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Protein

Ubiquitin thioesterase OTU1

Gene

yod1

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by triming the ubiquitin chain on the associated substrate to facilitate their threading through the VCP/p97 pore. Ubiquitin moieties on substrates may present a steric impediment to the threading process when the substrate is transferred to the VCP pore and threaded through VCP's axial channel. Mediates deubiquitination of 'Lys-27'-, 'Lys-29'- and 'Lys-33'-linked polyubiquitin chains. Also able to hydrolyze 'Lys-11'-linked ubiquitin chains. Cleaves both polyubiquitin and di-ubiquitin (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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei110 – 1101By similarity
Active sitei113 – 1131NucleophileBy similarity
Binding sitei219 – 2191Substrate; via carbonyl oxygenBy similarity
Active sitei220 – 2201By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri271 – 29525C2H2-typeAdd
BLAST

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. ubiquitin-specific protease activity Source: UniProtKB

GO - Biological processi

  1. endoplasmic reticulum unfolded protein response Source: UniProtKB
  2. ER-associated ubiquitin-dependent protein catabolic process Source: UniProtKB
  3. protein K11-linked deubiquitination Source: UniProtKB
  4. protein K27-linked deubiquitination Source: UniProtKB
  5. protein K29-linked deubiquitination Source: UniProtKB
  6. protein K33-linked deubiquitination Source: UniProtKB
  7. protein K48-linked deubiquitination Source: UniProtKB
  8. protein K63-linked deubiquitination Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway, Unfolded protein response

Keywords - Ligandi

Metal-binding, Zinc

Protein family/group databases

MEROPSiC85.007.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin thioesterase OTU1 (EC:3.4.19.12)
Gene namesi
Name:yod1
ORF Names:zgc:112182
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437 Componenti: Chromosome 11

Organism-specific databases

ZFINiZDB-GENE-050417-217. yod1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 301301Ubiquitin thioesterase OTU1PRO_0000282360Add
BLAST

Proteomic databases

PRIDEiQ567B1.

Expressioni

Gene expression databases

BgeeiQ567B1.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000003565.

Structurei

3D structure databases

ProteinModelPortaliQ567B1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini102 – 227126OTUPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni5 – 8379UBX-likeAdd
BLAST
Regioni107 – 1137Cys-loopBy similarity
Regioni166 – 17611Variable-loopBy similarityAdd
BLAST
Regioni216 – 2205His-loopBy similarity
Regioni244 – 2496S2 siteBy similarity

Domaini

The C2H2-type zinc finger mediates specificity for 'Lys-27'-, 'Lys-29'- and 'Lys-33'-linked polyubiquitin chains but not for 'Lys-11'-linked ubiquitin chains. Selectivity for 'Lys-11'-linked ubiquitin chains is provided by recognition of the sequence surrounding 'Lys-11' in ubiquitin. The S2 site region provides specificity for longer 'Lys-11'-linked ubiquitin chains (By similarity).By similarity

Sequence similaritiesi

Contains 1 C2H2-type zinc finger.Curated
Contains 1 OTU domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri271 – 29525C2H2-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG5539.
GeneTreeiENSGT00390000009989.
HOGENOMiHOG000193461.
HOVERGENiHBG097006.
InParanoidiQ567B1.
KOiK13719.
OMAiYDPLERR.
OrthoDBiEOG7J1808.
PhylomeDBiQ567B1.
TreeFamiTF323700.

Family and domain databases

InterProiIPR003323. OTU.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
[Graphical view]
PfamiPF02338. OTU. 1 hit.
PF14560. Ubiquitin_2. 1 hit.
[Graphical view]
SMARTiSM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS50802. OTU. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q567B1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLRLRCKAKN GTHLMQGLTH QSCVQELKDK IEELTGIPCD VQKIMVGYPP
60 70 80 90 100
SSLDLRNGEA HLKDYPIKSG DTLIVEEEKN KPKPPVQPTV TKGPSFEVTP
110 120 130 140 150
VVERRVVPAD NSCLFTSVNY VMEGGVYDPA CASEMRGLIA QIVASDPTAY
160 170 180 190 200
SEAVLGKTNE EYCTWIRRDD TWGGAIEVSI LSKFYQCEIC VVDTQTVRVD
210 220 230 240 250
RFGEDAGYTK RVLLIYDGIH YDPLQKVLPG SDVPAQTVFS TVDDVILAQA
260 270 280 290 300
LELADEARRK RQFTDVNRFA LRCMVCQTGL VGQKEAREHA KETGHTNFGE

V
Length:301
Mass (Da):33,486
Last modified:May 9, 2005 - v1
Checksum:i70D85A2694B56198
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC093247 mRNA. Translation: AAH93247.1.
RefSeqiNP_001017716.1. NM_001017716.2.
UniGeneiDr.104832.

Genome annotation databases

EnsembliENSDART00000023388; ENSDARP00000003565; ENSDARG00000008542.
GeneIDi550411.
KEGGidre:550411.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC093247 mRNA. Translation: AAH93247.1.
RefSeqiNP_001017716.1. NM_001017716.2.
UniGeneiDr.104832.

3D structure databases

ProteinModelPortaliQ567B1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000003565.

Protein family/group databases

MEROPSiC85.007.

Proteomic databases

PRIDEiQ567B1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000023388; ENSDARP00000003565; ENSDARG00000008542.
GeneIDi550411.
KEGGidre:550411.

Organism-specific databases

CTDi55432.
ZFINiZDB-GENE-050417-217. yod1.

Phylogenomic databases

eggNOGiCOG5539.
GeneTreeiENSGT00390000009989.
HOGENOMiHOG000193461.
HOVERGENiHBG097006.
InParanoidiQ567B1.
KOiK13719.
OMAiYDPLERR.
OrthoDBiEOG7J1808.
PhylomeDBiQ567B1.
TreeFamiTF323700.

Miscellaneous databases

NextBioi20879660.
PROiQ567B1.

Gene expression databases

BgeeiQ567B1.

Family and domain databases

InterProiIPR003323. OTU.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
[Graphical view]
PfamiPF02338. OTU. 1 hit.
PF14560. Ubiquitin_2. 1 hit.
[Graphical view]
SMARTiSM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS50802. OTU. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Embryo.

Entry informationi

Entry nameiOTU1_DANRE
AccessioniPrimary (citable) accession number: Q567B1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 2, 2007
Last sequence update: May 9, 2005
Last modified: January 6, 2015
This is version 63 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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.