Gene: Yod1

Basic information

Tag Content
Uniprot ID Q8CB27; B2RSW9; Q8BPM9; Q8CB24;
Entrez ID 226418
Genbank protein ID BAC35495.1; BAC29661.1; BAC29646.1; AAI39035.1;
Genbank nucleotide ID NM_178691.4
Ensembl protein ID ENSMUSP00000055318
Ensembl nucleotide ID ENSMUSG00000046404
Gene name Ubiquitin thioesterase OTU1
Gene symbol Yod1
Organism Mus musculus
NCBI taxa ID 10090
Cleft type
Developmental stage
Data sources Homology search
Reference
Functional description 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. May play a role in macroautophagy, regulating for instance the clearance of damaged lysosomes. May recruit PLAA, UBXN6 and VCP to damaged lysosome membranes decorated with K48-linked ubiquitin chains and remove these chains allowing autophagosome formation.
Sequence
MFGGAKGGHF GVPPAGYSGA VPQSEAGTKA GPAGGRPADT MWRVRCKAKG GTHLLQGLSS 60
RTRLRELQGQ IAAITGIAPG SQRILVGYPP ECLDLSDRDI TLGDLPIQSG DMLIVEEDQT 120
RPKASPAFSK YGAPSYVREA LPVLTRTAVP ADNSCLFTSV YYVVEGGVLN PACAPEMRRL 180
IAQIVASDPV LYSEAILGKT NEDYCDWIRR DDTWGGAIEI SILSKFYQCE ICVVDTQTVR 240
IDRFGEDAGY TKRVLLIYDG IHYDPLQRNF PDPDTPPLTI FSSNDDIVLV QALELADEAR 300
RKRQFTDVNR FTLRCMICQK GLTGQAEARD HARETGHTNF GEV 343

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Protein structural annotations

3D structure in PDB database


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Protein disorder information

Orthologous information

Relation Gene symbol Entrez ID UniProt ID Cleft type Developmental stage Species Evidence Details
1:1 orthologYOD1539931Q05B57Bos taurusPredictionMore>>
1:1 orthologYOD1490268E2R1N1Canis lupus familiarisPredictionMore>>
1:1 orthologYOD1102177549A0A452EJV7Capra hircusPredictionMore>>
1:1 orthologYOD155432Q5VVQ6Homo sapiensPublicationMore>>
1:1 orthologYod1226418Q8CB27Mus musculusPredictionMore>>
1:1 orthologYOD1469659G2HE61Pan troglodytesPredictionMore>>
1:1 orthologYOD1100520400F1RTR7Sus scrofaPredictionMore>>
1:1 orthologYOD1U3KMW5Oryctolagus cuniculusPredictionMore>>
1:1 orthologYod1363982Q32Q05Rattus norvegicusPredictionMore>>
1:1 orthologyod1550411Q567B1Danio rerioPredictionMore>>

Identified variants/mutations related to cleft phenotype

Gene symbol Significant Variants/SNPS Methods PubMed ID
YOD1c.54G>T; p.F18LWES and Sanger sequencing26449438

Other genetic variants/mutations

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Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID GO Term Evidence
GO:0003676 nucleic acid bindingIEA
GO:0004843 thiol-dependent ubiquitin-specific protease activityISS
GO:0004843 thiol-dependent ubiquitin-specific protease activityISO
GO:0004843 thiol-dependent ubiquitin-specific protease activityIBA
GO:0031625 ubiquitin protein ligase bindingISO
GO:0046872 metal ion bindingIEA
GO:1990380 Lys48-specific deubiquitinase activityISO

GO:Biological Process

GO ID GO Term Evidence
GO:0016236 macroautophagyISS
GO:0016236 macroautophagyISO
GO:0016579 protein deubiquitinationIBA
GO:0030433 ubiquitin-dependent ERAD pathwayISS
GO:0030433 ubiquitin-dependent ERAD pathwayISO
GO:0030433 ubiquitin-dependent ERAD pathwayIBA
GO:0030968 endoplasmic reticulum unfolded protein responseISS
GO:0030968 endoplasmic reticulum unfolded protein responseISO
GO:0030968 endoplasmic reticulum unfolded protein responseIBA
GO:0035523 protein K29-linked deubiquitinationISS
GO:0035523 protein K29-linked deubiquitinationISO
GO:0035871 protein K11-linked deubiquitinationISS
GO:0035871 protein K11-linked deubiquitinationISO
GO:0070536 protein K63-linked deubiquitinationISS
GO:0070536 protein K63-linked deubiquitinationISO
GO:0071108 protein K48-linked deubiquitinationISS
GO:0071108 protein K48-linked deubiquitinationISO
GO:1904153 negative regulation of retrograde protein transport, ER to cytosolISO
GO:1990167 protein K27-linked deubiquitinationISS
GO:1990167 protein K27-linked deubiquitinationISO
GO:1990168 protein K33-linked deubiquitinationISS
GO:1990168 protein K33-linked deubiquitinationISO

GO:Cellular Component

GO ID GO Term Evidence
GO:0005737 cytoplasmISS
GO:0005737 cytoplasmISO
GO:0005829 cytosolIBA

Reactome Pathway

Reactome ID Reactome Term Evidence
R-MMU-392499 Metabolism of proteinsIEA
R-MMU-5688426 DeubiquitinationIEA
R-MMU-5689896 Ovarian tumor domain proteasesIEA
R-MMU-597592 Post-translational protein modificationIEA

Functional annotations

Keywords

Keyword ID Keyword Term
KW-0002 3D-structure
KW-0963 Cytoplasm
KW-0378 Hydrolase
KW-0479 Metal-binding
KW-0645 Protease
KW-1185 Reference proteome
KW-0788 Thiol protease
KW-0833 Ubl conjugation pathway
KW-0834 Unfolded protein response
KW-0862 Zinc
KW-0863 Zinc-finger

Interpro

InterPro ID InterPro Term
IPR039138 OTU1_2_3
IPR003323 OTU_dom
IPR038765 Papain-like_cys_pep_sf
IPR029071 Ubiquitin-like_domsf
IPR013087 Znf_C2H2_type

PROSITE

PROSITE ID PROSITE Term
PS50802 OTU
PS00028 ZINC_FINGER_C2H2_1

Pfam

Pfam ID Pfam Term
PF02338 OTU

Protein-miRNA interaction