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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).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 sitei345 – 3451NucleophilePROSITE-ProRule annotation
Active sitei823 – 8231Proton acceptorPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri209 – 28173UBP-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
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 13PRO_0000418010Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei114 – 1141PhosphoserineBy similarity
Modified residuei122 – 1221PhosphothreonineBy similarity

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

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

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini336 – 861526USPAdd
BLAST
Domaini652 – 69342UBA 1PROSITE-ProRule annotationAdd
BLAST
Domaini727 – 76741UBA 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 fingeri209 – 28173UBP-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000000874.
InParanoidiE1BMF7.
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

« Hide

        10         20         30         40         50
MQRRGALFGM PGGSGSRKMA AGDIGELLVP HMPTIRVPRS GDRVYKNECA
60 70 80 90 100
FSYDSPNSEG GLYVCMNTFL AFGREHVERH FRKTGQSVYM HLKRHVREKV
110 120 130 140 150
RGASGGALPK RRNSKMFLDL DTDDDLNSDD YEYEDEAKLV IFPDHYEIAL
160 170 180 190 200
PNIEELPALV TIACDAVLSS KSPYRKQDPD TWENELPVSK YANNLTQLDN
210 220 230 240 250
GVRIPPSGWK CARCDLRENL WLNLTDGSVL CGKWFFDSSG GNGHALEHYR
260 270 280 290 300
DTGYPLAVKL GTITPDGADV YSFQEEEAVL DPHLAKHLAH FGIDMLHMHG
310 320 330 340 350
TENGLQDNDI KPRVSEWEVI QETGTKLKPM YGPGYTGLKN LGNSCYLSSV
360 370 380 390 400
MQAIFSIPEF QRAYVGNLPR IFDYSPLDPT QDFNTQMTKL GHGLLSGQYS
410 420 430 440 450
KPPVKSELIE QVMKEEHKPQ QNGISPRMFK AFVSKSHPEF SSNRQQDAQE
460 470 480 490 500
FFLHLVNLVE RNRIGSENPS DVFRFLVEER IQCCQTRKVR YTERVDYLMQ
510 520 530 540 550
LPVAMEAATN KDELIAYELT RREAESNRRP LPELVRAKIP FSACLQAFSE
560 570 580 590 600
PENVDDFWSS ALQAKSAGVK TSRFASFPEY LVVQIKKFTF GLDWVPKKFD
610 620 630 640 650
VSVDMPDLLD INHLRARGLQ PGEEELPDIS PPIVIPDDSK DRLMTQLIDP
660 670 680 690 700
SDIDESSVMQ LAEMGFPLEA CRKAVYFTGN MGAEVAFNWI VVHMEEPDFA
710 720 730 740 750
EPLTMPGYGG AASAGASVFG ATGLDNQPPE ETVAIITSMG FHRNQAIQAL
760 770 780 790 800
RATNSNLERA LDWIFSHPEF EEDSDFVIEM ENNANANIVS EAKPEGPRVK
810 820 830 840 850
DGSGMYELFA FISHMGTSTM SGHYVCHIKK EGRWVIYNDH KVCASERPPK
860
DLGYMYFYRR IPS
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...
MobiDBi Search...

Protein family/group databases

MEROPSi C19.012.

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.
InParanoidi E1BMF7.
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: October 29, 2014
This is version 32 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