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P43593 (UBP6_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 135. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:UBP6
Ordered Locus Names:YFR010W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length499 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.3 Ref.4 Ref.7 Ref.9 Ref.10 Ref.11

Catalytic activity

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 regulation

Activated by it's association with the proteasome. Ref.7

Subunit structure

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

Domain

The N-terminal ubiquitin-like domain is required for proteasome association and UBP6 activation at the proteasome. Ref.5 Ref.7

Miscellaneous

Present with 6770 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the peptidase C19 family. USP14/UBP6 subfamily.

Contains 1 ubiquitin-like domain.

Contains 1 USP domain.

Biophysicochemical properties

pH dependence:

Optimum pH is 8.5-9. Ref.3

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 499499Ubiquitin carboxyl-terminal hydrolase 6
PRO_0000080591

Regions

Domain6 – 8075Ubiquitin-like
Domain109 – 497389USP

Sites

Active site1181Nucleophile By similarity
Active site4471Proton acceptor By similarity

Amino acid modifications

Modified residue3891Phosphothreonine Ref.12 Ref.13 Ref.14
Modified residue4701Phosphoserine Ref.13

Secondary structure

......................................................... 499
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P43593 [UniParc].

Last modified November 1, 1995. Version 1.
Checksum: DAE54D1F8AC9960C

FASTA49957,111
        10         20         30         40         50         60 
MSGETFEFNI RHSGKVYPIT LSTDATSADL KSKAEELTQV PSARQKYMVK GGLSGEESIK 

        70         80         90        100        110        120 
IYPLIKPGST VMLLGTPDAN LISKPAKKNN FIEDLAPEQQ VQQFAQLPVG FKNMGNTCYL 

       130        140        150        160        170        180 
NATLQALYRV NDLRDMILNY NPSQGVSNSG AQDEEIHKQI VIEMKRCFEN LQNKSFKSVL 

       190        200        210        220        230        240 
PIVLLNTLRK CYPQFAERDS QGGFYKQQDA EELFTQLFHS MSIVFGDKFS EDFRIQFKTT 

       250        260        270        280        290        300 
IKDTANDNDI TVKENESDSK LQCHISGTTN FMRNGLLEGL NEKIEKRSDL TGANSIYSVE 

       310        320        330        340        350        360 
KKISRLPKFL TVQYVRFFWK RSTNKKSKIL RKVVFPFQLD VADMLTPEYA AEKVKVRDEL 

       370        380        390        400        410        420 
RKVEKEKNEK EREIKRRKFD PSSSENVMTP REQYETQVAL NESEKDQWLE EYKKHFPPNL 

       430        440        450        460        470        480 
EKGENPSCVY NLIGVITHQG ANSESGHYQA FIRDELDENK WYKFNDDKVS VVEKEKIESL 

       490 
AGGGESDSAL ILMYKGFGL 

« Hide

References

« Hide 'large scale' references
[1]"Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae."
Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S., Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K., Yamazaki M., Tashiro H., Eki T.
Nat. Genet. 10:261-268(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[2]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
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]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D50617 Genomic DNA. Translation: BAA09249.1.
BK006940 Genomic DNA. Translation: DAA12450.1.
PIRS56265.
RefSeqNP_116665.1. NM_001179975.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1VJVX-ray1.74A97-499[»]
ProteinModelPortalP43593.
SMRP43593. Positions 103-499.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31160. 360 interactions.
DIPDIP-6731N.
IntActP43593. 25 interactions.
MINTMINT-619095.
STRING4932.YFR010W.

Protein family/group databases

MEROPSC19.079.

Proteomic databases

MaxQBP43593.
PaxDbP43593.
PeptideAtlasP43593.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYFR010W; YFR010W; YFR010W.
GeneID850562.
KEGGsce:YFR010W.

Organism-specific databases

CYGDYFR010w.
SGDS000001906. UBP6.

Phylogenomic databases

eggNOGNOG286607.
GeneTreeENSGT00390000009615.
HOGENOMHOG000202292.
KOK11843.
OMAELCTTEL.
OrthoDBEOG789CMF.

Enzyme and pathway databases

BioCycYEAST:G3O-30463-MONOMER.

Gene expression databases

GenevestigatorP43593.

Family and domain databases

InterProIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR028889. UCH/PAN2.
[Graphical view]
PfamPF00443. UCH. 1 hit.
[Graphical view]
SMARTSM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMSSF54236. SSF54236. 1 hit.
PROSITEPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP43593.
NextBio966361.
PROP43593.

Entry information

Entry nameUBP6_YEAST
AccessionPrimary (citable) accession number: P43593
Secondary accession number(s): D6VTP0
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: June 11, 2014
This is version 135 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome VI

Yeast (Saccharomyces cerevisiae) chromosome VI: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references