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Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

Usp13

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Deubiquitinase that mediates deubiquitination of target proteins such as BECN1, MITF, SKP2 and USP10 and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD). Component of a regulatory loop that controls autophagy and p53/TP53 levels: mediates deubiquitination of BECN1, a key regulator of autophagy, leading to stabilize the PIK3C3/VPS34-containing complexes. Also deubiquitinates USP10, an essential regulator of p53/TP53 stability. In turn, PIK3C3/VPS34-containing complexes regulate USP13 stability, suggesting the existence of a regulatory system by which PIK3C3/VPS34-containing complexes regulate p53/TP53 protein levels via USP10 and USP13. Recruited by nuclear UFD1 and mediates deubiquitination of SKP2, thereby regulating endoplasmic reticulum-associated degradation (ERAD). Also regulates ERAD through the deubiquitination of UBL4A a component of the BAG6/BAT3 complex. Mediates stabilization of SIAH2 independently of deubiquitinase activity: binds ubiquitinated SIAH2 and acts by impairing SIAH2 autoubiquitination. Has a weak deubiquitinase activity in vitro and preferentially cleaves 'Lys-63'-linked polyubiquitin chains. In contrast to USP5, it is not able to mediate unanchored polyubiquitin disassembly. Able to cleave ISG15 in vitro; however, additional experiments are required to confirm such data.By similarity

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).

Enzyme regulationi

Specifically inhibited by spautin-1 (specific and potent autophagy inhibitor-1), a derivative of MBCQ that binds to USP13 and inhibits deubiquitinase activity. Regulated by PIK3C3/VPS34-containing complexes. The weak deubiquitinase activity in vitro suggests the existence of some mechanism that activates the enzyme (By similarity).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei343NucleophilePROSITE-ProRule annotation1
Active sitei818Proton acceptorPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri207 – 279UBP-typePROSITE-ProRule annotationAdd BLAST73

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase, Protease, Thiol protease
Biological processAutophagy, Ubl conjugation pathway
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-5689880. Ub-specific processing proteases.
R-MMU-8948751. Regulation of PTEN stability and activity.

Protein family/group databases

MEROPSiC19.012.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 13 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 13
Ubiquitin thioesterase 13
Ubiquitin-specific-processing protease 13
Gene namesi
Name:Usp13
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 3

Organism-specific databases

MGIiMGI:1919857. Usp13.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004180111 – 858Ubiquitin carboxyl-terminal hydrolase 13Add BLAST858

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei112PhosphoserineBy similarity1
Cross-linki309Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki403Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ5BKP2.
PaxDbiQ5BKP2.
PRIDEiQ5BKP2.

PTM databases

iPTMnetiQ5BKP2.
PhosphoSitePlusiQ5BKP2.

Expressioni

Gene expression databases

BgeeiENSMUSG00000056900.
ExpressionAtlasiQ5BKP2. baseline and differential.
GenevisibleiQ5BKP2. MM.

Interactioni

Subunit structurei

Interacts with UFD1. Interacts (via UBA domains) with SIAH2 (when ubiquitinated). Interacts with BAG6; the interaction is direct and may mediate UBL4A deubiquitination. Interacts (via UBA 2 domain) with AMFR; the interaction is direct. Interacts with UBL4A; may be indirect via BAG6.By similarity

GO - Molecular functioni

Protein-protein interaction databases

BioGridi215466. 1 interactor.
STRINGi10090.ENSMUSP00000072155.

Structurei

3D structure databases

ProteinModelPortaliQ5BKP2.
SMRiQ5BKP2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini334 – 856USPAdd BLAST523
Domaini650 – 691UBA 1PROSITE-ProRule annotationAdd BLAST42
Domaini722 – 762UBA 2PROSITE-ProRule annotationAdd BLAST41

Domaini

The UBP-type zinc finger has lost its ability to bind ubiquitin and USP13 is not activated by unanchored ubiquitin.By similarity
The UBA domains mediate binding to ubiquitin.By similarity

Sequence similaritiesi

Belongs to the peptidase C19 family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri207 – 279UBP-typePROSITE-ProRule annotationAdd BLAST73

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG0944. Eukaryota.
COG5207. LUCA.
GeneTreeiENSGT00390000000874.
HOGENOMiHOG000162311.
HOVERGENiHBG002833.
InParanoidiQ5BKP2.
KOiK11836.
OMAiMKEEHKP.
OrthoDBiEOG091G01W3.
PhylomeDBiQ5BKP2.
TreeFamiTF300576.

