., Brown A., Love S., Urquhart K., Muir T., Baker R., Mayer R.J.
    Anal. Biochem. 274:40-49(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "The Ubp6 family of deubiquitinating enzymes contains a ubiquitin-like domain: SUb."
    Wyndham A.M., Baker R.T., Chelvanayagam G.
    Protein Sci. 8:1268-1275(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: DOMAIN.
  6. "Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes."
    Verma R., Chen S., Feldman R., Schieltz D., Yates J., Dohmen J., Deshaies R.J.
    Mol. Biol. Cell 11:3425-3439(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: ASSOCIATION WITH THE 26S PROTEASOME, IDENTIFICATION BY MASS SPECTROMETRY.
  7. "Multiple associated proteins regulate proteasome structure and function."
    Leggett D.S., Hanna J., Borodovsky A., Crosas B., Schmidt M., Baker R.T., Walz T., Ploegh H., Finley D.
    Mol. Cell 10:495-507(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, ASSOCIATION WITH THE 26S PROTEASOME, FUNCTION, ENZYME REGULATION, DOMAIN.
  8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  9. "Complementary roles for Rpn11 and Ubp6 in deubiquitination and proteolysis by the proteasome."
    Guterman A., Glickman M.H.
    J. Biol. Chem. 279:1729-1738(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation."
    Hanna J., Hathaway N.A., Tone Y., Crosas B., Elsasser S., Kirkpatrick D.S., Leggett D.S., Gygi S.P., King R.W., Finley D.
    Cell 127:99-111(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  11. "Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities."
    Crosas B., Hanna J., Kirkpatrick D.S., Zhang D.P., Tone Y., Hathaway N.A., Buecker C., Leggett D.S., Schmidt M., King R.W., Gygi S.P., Finley D.
    Cell 127:1401-1413(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  12. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-389, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  13. "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(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-389 AND SER-470, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-389, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  15. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. "Crystal structure of ubiquitin carboxyl-terminal hydrolase 6 (yfr010w) from saccharomyces cerevisiae at 1.74 a resolution."
    Joint center for structural genomics (JCSG)
    Submitted (JUN-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.74 ANGSTROMS) OF 97-499.

Entry informationi

Entry nameiUBP6_YEAST
AccessioniPrimary (citable) accession number: P43593
Secondary accession number(s): D6VTP0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 1995
Last sequence update: October 31, 1995
Last modified: February 3, 2015
This is version 141 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

External Data

Dasty 3

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 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.