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Protein

Ubiquitin thioesterase OTU1

Gene

Yod1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 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 sitei152 – 1521By similarity
Active sitei155 – 1551NucleophileBy similarity
Binding sitei261 – 2611Substrate; via carbonyl oxygenBy similarity
Active sitei262 – 2621By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri313 – 33725C2H2-typeAdd
BLAST

GO - Molecular functioni

  1. Lys48-specific deubiquitinase activity Source: Ensembl
  2. metal ion binding Source: UniProtKB-KW
  3. 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
Synonyms:Hshin7
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494: Chromosome 13

Organism-specific databases

RGDi1359726. Yod1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 343343Ubiquitin thioesterase OTU1PRO_0000282358Add
BLAST

Proteomic databases

PRIDEiQ32Q05.

PTM databases

PhosphoSiteiQ32Q05.

Expressioni

Gene expression databases

GenevestigatoriQ32Q05.

Interactioni

Subunit structurei

Interacts with VCP; the interaction is direct. Interacts with FAF2/UBXD8. Interacts with DERL1; however interaction is dependent on the UBAX-like region, suggesting that it may be indirect (By similarity).By similarity

Protein-protein interaction databases

BioGridi264526. 1 interaction.
STRINGi10116.ENSRNOP00000031836.

Structurei

3D structure databases

ProteinModelPortaliQ32Q05.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini144 – 269126OTUPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni45 – 12379UBX-likeAdd
BLAST
Regioni149 – 1557Cys-loopBy similarity
Regioni208 – 21811Variable-loopBy similarityAdd
BLAST
Regioni258 – 2625His-loopBy similarity
Regioni286 – 2916S2 siteBy similarity

Domaini

The UBAX-like region mediates the interaction with VCP.By similarity
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 fingeri313 – 33725C2H2-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG5539.
GeneTreeiENSGT00390000009989.
HOGENOMiHOG000193461.
HOVERGENiHBG097006.
InParanoidiQ32Q05.
KOiK13719.
OMAiSNAEYCA.
OrthoDBiEOG7J1808.
PhylomeDBiQ32Q05.
TreeFamiTF323700.

Family and domain databases

InterProiIPR003323. OTU.
IPR029071. Ubiquitin-rel_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
[Graphical view]
PfamiPF02338. OTU. 1 hit.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 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.

Q32Q05-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MFGGAKGGHF GVPPAGCSGA VSQAAAGTKA GPAGGRPADT MWRLRCKAKG
60 70 80 90 100
GTHVLQGLSN RTRLRELQGQ IAAITGIAPG SQRILVGYPP ECLDLSDRDI
110 120 130 140 150
TLGDLPIQSG DMLIVEEDQT RPKASPAFSK HGAPSYVRET LPVLTRTAVP
160 170 180 190 200
ADNSCLFTSV YYVVEGGVLN PACAPEMRRL IAQIVASDPD LYSEAILGKT
210 220 230 240 250
NEEYCDWIRR DDTWGGAIEI SILSKFYQCE ICVVDTQTVR IDRFGEDAGY
260 270 280 290 300
TKRVLLIYDG IHYDPLQRNF PDPDTPPLTI FSSNDDIVLV QALELADEAR
310 320 330 340
RKRQFTDVNR FTLRCMLCQK GLTGQAEARD HARETGHTNF GEV
Length:343
Mass (Da):37,402
Last modified:December 6, 2005 - v1
Checksum:iAD23FFBF8A4AC502
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC107904 mRNA. Translation: AAI07905.1.
BN000319 mRNA. Translation: CAE48374.1.
RefSeqiNP_001008889.1. NM_001008889.1.
UniGeneiRn.212904.

Genome annotation databases

EnsembliENSRNOT00000030476; ENSRNOP00000031836; ENSRNOG00000025704.
GeneIDi363982.
KEGGirno:363982.
UCSCiRGD:1359726. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC107904 mRNA. Translation: AAI07905.1.
BN000319 mRNA. Translation: CAE48374.1.
RefSeqiNP_001008889.1. NM_001008889.1.
UniGeneiRn.212904.

3D structure databases

ProteinModelPortaliQ32Q05.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi264526. 1 interaction.
STRINGi10116.ENSRNOP00000031836.

Protein family/group databases

MEROPSiC85.007.

PTM databases

PhosphoSiteiQ32Q05.

Proteomic databases

PRIDEiQ32Q05.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000030476; ENSRNOP00000031836; ENSRNOG00000025704.
GeneIDi363982.
KEGGirno:363982.
UCSCiRGD:1359726. rat.

Organism-specific databases

CTDi55432.
RGDi1359726. Yod1.

Phylogenomic databases

eggNOGiCOG5539.
GeneTreeiENSGT00390000009989.
HOGENOMiHOG000193461.
HOVERGENiHBG097006.
InParanoidiQ32Q05.
KOiK13719.
OMAiSNAEYCA.
OrthoDBiEOG7J1808.
PhylomeDBiQ32Q05.
TreeFamiTF323700.

Miscellaneous databases

NextBioi684590.
PROiQ32Q05.

Gene expression databases

GenevestigatoriQ32Q05.

Family and domain databases

InterProiIPR003323. OTU.
IPR029071. Ubiquitin-rel_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
[Graphical view]
PfamiPF02338. OTU. 1 hit.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS50802. OTU. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Testis.
  2. "A genomic analysis of rat proteases and protease inhibitors."
    Puente X.S., Lopez-Otin C.
    Genome Res. 14:609-622(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.

Entry informationi

Entry nameiOTU1_RAT
AccessioniPrimary (citable) accession number: Q32Q05
Secondary accession number(s): Q6IE74
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: December 6, 2005
Last modified: January 7, 2015
This is version 64 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.