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Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

usp13

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

Functioni

Deubiquitinase that mediates deubiquitination of target proteins and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD).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.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei327NucleophilePROSITE-ProRule annotation1
Active sitei819Proton acceptorPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri190 – 262UBP-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-DRE-5689880 Ub-specific processing proteases
R-DRE-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
ORF Names:wu:fc61g08
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Chromosome 6

Organism-specific databases

ZFINiZDB-GENE-080724-7 usp13

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004180131 – 860Ubiquitin carboxyl-terminal hydrolase 13Add BLAST860

Proteomic databases

PaxDbiF1QFS9

Expressioni

Gene expression databases

BgeeiENSDARG00000079198

Interactioni

GO - Molecular functioni

Protein-protein interaction databases

BioGridi284243, 1 interactor
STRINGi7955.ENSDARP00000065292

Structurei

3D structure databases

SMRiF1QFS9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini318 – 857USPAdd BLAST540
Domaini635 – 676UBA 1PROSITE-ProRule annotationAdd BLAST42
Domaini710 – 750UBA 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 fingeri190 – 262UBP-typePROSITE-ProRule annotationAdd BLAST73

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG0944 Eukaryota
COG5207 LUCA
GeneTreeiENSGT00390000000874
HOGENOMiHOG000162311
InParanoidiF1QFS9
KOiK11836
OMAiMKEEHKP
OrthoDBiEOG091G01W3
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
PS00973 USP_2, 1 hit
PS50235 USP_3, 1 hit
PS50271 ZF_UBP, 1 hit

Sequencei

Sequence statusi: Complete.

F1QFS9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATDLGELLV PYMPTIRVPR TGDRVFKSEC AFSYDSPESE GGLYVCMNSF
60 70 80 90 100
LGFGREHVER HYRKTGQSVY MHLKRHVKEK ATGAAGGAIP RRRNGKVFLD
110 120 130 140 150
LELNRDFNGD DYEYEDEAKL VIFPDHYEIP LPNIEELPAL VTIACDAVLN
160 170 180 190 200
APSPYKKQES DSWEEEIQVS RHARSLRQLD NGVRIPPSGW KCAKCEMREN
210 220 230 240 250
LWLNLTDGSV LCGKWFFDGS GGNGHALEHY RESNFPLAVK LNTITPDGAD
260 270 280 290 300
IYSFDEEEAV LDPHISEHLL HFGIDMLQMQ RTENGHHTDN HVQPRISDWE
310 320 330 340 350
VIQEAGLKLK PVYGSGYTGI KNLGNSCYLS TTMQVLFSIP EFQRAYAGNL
360 370 380 390 400
QRIFDYSPLD PTQDFNTQMA KLGHGLLSGQ YSKPPMKSEL IEQVMKEEHK
410 420 430 440 450
QQQQRGISPK MFKALVSKGH PEFSSNRQQD AHEFLLHLIN LVERNNSGSE
460 470 480 490 500
NPSDVFRFIV EERTQCCQSQ KVRYTQRVDY LMQLPVPLEA ASNREELIAY
510 520 530 540 550
EGKRKEAEEN MRPLPEVVRA RVPFTACLQA FTEPENVPDF WSSALQAKSA
560 570 580 590 600
GVKTSRFATF PEYMIVQLKK FTFGVDWVPK KLDMSVDVPD FLDLNRLRAT
610 620 630 640 650
GLQAGEEELP DLTPPIVIPE DTRDSSTNNS LESPEIDESS VMQLAEMGFP
660 670 680 690 700
LEACRKAVYY TGNMGAEMAF NWIIAHMEEP DFAEPLAVPT YMESDLPSPS
710 720 730 740 750
LPTTSALDNQ PPEESISILT SMGFPRHHTI QALKASNNNL ERALDWIFTH
760 770 780 790 800
PDCEDESEAM SDTADTEPND NSFSNANAHT DSSLSPDQDL SSPRVRDGPG
810 820 830 840 850
RYELFAFISH MGTSTMSGHY VCHIKKEGRW LIYNDHKVCL SERPPKDLGY
860
MYFYRRLSSC
Length:860
Mass (Da):97,452
Last modified:May 3, 2011 - v1
Checksum:i456C6827F7D0DCC1
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti731Q → R in AAI41801 (Ref. 2) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL928701 Genomic DNA No translation available.
CU459215 Genomic DNA No translation available.
BC141800 mRNA Translation: AAI41801.1
RefSeqiNP_001091856.1, NM_001098386.1
UniGeneiDr.115281

Genome annotation databases

EnsembliENSDART00000065293; ENSDARP00000065292; ENSDARG00000079198
GeneIDi558011
KEGGidre:558011

Similar proteinsi

Entry informationi

Entry nameiUBP13_DANRE
AccessioniPrimary (citable) accession number: F1QFS9
Secondary accession number(s): A5D8T1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 13, 2012
Last sequence update: May 3, 2011
Last modified: May 23, 2018
This is version 50 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. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

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