2KZR | pdb_00002kzr

Solution NMR Structure of Ubiquitin thioesterase OTU1 (EC 3.1.2.-) from Mus musculus, Northeast Structural Genomics Consortium Target MmT2A

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	OTU1_UBXL	e2kzrA1	A: a/b three-layered sandwiches	X: Cystatin-like	H: Cytochrome b5-like heme/steroid binding domain	T: Cytochrome b5-like heme/steroid binding domain	F: OTU1_UBXL	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21403	OTU1, UBXL domain (OTU1_UBXL)	OTU1, UBXL domain	OTU1 is a deubiquitinating enzyme that may play an important regulatory role at the level of protein turnover by preventing degradation. This entry represents the ubiquitin regulatory X-like (UBXL) which interacts with the N-terminal domain of VCP [1 ...	OTU1 is a deubiquitinating enzyme that may play an important regulatory role at the level of protein turnover by preventing degradation. This entry represents the ubiquitin regulatory X-like (UBXL) which interacts with the N-terminal domain of VCP [1] and removes ubiquitin chains using the OTU domain. This domain is also found in VCIP1, a known UBXL-containing protein that functions in p97/p47-mediated Golgi reassembly.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin thioesterase OTU1	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity K48-linked deubiquitinase activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity K48-linked deubiquitinase activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	protein deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification protein K27-linked deubiquitination metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal catabolic process macroautophagy protein deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification protein K27-linked deubiquitination metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal catabolic process macroautophagy autophagy process utilizing autophagic mechanism protein K11-linked deubiquitination cellular response to stimulus response to stimulus proteasomal protein catabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress response to endoplasmic reticulum stress protein K48-linked deubiquitination protein K29-linked deubiquitination protein K33-linked deubiquitination negative regulation of protein transport regulation of localization establishment of protein localization regulation of cellular process negative regulation of biological process negative regulation of intracellular protein transport negative regulation of transport localization establishment of localization in cell intracellular protein localization negative regulation of protein exit from endoplasmic reticulum regulation of intracellular transport regulation of biological process negative regulation of establishment of protein localization intracellular transport establishment of localization regulation of intracellular protein transport intracellular protein transport regulation of protein exit from endoplasmic reticulum protein exit from endoplasmic reticulum cellular localization regulation of protein localization transport regulation of retrograde protein transport, ER to cytosol negative regulation of cellular process negative regulation of protein localization negative regulation of intracellular transport endoplasmic reticulum to cytosol transport regulation of transport biological regulation regulation of establishment of protein localization regulation of protein transport protein transport regulation of cellular localization macromolecule localization retrograde protein transport, ER to cytosol negative regulation of retrograde protein transport, ER to cytosol protein K63-linked deubiquitination cellular response to topologically incorrect protein signaling endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein intracellular signal transduction cell communication response to topologically incorrect protein signal transduction	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013087	Zinc finger C2H2-type	Domain
A	IPR003323	OTU domain	Domain
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR057766	OTU1-like, C-terminal C2H2-type zinc finger	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A	IPR048857	OTU1, Ubl domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.