4PQT

Insights into the mechanism of deubiquitination by JAMM deubiquitinases from co-crystal structures of enzyme with substrate and product

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4pqtb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	JAB1/MPN domain-like	8053259	3001105	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF01398	e4pqtA1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: PF01398	ECOD (1.6)
B	PF00240	e4pqtB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01398	JAB1/Mov34/MPN/PAD-1 ubiquitin protease (JAB)	JAB1/Mov34/MPN/PAD-1 ubiquitin protease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	AMSH-like protease sst2	K63-linked deubiquitinase activity ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity protein binding binding ubiquitin binding ubiquitin-like protein binding polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding K63-linked deubiquitinase activity ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity protein binding binding ubiquitin binding ubiquitin-like protein binding polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding metal-dependent deubiquitinase activity metallopeptidase activity	localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway endosome transport via multivesicular body sorting pathway localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway endosome transport via multivesicular body sorting pathway protein localization establishment of protein localization catabolic process nitrogen compound transport proteolysis involved in protein catabolic process establishment of protein localization to vacuole macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process proteolysis cellular macromolecule localization protein metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process organic substance transport protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway primary metabolic process protein localization to vacuole protein catabolic process establishment of protein localization to organelle protein transport modification-dependent protein catabolic process macromolecule localization protein localization to organelle ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process metabolic process macromolecule metabolic process organic substance catabolic process intracellular protein transport protein targeting cytoplasm to vacuole targeting by the NVT pathway protein targeting to vacuole	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle cell division site
B	Protein UBBP4	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015063	USP8 dimerisation domain	Domain
A	IPR044098	STAMBP/STALP-like, MPN domain	Domain
A	IPR037518	MPN domain	Domain
A	IPR000555	JAB1/MPN/MOV34 metalloenzyme 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 R01GM133198.