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E1BMF7 (UBP13_BOVIN) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 30. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:USP13
OrganismBos taurus (Bovine) [Reference proteome]
Taxonomic identifier9913 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos

Protein attributes

Sequence length863 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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.

Catalytic activity

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 regulation

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.

Subunit structure

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

Domain

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 similarities

Belongs to the peptidase C19 family.

Contains 2 UBA domains.

Contains 1 UBP-type zinc finger.

Contains 1 USP domain.

Ontologies

Keywords
   Biological processAutophagy
Ubl conjugation pathway
   DomainRepeat
Zinc-finger
   LigandMetal-binding
Zinc
   Molecular functionHydrolase
Protease
Thiol protease
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processautophagy

Inferred from electronic annotation. Source: UniProtKB-KW

cell proliferation

Inferred from sequence or structural similarity. Source: UniProtKB

protein K63-linked deubiquitination

Inferred from sequence or structural similarity. Source: UniProtKB

protein stabilization

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of autophagy

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of transcription, DNA-templated

Inferred from sequence or structural similarity. Source: UniProtKB

ubiquitin-dependent protein catabolic process

Inferred from electronic annotation. Source: InterPro

   Molecular_functioncysteine-type endopeptidase activity

Inferred from sequence or structural similarity. Source: UniProtKB

omega peptidase activity

Inferred from electronic annotation. Source: InterPro

ubiquitin binding

Inferred from sequence or structural similarity. Source: UniProtKB

ubiquitin thiolesterase activity

Inferred from sequence or structural similarity. Source: UniProtKB

ubiquitin-specific protease activity

Inferred from sequence or structural similarity. Source: UniProtKB

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 863863Ubiquitin carboxyl-terminal hydrolase 13
PRO_0000418010

Regions

Domain336 – 861526USP
Domain652 – 69342UBA 1
Domain727 – 76741UBA 2
Zinc finger209 – 28173UBP-type

Sites

Active site3451Nucleophile By similarity
Active site8231Proton acceptor By similarity

Amino acid modifications

Modified residue1141Phosphoserine By similarity
Modified residue1221Phosphothreonine By similarity

Sequences

Sequence LengthMass (Da)Tools
E1BMF7 [UniParc].

Last modified November 16, 2011. Version 2.
Checksum: 04357616964550B5

FASTA86397,278
        10         20         30         40         50         60 
MQRRGALFGM PGGSGSRKMA AGDIGELLVP HMPTIRVPRS GDRVYKNECA FSYDSPNSEG 

        70         80         90        100        110        120 
GLYVCMNTFL AFGREHVERH FRKTGQSVYM HLKRHVREKV RGASGGALPK RRNSKMFLDL 

       130        140        150        160        170        180 
DTDDDLNSDD YEYEDEAKLV IFPDHYEIAL PNIEELPALV TIACDAVLSS KSPYRKQDPD 

       190        200        210        220        230        240 
TWENELPVSK YANNLTQLDN GVRIPPSGWK CARCDLRENL WLNLTDGSVL CGKWFFDSSG 

       250        260        270        280        290        300 
GNGHALEHYR DTGYPLAVKL GTITPDGADV YSFQEEEAVL DPHLAKHLAH FGIDMLHMHG 

       310        320        330        340        350        360 
TENGLQDNDI KPRVSEWEVI QETGTKLKPM YGPGYTGLKN LGNSCYLSSV MQAIFSIPEF 

       370        380        390        400        410        420 
QRAYVGNLPR IFDYSPLDPT QDFNTQMTKL GHGLLSGQYS KPPVKSELIE QVMKEEHKPQ 

       430        440        450        460        470        480 
QNGISPRMFK AFVSKSHPEF SSNRQQDAQE FFLHLVNLVE RNRIGSENPS DVFRFLVEER 

       490        500        510        520        530        540 
IQCCQTRKVR YTERVDYLMQ LPVAMEAATN KDELIAYELT RREAESNRRP LPELVRAKIP 

       550        560        570        580        590        600 
FSACLQAFSE PENVDDFWSS ALQAKSAGVK TSRFASFPEY LVVQIKKFTF GLDWVPKKFD 

       610        620        630        640        650        660 
VSVDMPDLLD INHLRARGLQ PGEEELPDIS PPIVIPDDSK DRLMTQLIDP SDIDESSVMQ 

       670        680        690        700        710        720 
LAEMGFPLEA CRKAVYFTGN MGAEVAFNWI VVHMEEPDFA EPLTMPGYGG AASAGASVFG 

       730        740        750        760        770        780 
ATGLDNQPPE ETVAIITSMG FHRNQAIQAL RATNSNLERA LDWIFSHPEF EEDSDFVIEM 

       790        800        810        820        830        840 
ENNANANIVS EAKPEGPRVK DGSGMYELFA FISHMGTSTM SGHYVCHIKK EGRWVIYNDH 

       850        860 
KVCASERPPK DLGYMYFYRR IPS 

« Hide

References

[1]"A whole-genome assembly of the domestic cow, Bos taurus."
Zimin A.V., Delcher A.L., Florea L., Kelley D.R., Schatz M.C., Puiu D., Hanrahan F., Pertea G., Van Tassell C.P., Sonstegard T.S., Marcais G., Roberts M., Subramanian P., Yorke J.A., Salzberg S.L.
Genome Biol. 10:R42.01-R42.10(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Hereford.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
DAAA02001954 Genomic DNA. No translation available.
DAAA02001955 Genomic DNA. No translation available.
DAAA02001956 Genomic DNA. No translation available.
DAAA02001957 Genomic DNA. No translation available.
DAAA02001958 Genomic DNA. No translation available.
RefSeqNP_001178195.1. NM_001191266.1.
UniGeneBt.74584.

3D structure databases

ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSBTAT00000061390; ENSBTAP00000053221; ENSBTAG00000005946.
GeneID100141289.
KEGGbta:100141289.

Organism-specific databases

CTD8975.

Phylogenomic databases

GeneTreeENSGT00390000000874.
KOK11836.
OMAPRMFKAF.
OrthoDBEOG7CNZF3.
TreeFamTF300576.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
InterProIPR018200. 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]
PfamPF00627. UBA. 2 hits.
PF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view]
PIRSFPIRSF016308. UBP. 1 hit.
SMARTSM00165. UBA. 2 hits.
SM00290. ZnF_UBP. 1 hit.
[Graphical view]
SUPFAMSSF46934. SSF46934. 1 hit.
PROSITEPS50030. 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]
ProtoNetSearch...

Other

NextBio20791338.

Entry information

Entry nameUBP13_BOVIN
AccessionPrimary (citable) accession number: E1BMF7
Entry history
Integrated into UniProtKB/Swiss-Prot: June 13, 2012
Last sequence update: November 16, 2011
Last modified: May 14, 2014
This is version 30 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries