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Q5BKP2

- UBP13_MOUSE

UniProt

Q5BKP2 - UBP13_MOUSE

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Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

Usp13

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript 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). 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).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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei343 – 3431NucleophilePROSITE-ProRule annotation
Active sitei818 – 8181Proton acceptorPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri207 – 27973UBP-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. cysteine-type endopeptidase activity Source: UniProtKB
  2. omega peptidase activity Source: InterPro
  3. ubiquitin binding Source: UniProtKB
  4. ubiquitin-specific protease activity Source: UniProtKB
  5. ubiquitin thiolesterase activity Source: UniProtKB
  6. zinc ion binding Source: InterPro

GO - Biological processi

  1. autophagy Source: UniProtKB-KW
  2. cell proliferation Source: UniProtKB
  3. protein K63-linked deubiquitination Source: UniProtKB
  4. protein stabilization Source: UniProtKB
  5. regulation of autophagy Source: UniProtKB
  6. regulation of transcription, DNA-templated Source: UniProtKB
  7. ubiquitin-dependent protein catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Autophagy, Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 3

Organism-specific databases

MGIiMGI:1919857. Usp13.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 858858Ubiquitin carboxyl-terminal hydrolase 13PRO_0000418011Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei112 – 1121PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ5BKP2.
PaxDbiQ5BKP2.
PRIDEiQ5BKP2.

PTM databases

PhosphoSiteiQ5BKP2.

Expressioni

Gene expression databases

BgeeiQ5BKP2.
ExpressionAtlasiQ5BKP2. baseline and differential.
GenevestigatoriQ5BKP2.

Interactioni

Subunit structurei

Interacts with UFD1. Interacts (via UBA domains) with SIAH2 (when ubiquitinated) (By similarity).By similarity

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000072155.

Structurei

3D structure databases

ProteinModelPortaliQ5BKP2.
SMRiQ5BKP2. Positions 24-858.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini334 – 856523USPAdd
BLAST
Domaini650 – 69142UBA 1PROSITE-ProRule annotationAdd
BLAST
Domaini722 – 76241UBA 2PROSITE-ProRule annotationAdd
BLAST

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
Contains 2 UBA domains.PROSITE-ProRule annotation
Contains 1 UBP-type zinc finger.PROSITE-ProRule annotation
Contains 1 USP domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri207 – 27973UBP-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG5207.
GeneTreeiENSGT00390000000874.
HOGENOMiHOG000162311.
HOVERGENiHBG002833.
InParanoidiQ5BKP2.
KOiK11836.
OMAiPRMFKAF.
OrthoDBiEOG7CNZF3.
PhylomeDBiQ5BKP2.
TreeFamiTF300576.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR009060. UBA-like.
IPR015940. UBA/transl_elong_EF1B_N_euk.
IPR000449. UBA/Ts_N.
IPR016652. Ubiquitinyl_hydrolase.
IPR028889. UCH/PAN2.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view]
PfamiPF00627. UBA. 2 hits.
PF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view]
PIRSFiPIRSF016308. UBP. 1 hit.
SMARTiSM00165. UBA. 2 hits.
SM00290. ZnF_UBP. 1 hit.
[Graphical view]
SUPFAMiSSF46934. SSF46934. 1 hit.
PROSITEiPS50030. UBA. 2 hits.
PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.
[Graphical view]

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.
uc008ows.1. mouse.

Cross-referencesi

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 .
CCDSi CCDS17301.1.
RefSeqi NP_001013042.1. NM_001013024.2.
UniGenei Mm.316153.

3D structure databases

ProteinModelPortali Q5BKP2.
SMRi Q5BKP2. Positions 24-858.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 10090.ENSMUSP00000072155.

Protein family/group databases

MEROPSi C19.012.

PTM databases

PhosphoSitei Q5BKP2.

Proteomic databases

MaxQBi Q5BKP2.
PaxDbi Q5BKP2.
PRIDEi Q5BKP2.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000072312 ; ENSMUSP00000072155 ; ENSMUSG00000056900 .
GeneIDi 72607.
KEGGi mmu:72607.
UCSCi uc008owr.1. mouse.
uc008ows.1. mouse.

Organism-specific databases

CTDi 8975.
MGIi MGI:1919857. Usp13.

Phylogenomic databases

eggNOGi COG5207.
GeneTreei ENSGT00390000000874.
HOGENOMi HOG000162311.
HOVERGENi HBG002833.
InParanoidi Q5BKP2.
KOi K11836.
OMAi PRMFKAF.
OrthoDBi EOG7CNZF3.
PhylomeDBi Q5BKP2.
TreeFami TF300576.

Miscellaneous databases

NextBioi 336585.
PROi Q5BKP2.
SOURCEi Search...

Gene expression databases

Bgeei Q5BKP2.
ExpressionAtlasi Q5BKP2. baseline and differential.
Genevestigatori Q5BKP2.

Family and domain databases

Gene3Di 3.30.40.10. 1 hit.
InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR009060. UBA-like.
IPR015940. UBA/transl_elong_EF1B_N_euk.
IPR000449. UBA/Ts_N.
IPR016652. Ubiquitinyl_hydrolase.
IPR028889. UCH/PAN2.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view ]
Pfami PF00627. UBA. 2 hits.
PF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view ]
PIRSFi PIRSF016308. UBP. 1 hit.
SMARTi SM00165. UBA. 2 hits.
SM00290. ZnF_UBP. 1 hit.
[Graphical view ]
SUPFAMi SSF46934. SSF46934. 1 hit.
PROSITEi PS50030. UBA. 2 hits.
PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  2. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Heart.

Entry informationi

Entry nameiUBP13_MOUSE
AccessioniPrimary (citable) accession number: Q5BKP2
Secondary accession number(s): D3YYG7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 13, 2012
Last sequence update: April 12, 2005
Last modified: October 29, 2014
This is version 86 of the entry and version 1 of the sequence. [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

External Data

Dasty 3