Ubiquitin carboxyl-terminal hydrolase 6 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P43593 (UBP6_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 124. History...

Clusters with 100%, 90%, 50% identity |

Documents (5) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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 names

Name:	UBP6
Ordered Locus Names:	YFR010W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	499 AA.
Sequence status	Complete.
Protein existence	Evidence 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.
Biophysicochemical properties	pH dependence: Optimum pH is 8.5-9. Ref.3

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Molecular function	Hydrolase Protease Thiol protease
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	protein deubiquitination Inferred from mutant phenotype Ref.7. Source: SGD ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	proteasome regulatory particle Inferred from physical interaction Ref.6. Source: SGD
Molecular_function	ubiquitin thiolesterase activity Inferred from electronic annotation. Source: InterPro ubiquitin-specific protease activity Inferred from mutant phenotype Ref.7. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 499

499

Ubiquitin carboxyl-terminal hydrolase 6

PRO_0000080591

Regions

Domain

6 – 80

Ubiquitin-like

Sites

Active site

118

Nucleophile By similarity

Active site

447

Proton acceptor By similarity

Amino acid modifications

Modified residue

298

Phosphoserine Ref.14

Modified residue

383

Phosphoserine Ref.13 Ref.14

Modified residue

389

Phosphothreonine Ref.12 Ref.13 Ref.14

Modified residue

470

Phosphoserine Ref.13 Ref.14

Secondary structure

499

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P43593 [UniParc].

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

499

57,111

        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' referencesShow '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 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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, 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, MASS SPECTROMETRY. Strain: ADR376.
[13]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-383; THR-389 AND SER-470, MASS SPECTROMETRY.
[14]	"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 SER-298; SER-383; THR-389 AND SER-470, MASS SPECTROMETRY.
[15]	"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.

PIR

S56265.

RefSeq

NP_116665.1. NM_001179975.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1VJV	X-ray	1.74	A	97-499	[»]

ProteinModelPortal

P43593.

SMR

P43593. Positions 103-499.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6731N.

IntAct

P43593. 24 interactions.

MINT

MINT-619095.

STRING

4932.YFR010W.

Protein family/group databases

MEROPS

C19.079.

Proteomic databases

PaxDb

P43593.

PeptideAtlas

P43593.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YFR010W; YFR010W; YFR010W.

GeneID

850562.

KEGG

sce:YFR010W.

Organism-specific databases

CYGD

YFR010w.

SGD

S000001906. UBP6.

Phylogenomic databases

eggNOG

NOG286607.

GeneTree

ENSGT00390000009615.

HOGENOM

HOG000202292.

K11843.

OMA

ELCTTEL.

OrthoDB

EOG4M951J.

Gene expression databases

Genevestigator

P43593.

GermOnline

YFR010W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19.
IPR000626. Ubiquitin.
[Graphical view]

Pfam

PF00443. UCH. 1 hit.
[Graphical view]

SMART

SM00213. UBQ. 1 hit.
[Graphical view]

PROSITE

PS00299. UBIQUITIN_1. False negative.
PS50053. UBIQUITIN_2. False negative.
PS00972. UCH_2_1. 1 hit.
PS00973. UCH_2_2. 1 hit.
PS50235. UCH_2_3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P43593.

NextBio

966361.

Entry information

Entry name

UBP6_YEAST

Accession

Primary (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:	May 1, 2013
This is version 124 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome VI

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

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protein family/group databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents