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Protein

Ubiquitin carboxyl-terminal hydrolase 10

Gene

UBP10

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

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei371NucleophilePROSITE-ProRule annotation1
Active sitei691Proton acceptorPROSITE-ProRule annotation1

GO - Molecular functioni

  • thiol-dependent ubiquitin-specific protease activity Source: SGD

GO - Biological processi

  • chromatin silencing at subtelomere Source: SGD
  • chromatin silencing at telomere Source: SGD
  • histone deubiquitination Source: SGD
  • protein deubiquitination Source: SGD
  • ubiquitin-dependent protein catabolic process Source: InterPro

Keywordsi

Molecular functionHydrolase, Protease, Thiol protease
Biological processUbl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-33197-MONOMER

Protein family/group databases

MEROPSiC19.088

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
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL186W
SGDiS000005130 UBP10

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; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Nucleus, Telomere

Pathology & 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 keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi371C → A or S: Abolishes deubiquitinating activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000805951 – 792Ubiquitin carboxyl-terminal hydrolase 10Add BLAST792

Proteomic databases

MaxQBiP53874
PaxDbiP53874
PRIDEiP53874

PTM databases

iPTMnetiP53874

Interactioni

Subunit structurei

Interacts with SIR4 (PubMed:10490600, PubMed:26149687). Interacts with the proliferating-cell nuclear antigen PCNA/POL30 (PubMed:22829782). Interacts with DHR2 and UTP22 (PubMed:22902402, PubMed:26149687).3 Publications

Protein-protein interaction databases

BioGridi35647, 222 interactors
DIPiDIP-6664N
IntActiP53874, 22 interactors
MINTiP53874
STRINGi4932.YNL186W

Structurei

3D structure databases

ProteinModelPortaliP53874
SMRiP53874
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini362 – 733USPPROSITE-ProRule annotationAdd BLAST372

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 27DHR2-binding module1 PublicationAdd BLAST26
Regioni109 – 145SIR4-binding module1 PublicationAdd BLAST37
Regioni167 – 208UTP22-binding module1 PublicationAdd BLAST42

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi116 – 310Glu-richPROSITE-ProRule annotationAdd BLAST195

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

GeneTreeiENSGT00880000138891
HOGENOMiHOG000248158
InParanoidiP53874
KOiK11873
OMAiYVCEKCH
OrthoDBiEOG092C5R71

Family and domain databases

InterProiView protein in InterPro
IPR001394 Peptidase_C19_UCH
IPR018200 USP_CS
IPR028889 USP_dom
PfamiView protein in Pfam
PF00443 UCH, 1 hit
PROSITEiView protein in PROSITE
PS00973 USP_2, 1 hit
PS50235 USP_3, 1 hit

Sequencei

Sequence statusi: Complete.

P53874-1 [UniParc]FASTAAdd to basket

« Hide

        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
Length:792
Mass (Da):88,531
Last modified:September 21, 2011 - v2
Checksum:iAA2DE6DB0C560E37
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti310E → D in CAA96080 (PubMed:9169873).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71462 Genomic DNA Translation: CAA96080.1
BK006947 Genomic DNA Translation: DAA10367.2
PIRiS63141
RefSeqiNP_014213.2, NM_001183024.2

Genome annotation databases

EnsemblFungiiYNL186W; YNL186W; YNL186W
GeneIDi855535
KEGGisce:YNL186W

Similar proteinsi

Entry informationi

Entry nameiUBP10_YEAST
AccessioniPrimary (citable) accession number: P53874
Secondary accession number(s): D6W101
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: September 21, 2011
Last modified: May 23, 2018
This is version 152 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

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