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P43593

- UBP6_YEAST

UniProt

P43593 - UBP6_YEAST

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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: 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.

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: 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. 365 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 – 12912
Helixi131 – 1388
Helixi142 – 1443
Helixi154 – 17219
Helixi182 – 19110
Helixi193 – 1964
Helixi210 – 22516
Helixi227 – 2304
Turni231 – 2333
Beta strandi235 – 2439
Beta strandi246 – 2538
Beta strandi257 – 2593
Beta strandi261 – 2633
Helixi272 – 2809
Beta strandi297 – 3059
Beta strandi307 – 3148
Beta strandi317 – 3204
Turni321 – 3244
Beta strandi325 – 3284
Beta strandi337 – 3404
Helixi342 – 3443
Helixi347 – 36923
Helixi390 – 41324
Beta strandi426 – 44217
Beta strandi445 – 4539
Beta strandi461 – 4655
Beta strandi468 – 4725
Helixi474 – 4785
Helixi479 – 4813
Beta strandi488 – 4969

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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

InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR028889. UCH/PAN2.
[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:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
D50617 Genomic DNA. Translation: BAA09249.1 .
BK006940 Genomic DNA. Translation: DAA12450.1 .
PIRi S56265.
RefSeqi NP_116665.1. NM_001179975.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1VJV X-ray 1.74 A 97-499 [» ]
ProteinModelPortali P43593.
SMRi P43593. Positions 103-499.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31160. 365 interactions.
DIPi DIP-6731N.
IntActi P43593. 25 interactions.
MINTi MINT-619095.
STRINGi 4932.YFR010W.

Protein family/group databases

MEROPSi C19.079.

Proteomic databases

MaxQBi P43593.
PaxDbi P43593.
PeptideAtlasi P43593.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YFR010W ; YFR010W ; YFR010W .
GeneIDi 850562.
KEGGi sce:YFR010W.

Organism-specific databases

CYGDi YFR010w.
SGDi S000001906. UBP6.

Phylogenomic databases

eggNOGi NOG286607.
GeneTreei ENSGT00390000009615.
HOGENOMi HOG000202292.
InParanoidi P43593.
KOi K11843.
OMAi ELCTTEL.
OrthoDBi EOG789CMF.

Enzyme and pathway databases

BioCyci YEAST:G3O-30463-MONOMER.

Miscellaneous databases

EvolutionaryTracei P43593.
NextBioi 966361.
PROi P43593.

Gene expression databases

Genevestigatori P43593.

Family and domain databases

InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR028889. UCH/PAN2.
[Graphical view ]
Pfami PF00443. UCH. 1 hit.
[Graphical view ]
SMARTi SM00213. UBQ. 1 hit.
[Graphical view ]
SUPFAMi SSF54236. SSF54236. 1 hit.
PROSITEi PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 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. "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(1997) [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(1999) [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(1999) [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(2000) [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(2002) [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(2004) [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(2006) [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(2006) [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(2007) [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(2008) [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(2009) [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 (JUL-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: November 1, 1995
Last sequence update: November 1, 1995
Last modified: October 29, 2014
This is version 138 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