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E1BMF7

- UBP13_BOVIN

UniProt

E1BMF7 - UBP13_BOVIN

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Protein
Ubiquitin carboxyl-terminal hydrolase 13
Gene
USP13
Organism
Bos taurus (Bovine)
Status
Reviewed - Annotation score: 4 out of 5 - Protein inferred from homologyi

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.

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei345 – 3451Nucleophile By similarity
Active sitei823 – 8231Proton acceptor By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri209 – 28173UBP-type
Add
BLAST

GO - Molecular functioni

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

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

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
OrganismiBos taurus (Bovine)
Taxonomic identifieri9913 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos
ProteomesiUP000009136: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 863863Ubiquitin carboxyl-terminal hydrolase 13
PRO_0000418010Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei114 – 1141Phosphoserine By similarity
Modified residuei122 – 1221Phosphothreonine By similarity

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

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

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini336 – 861526USP
Add
BLAST
Domaini652 – 69342UBA 1
Add
BLAST
Domaini727 – 76741UBA 2
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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.
Contains 2 UBA domains.
Contains 1 USP domain.

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000000874.
KOiK11836.
OMAiPRMFKAF.
OrthoDBiEOG7CNZF3.
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.

E1BMF7-1 [UniParc]FASTAAdd to Basket

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MQRRGALFGM PGGSGSRKMA AGDIGELLVP HMPTIRVPRS GDRVYKNECA    50
FSYDSPNSEG GLYVCMNTFL AFGREHVERH FRKTGQSVYM HLKRHVREKV 100
RGASGGALPK RRNSKMFLDL DTDDDLNSDD YEYEDEAKLV IFPDHYEIAL 150
PNIEELPALV TIACDAVLSS KSPYRKQDPD TWENELPVSK YANNLTQLDN 200
GVRIPPSGWK CARCDLRENL WLNLTDGSVL CGKWFFDSSG GNGHALEHYR 250
DTGYPLAVKL GTITPDGADV YSFQEEEAVL DPHLAKHLAH FGIDMLHMHG 300
TENGLQDNDI KPRVSEWEVI QETGTKLKPM YGPGYTGLKN LGNSCYLSSV 350
MQAIFSIPEF QRAYVGNLPR IFDYSPLDPT QDFNTQMTKL GHGLLSGQYS 400
KPPVKSELIE QVMKEEHKPQ QNGISPRMFK AFVSKSHPEF SSNRQQDAQE 450
FFLHLVNLVE RNRIGSENPS DVFRFLVEER IQCCQTRKVR YTERVDYLMQ 500
LPVAMEAATN KDELIAYELT RREAESNRRP LPELVRAKIP FSACLQAFSE 550
PENVDDFWSS ALQAKSAGVK TSRFASFPEY LVVQIKKFTF GLDWVPKKFD 600
VSVDMPDLLD INHLRARGLQ PGEEELPDIS PPIVIPDDSK DRLMTQLIDP 650
SDIDESSVMQ LAEMGFPLEA CRKAVYFTGN MGAEVAFNWI VVHMEEPDFA 700
EPLTMPGYGG AASAGASVFG ATGLDNQPPE ETVAIITSMG FHRNQAIQAL 750
RATNSNLERA LDWIFSHPEF EEDSDFVIEM ENNANANIVS EAKPEGPRVK 800
DGSGMYELFA FISHMGTSTM SGHYVCHIKK EGRWVIYNDH KVCASERPPK 850
DLGYMYFYRR IPS 863
Length:863
Mass (Da):97,278
Last modified:November 16, 2011 - v2
Checksum:i04357616964550B5
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
RefSeqiNP_001178195.1. NM_001191266.1.
UniGeneiBt.74584.

Genome annotation databases

EnsembliENSBTAT00000061390; ENSBTAP00000053221; ENSBTAG00000005946.
GeneIDi100141289.
KEGGibta:100141289.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
RefSeqi NP_001178195.1. NM_001191266.1.
UniGenei Bt.74584.

3D structure databases

ModBasei Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSBTAT00000061390 ; ENSBTAP00000053221 ; ENSBTAG00000005946 .
GeneIDi 100141289.
KEGGi bta:100141289.

Organism-specific databases

CTDi 8975.

Phylogenomic databases

GeneTreei ENSGT00390000000874.
KOi K11836.
OMAi PRMFKAF.
OrthoDBi EOG7CNZF3.
TreeFami TF300576.

Miscellaneous databases

NextBioi 20791338.

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: Hereford.

Entry informationi

Entry nameiUBP13_BOVIN
AccessioniPrimary (citable) accession number: E1BMF7
Entry historyi
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 statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata 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

External Data

Dasty 3

Similar proteinsi