UniProtKB - P53874 (UBP10_YEAST)
Protein
Ubiquitin carboxyl-terminal hydrolase 10
Gene
UBP10
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Functioni
Deubiquitinating enzyme involved in telomere and HM loci silencing, which is the repression of chromatin structure which leads to a stop in the transcription of nearby genes (PubMed:9755194, PubMed:10490600, PubMed:14623890). Targets histone H2B for deubiquitination, thus helping to localize SIR2 to the telomere (PubMed:15721261, PubMed:17028327, PubMed:22056669). At silent chromatin, including telomeres and the rDNA locus, not only maintains low H2B 'Lys-123' ubiquitination (H2BK123Ub), but also low H3 'Lys-4' and 'Lys-79' methylation (H3K4me and H3K79me, respectively) (PubMed:15721261, PubMed:15988024). Controls the proliferating-cell nuclear antigen PCNA/POL30 deubiquitination which is crucial for keeping TLS polymerases in check as well as for down-regulating the error-free bypass (PubMed:22829782). Deubiquitinates and stabilizes RPA190, the largest subunit of RNA polymerase I, to achieve optimal levels of ribosomes and cell growth (PubMed:22902402). Protects also nutrient transporters such as GAP1 from ubiquitin-dependent endocytosis (PubMed:11352638).10 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 EC:3.4.19.12
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 371 | NucleophilePROSITE-ProRule annotation | 1 | |
Active sitei | 691 | Proton acceptorPROSITE-ProRule annotation | 1 |
GO - Molecular functioni
- cysteine-type endopeptidase activity Source: GO_Central
- thiol-dependent ubiquitin-specific protease activity Source: SGD
GO - Biological processi
- chromatin silencing at telomere Source: SGD
- histone deubiquitination Source: SGD
- protein deubiquitination Source: SGD
- regulation of response to DNA damage stimulus Source: SGD
- subtelomeric heterochromatin assembly Source: SGD
- ubiquitin-dependent protein catabolic process Source: InterPro
Keywordsi
Molecular function | Hydrolase, Protease, Thiol protease |
Biological process | Ubl conjugation pathway |
Protein family/group databases
MEROPSi | C19.088 |
Names & Taxonomyi
Protein namesi | Recommended name: Ubiquitin carboxyl-terminal hydrolase 10 (EC:3.4.19.121 Publication)Alternative name(s): Deubiquitinating enzyme 10 Disrupter of telomere silencing protein 41 Publication Ubiquitin thioesterase 10 Ubiquitin-specific-processing protease 10 |
Gene namesi | Name:UBP10 Synonyms:DOT41 Publication Ordered Locus Names:YNL186W ORF Names:N1619 |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
EuPathDBi | FungiDB:YNL186W |
SGDi | S000005130, UBP10 |
Subcellular locationi
Cytosol
- cytosol Source: GO_Central
Nucleus
- nuclear replication fork Source: SGD
- nucleolus Source: SGD
- nucleus Source: SGD
Other locations
- chromosome, telomeric region Source: UniProtKB-SubCell
Keywords - Cellular componenti
Chromosome, Nucleus, TelomerePathology & Biotechi
Disruption phenotypei
Exhibits reduced silencing and a corresponding decrease in the level of SIR4 (PubMed:10490600). Reduces also the level of the low-affinity, high-capacity transporter of amino acids GAP1 (PubMed:11352638). Leads to alterations in expression of subtelomeric genes together with a broad change in the whole transcriptional profile, closely parallel to that induced by oxidative stress (PubMed:14623890). Results also in extrachromosomal rDNA circles (ERCs) accumulation (PubMed:17028327). Accumulates also mono- and di-ubiquitinated PCNA/POL30 in response to DNA damage and replicative stress (PubMed:22829782). Leads to reduced pre-rRNAs, mature rRNAs, and translating ribosomes (PubMed:22902402).6 Publications
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 371 | C → A or S: Abolishes deubiquitinating activity. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000080595 | 1 – 792 | Ubiquitin carboxyl-terminal hydrolase 10Add BLAST | 792 |
Proteomic databases
MaxQBi | P53874 |
PaxDbi | P53874 |
PRIDEi | P53874 |
PTM databases
iPTMneti | P53874 |
Interactioni
Subunit structurei
Protein-protein interaction databases
BioGRIDi | 35647, 231 interactors |
DIPi | DIP-6664N |
IntActi | P53874, 22 interactors |
MINTi | P53874 |
STRINGi | 4932.YNL186W |
Miscellaneous databases
RNActi | P53874, protein |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 362 – 733 | USPPROSITE-ProRule annotationAdd BLAST | 372 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 2 – 27 | DHR2-binding module1 PublicationAdd BLAST | 26 | |
Regioni | 109 – 145 | SIR4-binding module1 PublicationAdd BLAST | 37 | |
Regioni | 167 – 208 | UTP22-binding module1 PublicationAdd BLAST | 42 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 116 – 310 | Glu-richPROSITE-ProRule annotationAdd BLAST | 195 |
Domaini
Residues 2-27 within the N-terminal intrinsically disordered regions (IDR) constitute the binding module for DHR2 which is required to coordinate the UBP10-DHR2 interaction (PubMed:26149687).1 Publication
Residues 109-145 within the N-terminal intrinsically disordered regions (IDR) constitute the binding module for SIR4 which required to coordinate the UBP10-SIR4 interaction, but also to direct UBP10's functional role in telomere chromatin silencing (PubMed:26149687).1 Publication
Residues 167-208 within the N-terminal intrinsically disordered regions (IDR) constitute the binding module for UTP22 which is required to coordinate the UBP10-UTP22 interaction (PubMed:26149687).1 Publication
Sequence similaritiesi
Belongs to the peptidase C19 family.Curated
Phylogenomic databases
eggNOGi | KOG1870, Eukaryota |
HOGENOMi | CLU_016013_1_1_1 |
InParanoidi | P53874 |
OMAi | SVPKGHK |
Family and domain databases
DisProti | DP01189 |
InterProi | View protein in InterPro IPR038765, Papain-like_cys_pep_sf IPR001394, Peptidase_C19_UCH IPR018200, USP_CS IPR028889, USP_dom |
Pfami | View protein in Pfam PF00443, UCH, 1 hit |
SUPFAMi | SSF54001, SSF54001, 1 hit |
PROSITEi | View protein in PROSITE PS00973, USP_2, 1 hit PS50235, USP_3, 1 hit |
i Sequence
Sequence statusi: Complete.
