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Entry version 173 (05 Jun 2019)
Sequence version 1 (01 Jul 1993)
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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:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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 (PubMed:12778054, PubMed:17632125). Plays a role in regulation of silencing by interacting with SIR4 (PubMed:8752220). Also, in conjunction with BRE5, cleaves ubiquitin, leading to the subsequent mono-ubiquitination of SEC23 (PubMed:12778054). Required for ribophagy, a process which relocalizes ribosomal particles into the vacuole for degradation in response to starvation (PubMed:20508643).4 Publications

Miscellaneous

Present with 2210 molecules/cell in log phase SD medium.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei469NucleophilePROSITE-ProRule annotation1
Active sitei861Proton acceptorPROSITE-ProRule annotation1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionHydrolase, Protease, Thiol protease
Biological processUbl conjugation pathway

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:G3O-30312-MONOMER

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-SCE-5656169 Termination of translesion DNA synthesis

Protein family/group databases

MEROPS protease database

More...
MEROPSi
C19.004

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 3 (EC:3.4.19.122 Publications)
Alternative name(s):
Deubiquitinating enzyme 3
Ubiquitin thioesterase 3
Ubiquitin-specific-processing protease 3
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:UBP3
Ordered Locus Names:YER151C
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome V

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YER151C

Saccharomyces Genome Database

More...
SGDi
S000000953 UBP3

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000805881 – 912Ubiquitin carboxyl-terminal hydrolase 3Add BLAST912

Proteomic databases

MaxQB - The MaxQuant DataBase

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MaxQBi
Q01477

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
Q01477

PRoteomics IDEntifications database

More...
PRIDEi
Q01477

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q01477

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Heterotetramer with BRE5; contains two molecules of BRE5 and two molecules of UBP3 (PubMed:12778054, PubMed:17632125).

Forms a complex composed of CDC48, DOA1, deubiquitinase UBP3 and probably BRE5. Within the complex interacts directly with DOA1 and CDC48 in a BRE5-independent manner (PubMed:20508643).

3 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
36901, 1163 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-1412 UBP3-BRE5 ubiquitin hydrolase complex

Database of interacting proteins

More...
DIPi
DIP-4255N

Protein interaction database and analysis system

More...
IntActi
Q01477, 404 interactors

Molecular INTeraction database

More...
MINTi
Q01477

STRING: functional protein association networks

More...
STRINGi
4932.YER151C

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1912
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
Q01477

Database of comparative protein structure models

More...
ModBasei
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
Q01477

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini460 – 911USPAdd BLAST452

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the peptidase C19 family.Curated

Phylogenomic databases

Ensembl GeneTree

More...
GeneTreei
ENSGT00940000170514

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000141876

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q01477

KEGG Orthology (KO)

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KOi
K11841

Identification of Orthologs from Complete Genome Data

More...
OMAi
LDPFQTI

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR038765 Papain-like_cys_pep_sf
IPR001394 Peptidase_C19_UCH
IPR018200 USP_CS
IPR028889 USP_dom

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00443 UCH, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF54001 SSF54001, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00972 USP_1, 1 hit
PS00973 USP_2, 1 hit
PS50235 USP_3, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i337FD05527C5542D
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
M94917 Genomic DNA Translation: AAA35191.1
U18917 Genomic DNA Translation: AAB64678.1
BK006939 Genomic DNA Translation: DAA07812.1

Protein sequence database of the Protein Information Resource

More...
PIRi
B44450

NCBI Reference Sequences

More...
RefSeqi
NP_011078.3, NM_001179041.3

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YER151C_mRNA; YER151C_mRNA; YER151C

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
856895

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YER151C

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2QIYX-ray1.69C/D190-233[»]
SMRiQ01477
ModBaseiSearch...

Protein-protein interaction databases

BioGridi36901, 1163 interactors
ComplexPortaliCPX-1412 UBP3-BRE5 ubiquitin hydrolase complex
DIPiDIP-4255N
IntActiQ01477, 404 interactors
MINTiQ01477
STRINGi4932.YER151C

Protein family/group databases

MEROPSiC19.004

PTM databases

iPTMnetiQ01477

Proteomic databases

MaxQBiQ01477
PaxDbiQ01477
PRIDEiQ01477

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYER151C_mRNA; YER151C_mRNA; YER151C
GeneIDi856895
KEGGisce:YER151C

Organism-specific databases

EuPathDBiFungiDB:YER151C
SGDiS000000953 UBP3

Phylogenomic databases

GeneTreeiENSGT00940000170514
HOGENOMiHOG000141876
InParanoidiQ01477
KOiK11841
OMAiLDPFQTI

Enzyme and pathway databases

BioCyciYEAST:G3O-30312-MONOMER
ReactomeiR-SCE-5656169 Termination of translesion DNA synthesis

Miscellaneous databases

EvolutionaryTraceiQ01477

Protein Ontology

More...
PROi
PR:Q01477

Family and domain databases

InterProiView protein in InterPro
IPR038765 Papain-like_cys_pep_sf
IPR001394 Peptidase_C19_UCH
IPR018200 USP_CS
IPR028889 USP_dom
PfamiView protein in Pfam
PF00443 UCH, 1 hit
SUPFAMiSSF54001 SSF54001, 1 hit
PROSITEiView protein in PROSITE
PS00972 USP_1, 1 hit
PS00973 USP_2, 1 hit
PS50235 USP_3, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiUBP3_YEAST
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q01477
Secondary accession number(s): D3DM58
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 1, 1993
Last modified: June 5, 2019
This is version 173 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Peptidase families
    Classification of peptidase families and list of entries
  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
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