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F1QFS9

- UBP13_DANRE

UniProt

F1QFS9 - UBP13_DANRE

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Protein
Ubiquitin carboxyl-terminal hydrolase 13
Gene
usp13, wu:fc61g08
Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 4 out of 5 - 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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei327 – 3271Nucleophile By similarity
Active sitei819 – 8191Proton acceptor By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri190 – 26273UBP-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

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
ORF Names:wu:fc61g08
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437: Chromosome 6

Organism-specific databases

ZFINiZDB-GENE-080724-7. usp13.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 860860Ubiquitin carboxyl-terminal hydrolase 13
PRO_0000418013Add
BLAST

Expressioni

Gene expression databases

BgeeiF1QFS9.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000095070.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini318 – 857540USP
Add
BLAST
Domaini635 – 67642UBA 1
Add
BLAST
Domaini710 – 75041UBA 2
Add
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.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

F1QFS9-1 [UniParc]FASTAAdd to Basket

« Hide

MATDLGELLV PYMPTIRVPR TGDRVFKSEC AFSYDSPESE GGLYVCMNSF    50
LGFGREHVER HYRKTGQSVY MHLKRHVKEK ATGAAGGAIP RRRNGKVFLD 100
LELNRDFNGD DYEYEDEAKL VIFPDHYEIP LPNIEELPAL VTIACDAVLN 150
APSPYKKQES DSWEEEIQVS RHARSLRQLD NGVRIPPSGW KCAKCEMREN 200
LWLNLTDGSV LCGKWFFDGS GGNGHALEHY RESNFPLAVK LNTITPDGAD 250
IYSFDEEEAV LDPHISEHLL HFGIDMLQMQ RTENGHHTDN HVQPRISDWE 300
VIQEAGLKLK PVYGSGYTGI KNLGNSCYLS TTMQVLFSIP EFQRAYAGNL 350
QRIFDYSPLD PTQDFNTQMA KLGHGLLSGQ YSKPPMKSEL IEQVMKEEHK 400
QQQQRGISPK MFKALVSKGH PEFSSNRQQD AHEFLLHLIN LVERNNSGSE 450
NPSDVFRFIV EERTQCCQSQ KVRYTQRVDY LMQLPVPLEA ASNREELIAY 500
EGKRKEAEEN MRPLPEVVRA RVPFTACLQA FTEPENVPDF WSSALQAKSA 550
GVKTSRFATF PEYMIVQLKK FTFGVDWVPK KLDMSVDVPD FLDLNRLRAT 600
GLQAGEEELP DLTPPIVIPE DTRDSSTNNS LESPEIDESS VMQLAEMGFP 650
LEACRKAVYY TGNMGAEMAF NWIIAHMEEP DFAEPLAVPT YMESDLPSPS 700
LPTTSALDNQ PPEESISILT SMGFPRHHTI QALKASNNNL ERALDWIFTH 750
PDCEDESEAM SDTADTEPND NSFSNANAHT DSSLSPDQDL SSPRVRDGPG 800
RYELFAFISH MGTSTMSGHY VCHIKKEGRW LIYNDHKVCL SERPPKDLGY 850
MYFYRRLSSC 860
Length:860
Mass (Da):97,452
Last modified:May 3, 2011 - v1
Checksum:i456C6827F7D0DCC1
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti731 – 7311Q → R in AAI41801. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AL928701 Genomic DNA. No translation available.
CU459215 Genomic DNA. No translation available.
BC141800 mRNA. Translation: AAI41801.1 .
RefSeqi NP_001091856.1. NM_001098386.1.
UniGenei Dr.115281.

3D structure databases

ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 7955.ENSDARP00000095070.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSDART00000065293 ; ENSDARP00000065292 ; ENSDARG00000079198 .
GeneIDi 558011.
KEGGi dre:558011.

Organism-specific databases

CTDi 8975.
ZFINi ZDB-GENE-080724-7. usp13.

Phylogenomic databases

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

Miscellaneous databases

NextBioi 20882266.

Gene expression databases

Bgeei F1QFS9.

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.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  2. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Embryo.

Entry informationi

Entry nameiUBP13_DANRE
AccessioniPrimary (citable) accession number: F1QFS9
Secondary accession number(s): A5D8T1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 13, 2012
Last sequence update: May 3, 2011
Last modified: May 14, 2014
This is version 26 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. 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