P53874-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MTTQESIKPL VDRILSNPLQ FNAAMISNKS NNNDTSAAPE NSSYIVIGKQ
60 70 80 90 100
HNNNSNSTAI AATAESKQIK ENNLIDRPNG KKTNTVPKSM AEALLLYTSK
110 120 130 140 150
NDKDAADATG AKKSAELSTE LSTEPPSSSS EDDKVGKEEE EEGEIFHEAR
160 170 180 190 200
DYVEPRKASL KERDNADKGD GEDIGEDIGE DIGEDIGEDI GEDIGENLGS
210 220 230 240 250
PLATIDDSSN ENEKEKRKEL STSISSDDEI EDDEDEDDMD YDSSAMEKEL
260 270 280 290 300
PEEEENDSSS KISEGEKKSL YQDLMENSTV EVNRYEPVNN TKENGNRNPK
310 320 330 340 350
GEEEEEEEEE LKHKSRSITP PVTISNLSNF YQFNENINDR GSLNSTRIVK
360 370 380 390 400
NWGDKFTNLK PRGLLNHGVT CYTNAAVQAM LHIPSIQHYL FDILMGKYDS
410 420 430 440 450
TISKNSVSYT LAETSKKMWL PVSKNPRKNV SASYINPKHL ISRLDDINCM
460 470 480 490 500
MSEWQQEDSH EYFMSLMSRL QEDSVPKGHK LIESIIYDIF GGLLKQIVTC
510 520 530 540 550
KSCGSISKTE QPFYDLSLHL KGKKKLDPNS DLSSDSINGT SATTSTTTSN
560 570 580 590 600
AATKPSLSSS SSVNLNNGSP FAAASDLSSA NRRFSIEKSI KDFFNPELIK
610 620 630 640 650
VDKEQKGYVC EKCHKTTNAV KHSSILRAPE TLLVHLKKFR FNGTSSSKMK
660 670 680 690 700
QAVSYPMFLD LTEYCESKEL PVKYQLLSVV VHEGRSLSSG HYIAHCKQPD
710 720 730 740 750
GSWATYDDEY INIISERDVL KEPNAYYLLY TRLTPKSVPL PLAKSAMATG
760 770 780 790
NVTSKSKQEQ AVNEPNNRPL KINSKKNNRK KWKKNKKRKF TK
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 310 | E → D in CAA96080 (PubMed:9169873).Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | Z71462 Genomic DNA Translation: CAA96080.1 BK006947 Genomic DNA Translation: DAA10367.2 |
PIRi | S63141 |
RefSeqi | NP_014213.2, NM_001183024.2 |
Genome annotation databases
EnsemblFungii | YNL186W_mRNA; YNL186W; YNL186W |
GeneIDi | 855535 |
KEGGi | sce:YNL186W |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | Z71462 Genomic DNA Translation: CAA96080.1 BK006947 Genomic DNA Translation: DAA10367.2 |
PIRi | S63141 |
RefSeqi | NP_014213.2, NM_001183024.2 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
6RR0 | X-ray | 2.18 | H/I/J/K/L/M/N | 117-128 | [»] | |
SMRi | P53874 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 35647, 231 interactors |
DIPi | DIP-6664N |
IntActi | P53874, 22 interactors |
MINTi | P53874 |
STRINGi | 4932.YNL186W |
Protein family/group databases
MEROPSi | C19.088 |
PTM databases
iPTMneti | P53874 |
Proteomic databases
MaxQBi | P53874 |
PaxDbi | P53874 |
PRIDEi | P53874 |
Genome annotation databases
EnsemblFungii | YNL186W_mRNA; YNL186W; YNL186W |
GeneIDi | 855535 |
KEGGi | sce:YNL186W |
Organism-specific databases
EuPathDBi | FungiDB:YNL186W |
SGDi | S000005130, UBP10 |
Phylogenomic databases
eggNOGi | KOG1870, Eukaryota |
HOGENOMi | CLU_016013_1_1_1 |
InParanoidi | P53874 |
OMAi | SVPKGHK |
Miscellaneous databases
PROi | PR:P53874 |
RNActi | P53874, protein |
Family and domain databases
DisProti | DP01189 |
InterProi | View protein in InterPro IPR038765, Papain-like_cys_pep_sf IPR001394, Peptidase_C19_UCH IPR018200, USP_CS IPR028889, USP_dom |
Pfami | View protein in Pfam PF00443, UCH, 1 hit |
SUPFAMi | SSF54001, SSF54001, 1 hit |
PROSITEi | View protein in PROSITE PS00973, USP_2, 1 hit PS50235, USP_3, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | UBP10_YEAST | |
Accessioni | P53874Primary (citable) accession number: P53874 Secondary accession number(s): D6W101 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | October 1, 1996 |
Last sequence update: | September 21, 2011 | |
Last modified: | December 2, 2020 | |
This is version 170 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Yeast chromosome XIV
Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families - Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Peptidase families
Classification of peptidase families and list of entries