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Q01477 (UBP3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 123. 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·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ubiquitin carboxyl-terminal hydrolase 3

EC=3.4.19.12
Alternative name(s):
Deubiquitinating enzyme 3
Ubiquitin thioesterase 3
Ubiquitin-specific-processing protease 3
Gene names
Name:UBP3
Ordered Locus Names:YER151C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length912 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Has an ATP-independent isopeptidase activity, cleaving at the C-terminus of the ubiquitin moiety in natural or engineered linear fusion proteins, irrespective of their size or the presence of an N-terminal extension to ubiquitin. Plays a role in regulation of silencing by interacting with SIR4. Also, in conjunction with BRE5, cleaves ubiquitin, leading to the subsequent mono-ubiquitination of SEC23. Ref.5 Ref.8

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). Ref.8

Subunit structure

Heterotetramer with BRE5; contains two molecules of BRE5 and two molecules of UBP3. Ref.5 Ref.8

Miscellaneous

Present with 2210 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the peptidase C19 family.

Contains 1 USP domain.

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 912912Ubiquitin carboxyl-terminal hydrolase 3
PRO_0000080588

Regions

Domain460 – 911452USP

Sites

Active site4691Nucleophile By similarity
Active site8611Proton acceptor By similarity

Secondary structure

..... 912
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q01477 [UniParc].

Last modified July 1, 1993. Version 1.
Checksum: 337FD05527C5542D

FASTA912101,917
        10         20         30         40         50         60 
MNMQDANKEE SYSMYPKTSS PPPPTPTNMQ IPIYQAPLQM YGYTQAPYLY PTQIPAYSFN 

        70         80         90        100        110        120 
MVNQNQPIYH QSGSPHHLPP QNNINGGSTT NNNNINKKKW HSNGITNNNG SSGNQGANSS 

       130        140        150        160        170        180 
GSGMSYNKSH TYHHNYSNNH IPMMASPNSG SNAGMKKQTN SSNGNGSSAT SPSYSSYNSS 

       190        200        210        220        230        240 
SQYDLYKFDV TKLKNLKENS SNLIQLPLFI NTTEAEFAAA SVQRYELNMK ALNLNSESLE 

       250        260        270        280        290        300 
NSSVEKSSAH HHTKSHSIPK HNEEVKTETH GEEEDAHDKK PHASKDAHEL KKKTEVKKED 

       310        320        330        340        350        360 
AKQDRNEKVI QEPQATVLPV VDKKEPEESV EENTSKTSSP SPSPPAAKSW SAIASDAIKS 

       370        380        390        400        410        420 
RQASNKTVSG SMVTKTPISG TTAGVSSTNM AAATIGKSSS PLLSKQPQKK DKKYVPPSTK 

       430        440        450        460        470        480 
GIEPLGSIAL RMCFDPDFIS YVLRNKDVEN KIPVHSIIPR GIINRANICF MSSVLQVLLY 

       490        500        510        520        530        540 
CKPFIDVINV LSTRNTNSRV GTSSCKLLDA CLTMYKQFDK ETYEKKFLEN ADDAEKTTES 

       550        560        570        580        590        600 
DAKKSSKSKS FQHCATADAV KPDEFYKTLS TIPKFKDLQW GHQEDAEEFL THLLDQLHEE 

       610        620        630        640        650        660 
LISAIDGLTD NEIQNMLQSI NDEQLKVFFI RNLSRYGKAE FIKNASPRLK ELIEKYGVIN 

       670        680        690        700        710        720 
DDSTEENGWH EVSGSSKRGK KTKTAAKRTV EIVPSPISKL FGGQFRSVLD IPNNKESQSI 

       730        740        750        760        770        780 
TLDPFQTIQL DISDAGVNDL ETAFKKFSEY ELLPFKSSSG NDVEAKKQTF IDKLPQVLLI 

       790        800        810        820        830        840 
QFKRFSFINN VNKDNAMTNY NAYNGRIEKI RKKIKYGHEL IIPEESMSSI TLKNNTSGID 

       850        860        870        880        890        900 
DRRYKLTGVI YHHGVSSDGG HYTADVYHSE HNKWYRIDDV NITELEDDDV LKGGEEASDS 

       910 
RTAYILMYQK RN 

« Hide

References

« Hide 'large scale' references
[1]"Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family."
Baker R.T., Tobias J.W., Varshavsky A.
J. Biol. Chem. 267:23364-23375(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome V."
Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. expand/collapse author list , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W.
Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae."
Moazed D., Johnson D.
Cell 86:667-677(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
[5]"Ubp3 requires a cofactor, Bre5, to specifically de-ubiquitinate the COPII protein, Sec23."
Cohen M., Stutz F., Belgareh N., Haguenauer-Tsapis R., Dargemont C.
Nat. Cell Biol. 5:661-667(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBUNIT.
[6]"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].
[7]"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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"Molecular basis for bre5 cofactor recognition by the ubp3 deubiquitylating enzyme."
Li K., Ossareh-Nazari B., Liu X., Dargemont C., Marmorstein R.
J. Mol. Biol. 372:194-204(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF 190-233 IN COMPLEX WITH BRE5, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M94917 Genomic DNA. Translation: AAA35191.1.
U18917 Genomic DNA. Translation: AAB64678.1.
BK006939 Genomic DNA. Translation: DAA07812.1.
PIRB44450.
RefSeqNP_011078.3. NM_001179041.3.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2QIYX-ray1.69C/D190-233[»]
ProteinModelPortalQ01477.
SMRQ01477. Positions 460-489, 573-912.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid36901. 863 interactions.
DIPDIP-4255N.
IntActQ01477. 401 interactions.
MINTMINT-527025.
STRING4932.YER151C.

Protein family/group databases

MEROPSC19.004.

Proteomic databases

PaxDbQ01477.
PeptideAtlasQ01477.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYER151C; YER151C; YER151C.
GeneID856895.
KEGGsce:YER151C.

Organism-specific databases

CYGDYER151c.
SGDS000000953. UBP3.

Phylogenomic databases

eggNOGCOG5533.
GeneTreeENSGT00550000074994.
HOGENOMHOG000141876.
KOK11841.
OMAANICFMS.
OrthoDBEOG7F2546.

Enzyme and pathway databases

BioCycYEAST:G3O-30312-MONOMER.

Gene expression databases

GenevestigatorQ01477.

Family and domain databases

InterProIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
[Graphical view]
PfamPF00443. UCH. 1 hit.
[Graphical view]
PROSITEPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ01477.
NextBio983307.
PROQ01477.

Entry information

Entry nameUBP3_YEAST
AccessionPrimary (citable) accession number: Q01477
Secondary accession number(s): D3DM58
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 1, 1993
Last modified: April 16, 2014
This is version 123 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 V

Yeast (Saccharomyces cerevisiae) chromosome V: 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