Family and domain databases

Gene3Di3.30.40.10. 2 hits.
InterProiView protein in InterPro
IPR001394. Peptidase_C19_UCH.
IPR015940. UBA.
IPR009060. UBA-like_sf.
IPR016652. Ubiquitinyl_hydrolase.
IPR018200. USP_CS.
IPR028889. USP_dom.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
PfamiView protein in Pfam
PF00627. UBA. 2 hits.
PF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
PIRSFiPIRSF016308. UBP. 1 hit.
SMARTiView protein in SMART
SM00165. UBA. 2 hits.
SM00290. ZnF_UBP. 1 hit.
SUPFAMiSSF46934. SSF46934. 1 hit.
PROSITEiView protein in PROSITE
PS50030. UBA. 2 hits.
PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5BKP2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQRRGALFSV PGGGGKMAAG DLGELLVPHM PTIRVPRSGD RVYKNECAFS
60 70 80 90 100
YDSPNSEGGL YVCMNTFLAF GREHVERHFR KTGQSVYMHL KRHMREKVRG
110 120 130 140 150
ASGGALPKRR NSKIFLDLDM DDDLNSDDYE YEDEAKLVIF PDHYEIALPN
160 170 180 190 200
IEELPALVTI ACDAVLSSKS PYRKQDPDTW ENEVPVSKYA NNLVQLDNGV
210 220 230 240 250
RIPPSGWKCA RCDLRENLWL NLTDGSVLCG KWFFDSSGGN GHALEHYRDM
260 270 280 290 300
GYPLAVKLGT ITPDGADVYS FQEEGPVSDP HLAKHLAHFG IDMLHTQGTE
310 320 330 340 350
NGLRDNDIKP RVSEWEVIQE SGTKLKPMYG PGYTGLKNLG NSCYLSSVMQ
360 370 380 390 400
AIFSIPEFQR AYVGNLPRIF DYSPLDPTQD FNTQMTKLGH GLLSGQYSKP
410 420 430 440 450
PVKSELIEQV MKEEHKPQQN GISPRMFKAF VSKSHPEFSS NRQQDAQEFF
460 470 480 490 500
LHLVNLVERN RIGSENPSDV FRFLVEERIQ CCQTRKVRYT ERVDYLMQLP
510 520 530 540 550
VAMEAATNKD ELITYELMRR EAEANRRPLP ELVRAKIPFS ACLQAFAEPD
560 570 580 590 600
NVDDFWSSAL QAKSAGVKTS RFASFPEYLV VQIKKFTFGL DWVPRKFDVS
610 620 630 640 650
IDMPDLLDIS HLRARGLQPG EEELPDISPP IVIPDDSKDR LMNQLIDPSD
660 670 680 690 700
IDESSVMQLA EMGFPLEACR KAVYFTGNTG AEVAFNWIIV HMEEPDFAEP
710 720 730 740 750
LAIPGYGGAG ASVFGATGLD NQPPEEIVAI ITSMGFQRNQ AVQALQATNH
760 770 780 790 800
NLERALDWIF SHPEFEEDSD FVIEMENNAN ANIVSEAKPE GPRVKDGSGM
810 820 830 840 850
YELFAFISHM GTSTMSGHYV CHIKKEGRWV IYNDHKVCAS ERPPKDLGYM

YFYRRIPS
Length:858
Mass (Da):96,723
Last modified:April 12, 2005 - v1
Checksum:i04989BACB784192C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC111140 Genomic DNA. No translation available.
CH466530 Genomic DNA. Translation: EDL35015.1.
BC090999 mRNA. Translation: AAH90999.1.
CCDSiCCDS17301.1.
RefSeqiNP_001013042.1. NM_001013024.2.
UniGeneiMm.316153.

Genome annotation databases

EnsembliENSMUST00000072312; ENSMUSP00000072155; ENSMUSG00000056900.
GeneIDi72607.
KEGGimmu:72607.
UCSCiuc008owr.1. mouse.

Similar proteinsi

Entry informationi

Entry nameiUBP13_MOUSE
AccessioniPrimary (citable) accession number: Q5BKP2
Secondary accession number(s): D3YYG7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 13, 2012
Last sequence update: April 12, 2005
Last modified: November 22, 2017
This is version 110 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families