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Protein

Ubiquitin thioesterase OTU1

Gene

Yod1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein 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).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei152By similarity1
Active sitei155NucleophileBy similarity1
Binding sitei261Substrate; via carbonyl oxygenBy similarity1
Active sitei262By similarity1
Active sitei337By similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri313 – 337C2H2-typeAdd BLAST25

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway, Unfolded protein response

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-5689896. Ovarian tumor domain proteases.

Protein family/group databases

MEROPSiC85.007.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin thioesterase OTU1 (EC:3.4.19.12By similarity)
Gene namesi
Name:Yod1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 1

Organism-specific databases

MGIiMGI:2442596. Yod1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002823571 – 343Ubiquitin thioesterase OTU1Add BLAST343

Proteomic databases

MaxQBiQ8CB27.
PaxDbiQ8CB27.
PRIDEiQ8CB27.

PTM databases

iPTMnetiQ8CB27.
PhosphoSitePlusiQ8CB27.

Expressioni

Gene expression databases

BgeeiENSMUSG00000046404.
GenevisibleiQ8CB27. MM.

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

GO - Molecular functioni

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000055318.

Structurei

Secondary structure

1343
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi44 – 48Combined sources5
Beta strandi51 – 55Combined sources5
Helixi64 – 74Combined sources11
Turni79 – 81Combined sources3
Beta strandi85 – 88Combined sources4
Turni102 – 104Combined sources3
Beta strandi112 – 114Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KZRNMR-A42-126[»]
ProteinModelPortaliQ8CB27.
SMRiQ8CB27.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini144 – 269OTUPROSITE-ProRule annotationAdd BLAST126

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni45 – 123UBX-likeAdd BLAST79
Regioni149 – 155Cys-loopBy similarity7
Regioni208 – 218Variable-loopBy similarityAdd BLAST11
Regioni258 – 262His-loopBy similarity5
Regioni286 – 291S2 siteBy similarity6

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)DescriptionActionsGraphical viewLength
Zinc fingeri313 – 337C2H2-typeAdd BLAST25

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3288. Eukaryota.
COG5539. LUCA.
GeneTreeiENSGT00390000009989.
HOGENOMiHOG000193461.
HOVERGENiHBG097006.
InParanoidiQ8CB27.
KOiK13719.
OMAiGGHFGVP.
OrthoDBiEOG091G0CA6.
PhylomeDBiQ8CB27.
TreeFamiTF323700.

Family and domain databases

InterProiIPR003323. OTU_dom.
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.

Q8CB27-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFGGAKGGHF GVPPAGYSGA VPQSEAGTKA GPAGGRPADT MWRVRCKAKG
60 70 80 90 100
GTHLLQGLSS RTRLRELQGQ IAAITGIAPG SQRILVGYPP ECLDLSDRDI
110 120 130 140 150
TLGDLPIQSG DMLIVEEDQT RPKASPAFSK YGAPSYVREA LPVLTRTAVP
160 170 180 190 200
ADNSCLFTSV YYVVEGGVLN PACAPEMRRL IAQIVASDPV LYSEAILGKT
210 220 230 240 250
NEDYCDWIRR DDTWGGAIEI SILSKFYQCE ICVVDTQTVR IDRFGEDAGY
260 270 280 290 300
TKRVLLIYDG IHYDPLQRNF PDPDTPPLTI FSSNDDIVLV QALELADEAR
310 320 330 340
RKRQFTDVNR FTLRCMICQK GLTGQAEARD HARETGHTNF GEV
Length:343
Mass (Da):37,485
Last modified:March 1, 2003 - v1
Checksum:iC07F3F69F1CA86D8
GO

Sequence cautioni

The sequence BAC29661 differs from that shown. Reason: Frameshift at position 8.Curated
The sequence BAC35495 differs from that shown. Reason: Erroneous termination at position 344. Translated as stop.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK036938 mRNA. Translation: BAC29646.1.
AK036991 mRNA. Translation: BAC29661.1. Frameshift.
AK053730 mRNA. Translation: BAC35495.1. Sequence problems.
BC139034 mRNA. Translation: AAI39035.1.
CCDSiCCDS48351.1.
RefSeqiNP_848806.2. NM_178691.4.
UniGeneiMm.106553.
Mm.392991.
Mm.491203.

Genome annotation databases

EnsembliENSMUST00000049813; ENSMUSP00000055318; ENSMUSG00000046404.
GeneIDi226418.
KEGGimmu:226418.
UCSCiuc007cmh.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK036938 mRNA. Translation: BAC29646.1.
AK036991 mRNA. Translation: BAC29661.1. Frameshift.
AK053730 mRNA. Translation: BAC35495.1. Sequence problems.
BC139034 mRNA. Translation: AAI39035.1.
CCDSiCCDS48351.1.
RefSeqiNP_848806.2. NM_178691.4.
UniGeneiMm.106553.
Mm.392991.
Mm.491203.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KZRNMR-A42-126[»]
ProteinModelPortaliQ8CB27.
SMRiQ8CB27.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000055318.

Protein family/group databases

MEROPSiC85.007.

PTM databases

iPTMnetiQ8CB27.
PhosphoSitePlusiQ8CB27.

Proteomic databases

MaxQBiQ8CB27.
PaxDbiQ8CB27.
PRIDEiQ8CB27.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000049813; ENSMUSP00000055318; ENSMUSG00000046404.
GeneIDi226418.
KEGGimmu:226418.
UCSCiuc007cmh.2. mouse.

Organism-specific databases

CTDi55432.
MGIiMGI:2442596. Yod1.

Phylogenomic databases

eggNOGiKOG3288. Eukaryota.
COG5539. LUCA.
GeneTreeiENSGT00390000009989.
HOGENOMiHOG000193461.
HOVERGENiHBG097006.
InParanoidiQ8CB27.
KOiK13719.
OMAiGGHFGVP.
OrthoDBiEOG091G0CA6.
PhylomeDBiQ8CB27.
TreeFamiTF323700.

Enzyme and pathway databases

ReactomeiR-MMU-5689896. Ovarian tumor domain proteases.

Miscellaneous databases

PROiQ8CB27.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000046404.
GenevisibleiQ8CB27. MM.

Family and domain databases

InterProiIPR003323. OTU_dom.
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...

Entry informationi

Entry nameiOTU1_MOUSE
AccessioniPrimary (citable) accession number: Q8CB27
Secondary accession number(s): B2RSW9, Q8BPM9, Q8CB24
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: March 1, 2003
Last modified: November 30, 2016
This is version 114 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.