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Protein

Ubiquitin thioesterase OTU1

Gene

yod1

Organism
Xenopus laevis (African clawed frog)
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 sitei113 – 1131By similarity
Active sitei116 – 1161NucleophileBy similarity
Binding sitei222 – 2221Substrate; via carbonyl oxygenBy similarity
Active sitei223 – 2231By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri274 – 29825C2H2-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
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-998963. yod1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 304304Ubiquitin thioesterase OTU1PRO_0000282361Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliQ0IH43.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini105 – 230126OTUPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni5 – 8379UBX-likeAdd
BLAST
Regioni110 – 1167Cys-loopBy similarity
Regioni169 – 17911Variable-loopBy similarityAdd
BLAST
Regioni219 – 2235His-loopBy similarity
Regioni247 – 2526S2 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 fingeri274 – 29825C2H2-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOVERGENiHBG097006.
KOiK13719.

Family and domain databases

InterProiIPR003323. OTU.
IPR029071. Ubiquitin-rel_dom.
IPR007087. Znf_C2H2.
[Graphical view]
PfamiPF02338. OTU. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS50802. OTU. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q0IH43-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLRLRCKTRE GTQLLQGLTD RSSIRELQER IAGVTGISGP LQRVMVGFPP
60 70 80 90 100
LSLDLSDEEA TLKNMSIKSG DTLIVEEDKS KLRSATPPVS KTDIGNWNAP
110 120 130 140 150
AQPTIVRRVV PADNSCLFTS IYYVVEGGVY DPACALEMRS LIAEIVASDQ
160 170 180 190 200
SAYCDAVLGK SNEEYCSWIR REDTWGGAIE VSILSKFYQC EICVVDTQTV
210 220 230 240 250
RIDRFGEDSG YTKRVLLIYD GIHYDPLQRQ FPDPDMPPMT VFSTTDDEAL
260 270 280 290 300
VQAMELADDA RKKRQFTDVN QFALRCMACQ KGLTGQSAAR DHAKETGHTN

FGEV
Length:304
Mass (Da):33,807
Last modified:October 3, 2006 - v1
Checksum:i4A0FEDC19A47E0DE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC123321 mRNA. Translation: AAI23322.1.
RefSeqiNP_001090389.1. NM_001096920.1.
UniGeneiXl.59889.

Genome annotation databases

GeneIDi779300.
KEGGixla:779300.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC123321 mRNA. Translation: AAI23322.1.
RefSeqiNP_001090389.1. NM_001096920.1.
UniGeneiXl.59889.

3D structure databases

ProteinModelPortaliQ0IH43.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC85.007.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi779300.
KEGGixla:779300.

Organism-specific databases

CTDi55432.
XenbaseiXB-GENE-998963. yod1.

Phylogenomic databases

HOVERGENiHBG097006.
KOiK13719.

Family and domain databases

InterProiIPR003323. OTU.
IPR029071. Ubiquitin-rel_dom.
IPR007087. Znf_C2H2.
[Graphical view]
PfamiPF02338. OTU. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS50802. OTU. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. NIH - Xenopus Gene Collection (XGC) project
    Submitted (SEP-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Ovary.

Entry informationi

Entry nameiOTU1_XENLA
AccessioniPrimary (citable) accession number: Q0IH43
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: October 3, 2006
Last modified: January 7, 2015
This is version 47 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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.