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F1QFS9

- UBP13_DANRE

UniProt

F1QFS9 - UBP13_DANRE

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Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

usp13

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 – 3271NucleophilePROSITE-ProRule annotation
Active sitei819 – 8191Proton acceptorPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri190 – 26273UBP-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
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 13PRO_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 – 857540USPAdd
BLAST
Domaini635 – 67642UBA 1PROSITE-ProRule annotationAdd
BLAST
Domaini710 – 75041UBA 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 fingeri190 – 26273UBP-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000000874.
InParanoidiF1QFS9.
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

        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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti731 – 7311Q → R in AAI41801. 1 PublicationCurated

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.

Cross-referencesi

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 .
RefSeqi NP_001091856.1. NM_001098386.1.
UniGenei Dr.115281.

3D structure databases

ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 7955.ENSDARP00000095070.

Protein family/group databases

MEROPSi C19.012.

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.
InParanoidi F1QFS9.
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: October 29, 2014
This is version 28 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