4MSJ | pdb_00004msj

Crystal structure of S. pombe AMSH-like protease SST2 catalytic domain from P212121 space group

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	JAB1/MPN domain-like	8053259	3001105	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	JAB1/MPN domain-like	8053259	3001105	SCOP2B (2022-06-29)
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)
C	JAB_1	e4msjC1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: JAB_1	ECOD (1.6)
B	JAB_1	e4msjB1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: JAB_1	ECOD (1.6)
A	JAB_1	e4msjA1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: JAB_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
B	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
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, B, C	PF01398	JAB1/Mov34/MPN/PAD-1 ubiquitin protease (JAB)	JAB1/Mov34/MPN/PAD-1 ubiquitin protease	Proteins with this domain are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This domain is known as the MPN domain [3] and PAD-1-like domain [4], JABP1 domain [5] or J ...	Proteins with this domain are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This domain is known as the MPN domain [3] and PAD-1-like domain [4], JABP1 domain [5] or JAMM domain [7]. These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signalling and protein turnover pathways in eukaryotes [7]. Versions of the domain in prokaryotic cognates of the ubiquitin-modification pathway are shown to have a similar role, and the archaeal protein from Haloferax volcanii is found to cleave ubiquitin-like small archaeal modifier proteins (SAMP1/2) from protein conjugates [8,9].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	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 establishment of protein localization nitrogen compound transport protein targeting establishment of protein localization to vacuole protein localization to vacuole establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization intracellular protein localization cytoplasm to vacuole targeting by the NVT pathway protein targeting to vacuole intracellular protein transport catabolic process proteolysis involved in protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process proteolysis protein metabolic process protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway primary metabolic process protein catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process metabolic process macromolecule metabolic process protein deubiquitination protein K63-linked deubiquitination protein modification by small protein removal macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation or removal	cellular anatomical structure membrane 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR015063	USP8 dimerisation domain	Domain
A, B, C	IPR044098	STAMBP/STALP-like, MPN domain	Domain
A, B, C	IPR037518	MPN domain	Domain
A, B, C	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 R01GM157729.