Ubiquitin carboxyl-terminal hydrolase 3 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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Q01477 (UBP3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 113. History...

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

Documents (5) |

Third-party data

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

Names and origin

Protein names

Recommended 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

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	912 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

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 direct assay PubMed 18498751. Source: SGD regulation of ER to Golgi vesicle-mediated transport Inferred from mutant phenotype Ref.5. Source: SGD regulation of response to osmotic stress Inferred from mutant phenotype PubMed 21743437. Source: SGD ribophagy Inferred from mutant phenotype PubMed 18391941. Source: SGD ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred by curator Ref.1. Source: SGD
Molecular_function	mRNA binding Inferred from direct assay PubMed 20844764. Source: SGD ubiquitin thiolesterase activity Inferred from electronic annotation. Source: InterPro ubiquitin-specific protease activity Inferred from direct assay Ref.1. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
BRE5	P53741	5	EBI-19834,EBI-28528

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 912

912

Ubiquitin carboxyl-terminal hydrolase 3

PRO_0000080588

Sites

Active site

469

Nucleophile By similarity

Active site

861

Proton acceptor By similarity

Amino acid modifications

Modified residue

242

Phosphoserine Ref.7

Modified residue

243

Phosphoserine Ref.7

Modified residue

339

Phosphoserine Ref.7

Modified residue

400

Phosphoserine Ref.7

Secondary structure

912

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q01477 [UniParc].

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

FASTA

912

101,917

        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' referencesShow '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. Davis R.W. Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-242; SER-243; SER-339 AND SER-400, MASS SPECTROMETRY.
[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.

PIR

B44450.

RefSeq

NP_011078.3. NM_001179041.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2QIY	X-ray	1.69	C/D	190-233	[»]

ProteinModelPortal

Q01477.

SMR

Q01477. Positions 573-912.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-4255N.

IntAct

Q01477. 41 interactions.

MINT

MINT-527025.

STRING

4932.YER151C.

Protein family/group databases

MEROPS

C19.004.

Proteomic databases

PaxDb

Q01477.

PeptideAtlas

Q01477.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YER151C; YER151C; YER151C.

GeneID

856895.

KEGG

sce:YER151C.
sce:YER155C.

Organism-specific databases

CYGD

YER151c.

SGD

S000000953. UBP3.

Phylogenomic databases

eggNOG

COG5533.

GeneTree

ENSGT00550000074994.

HOGENOM

HOG000141876.

K11841.

OMA

ANICFMS.

OrthoDB

EOG4TJ035.

Gene expression databases

Genevestigator

Q01477.

GermOnline

YER151C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

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

Pfam

PF00443. UCH. 1 hit.
[Graphical view]

PROSITE

PS00972. UCH_2_1. 1 hit.
PS00973. UCH_2_2. 1 hit.
PS50235. UCH_2_3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q01477.

NextBio

983307.

Entry information

Entry name

UBP3_YEAST

Accession

Primary (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:	May 1, 2013
This is version 113 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 V

Yeast (Saccharomyces cerevisiae) chromosome V: 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·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

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