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Q01477

- UBP3_YEAST

UniProt

Q01477 - UBP3_YEAST

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Protein

Ubiquitin carboxyl-terminal hydrolase 3

Gene

UBP3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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 SEC23.2 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).1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei469 – 4691NucleophilePROSITE-ProRule annotation
Active sitei861 – 8611Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

  1. mRNA binding Source: SGD
  2. ubiquitin-specific protease activity Source: SGD

GO - Biological processi

  1. protein deubiquitination Source: SGD
  2. regulation of ER to Golgi vesicle-mediated transport Source: SGD
  3. regulation of response to osmotic stress Source: SGD
  4. ribophagy Source: SGD
  5. 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-30312-MONOMER.

Protein family/group databases

MEROPSiC19.004.

Names & Taxonomyi

Protein namesi
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 namesi
Name:UBP3
Ordered Locus Names:YER151C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome V

Organism-specific databases

CYGDiYER151c.
SGDiS000000953. UBP3.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: SGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 912912Ubiquitin carboxyl-terminal hydrolase 3PRO_0000080588Add
BLAST

Proteomic databases

MaxQBiQ01477.
PaxDbiQ01477.
PeptideAtlasiQ01477.

Expressioni

Gene expression databases

GenevestigatoriQ01477.

Interactioni

Subunit structurei

Heterotetramer with BRE5; contains two molecules of BRE5 and two molecules of UBP3.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
BRE5P537417EBI-19834,EBI-28528
CDC48P256944EBI-19834,EBI-4308
DOA1P360374EBI-19834,EBI-6017
HOG1P324853EBI-19834,EBI-8437

Protein-protein interaction databases

BioGridi36901. 866 interactions.
DIPiDIP-4255N.
IntActiQ01477. 401 interactions.
MINTiMINT-527025.
STRINGi4932.YER151C.

Structurei

Secondary structure

1
912
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi208 – 2125
Helixi214 – 22815

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2QIYX-ray1.69C/D190-233[»]
ProteinModelPortaliQ01477.
SMRiQ01477. Positions 573-912.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ01477.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini460 – 911452USPAdd
BLAST

Sequence similaritiesi

Belongs to the peptidase C19 family.Curated
Contains 1 USP domain.Curated

Phylogenomic databases

eggNOGiCOG5533.
GeneTreeiENSGT00550000074994.
HOGENOMiHOG000141876.
InParanoidiQ01477.
KOiK11841.
OMAiANICFMS.
OrthoDBiEOG7F2546.

Family and domain databases

InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q01477-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNMQDANKEE SYSMYPKTSS PPPPTPTNMQ IPIYQAPLQM YGYTQAPYLY
60 70 80 90 100
PTQIPAYSFN MVNQNQPIYH QSGSPHHLPP QNNINGGSTT NNNNINKKKW
110 120 130 140 150
HSNGITNNNG SSGNQGANSS GSGMSYNKSH TYHHNYSNNH IPMMASPNSG
160 170 180 190 200
SNAGMKKQTN SSNGNGSSAT SPSYSSYNSS SQYDLYKFDV TKLKNLKENS
210 220 230 240 250
SNLIQLPLFI NTTEAEFAAA SVQRYELNMK ALNLNSESLE NSSVEKSSAH
260 270 280 290 300
HHTKSHSIPK HNEEVKTETH GEEEDAHDKK PHASKDAHEL KKKTEVKKED
310 320 330 340 350
AKQDRNEKVI QEPQATVLPV VDKKEPEESV EENTSKTSSP SPSPPAAKSW
360 370 380 390 400
SAIASDAIKS RQASNKTVSG SMVTKTPISG TTAGVSSTNM AAATIGKSSS
410 420 430 440 450
PLLSKQPQKK DKKYVPPSTK GIEPLGSIAL RMCFDPDFIS YVLRNKDVEN
460 470 480 490 500
KIPVHSIIPR GIINRANICF MSSVLQVLLY CKPFIDVINV LSTRNTNSRV
510 520 530 540 550
GTSSCKLLDA CLTMYKQFDK ETYEKKFLEN ADDAEKTTES DAKKSSKSKS
560 570 580 590 600
FQHCATADAV KPDEFYKTLS TIPKFKDLQW GHQEDAEEFL THLLDQLHEE
610 620 630 640 650
LISAIDGLTD NEIQNMLQSI NDEQLKVFFI RNLSRYGKAE FIKNASPRLK
660 670 680 690 700
ELIEKYGVIN DDSTEENGWH EVSGSSKRGK KTKTAAKRTV EIVPSPISKL
710 720 730 740 750
FGGQFRSVLD IPNNKESQSI TLDPFQTIQL DISDAGVNDL ETAFKKFSEY
760 770 780 790 800
ELLPFKSSSG NDVEAKKQTF IDKLPQVLLI QFKRFSFINN VNKDNAMTNY
810 820 830 840 850
NAYNGRIEKI RKKIKYGHEL IIPEESMSSI TLKNNTSGID DRRYKLTGVI
860 870 880 890 900
YHHGVSSDGG HYTADVYHSE HNKWYRIDDV NITELEDDDV LKGGEEASDS
910
RTAYILMYQK RN
Length:912
Mass (Da):101,917
Last modified:July 1, 1993 - v1
Checksum:i337FD05527C5542D
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M94917 Genomic DNA. Translation: AAA35191.1.
U18917 Genomic DNA. Translation: AAB64678.1.
BK006939 Genomic DNA. Translation: DAA07812.1.
PIRiB44450.
RefSeqiNP_011078.3. NM_001179041.3.

Genome annotation databases

EnsemblFungiiYER151C; YER151C; YER151C.
GeneIDi856895.
KEGGisce:YER151C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M94917 Genomic DNA. Translation: AAA35191.1 .
U18917 Genomic DNA. Translation: AAB64678.1 .
BK006939 Genomic DNA. Translation: DAA07812.1 .
PIRi B44450.
RefSeqi NP_011078.3. NM_001179041.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2QIY X-ray 1.69 C/D 190-233 [» ]
ProteinModelPortali Q01477.
SMRi Q01477. Positions 573-912.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 36901. 866 interactions.
DIPi DIP-4255N.
IntActi Q01477. 401 interactions.
MINTi MINT-527025.
STRINGi 4932.YER151C.

Protein family/group databases

MEROPSi C19.004.

Proteomic databases

MaxQBi Q01477.
PaxDbi Q01477.
PeptideAtlasi Q01477.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YER151C ; YER151C ; YER151C .
GeneIDi 856895.
KEGGi sce:YER151C.

Organism-specific databases

CYGDi YER151c.
SGDi S000000953. UBP3.

Phylogenomic databases

eggNOGi COG5533.
GeneTreei ENSGT00550000074994.
HOGENOMi HOG000141876.
InParanoidi Q01477.
KOi K11841.
OMAi ANICFMS.
OrthoDBi EOG7F2546.

Enzyme and pathway databases

BioCyci YEAST:G3O-30312-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q01477.
NextBioi 983307.
PROi Q01477.

Gene expression databases

Genevestigatori Q01477.

Family and domain databases

InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
[Graphical view ]
Pfami PF00443. UCH. 1 hit.
[Graphical view ]
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. "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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. 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. 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.

Entry informationi

Entry nameiUBP3_YEAST
AccessioniPrimary (citable) accession number: Q01477
Secondary accession number(s): D3DM58
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 1, 1993
Last modified: October 29, 2014
This is version 129 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 2210 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 V
    Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

External Data

Dasty 3