3RZU | pdb_00003rzu

The Crystal Structure of the Catalytic Domain of AMSH

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3rzud_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	JAB1/MPN domain	Catalytic domain of AMSH	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3rzue_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	JAB1/MPN domain	Catalytic domain of AMSH	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d3rzug_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	JAB1/MPN domain	Catalytic domain of AMSH	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3rzuf_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	JAB1/MPN domain	Catalytic domain of AMSH	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3rzuc_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	JAB1/MPN domain	Catalytic domain of AMSH	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3rzub_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	JAB1/MPN domain	Catalytic domain of AMSH	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3rzua_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	JAB1/MPN domain	JAB1/MPN domain	Catalytic domain of AMSH	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)
D	SCOP2B Superfamily	JAB1/MPN domain-like	8053262	3001105	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	JAB1/MPN domain-like	8053262	3001105	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	JAB1/MPN domain-like	8053262	3001105	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	JAB1/MPN domain-like	8053262	3001105	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	JAB1/MPN domain-like	8053262	3001105	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	JAB1/MPN domain-like	8053262	3001105	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	JAB1/MPN domain-like	8053262	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)
D	JAB_1	e3rzuD1	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)
E	JAB_1	e3rzuE1	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)
G	JAB_1	e3rzuG1	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)
F	JAB_1	e3rzuF1	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)
C	JAB_1	e3rzuC1	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	e3rzuB1	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	e3rzuA1	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)
D	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
E	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
G	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
F	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
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, D, E A, B, C, D, E, F, G	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, D, E A, B, C, D, E, F, G	STAM-binding protein	protein binding binding protein domain specific binding ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity metal-dependent deubiquitinase activity metallopeptidase activity K63-linked deubiquitinase activity cation binding ion binding protein binding binding protein domain specific binding ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity metal-dependent deubiquitinase activity metallopeptidase activity K63-linked deubiquitinase activity cation binding ion binding metal ion binding small molecule binding	neuron apoptotic process hippocampal neuron apoptotic process cellular process apoptotic process cell death programmed cell death mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division cell cycle mitotic cell cycle cell cycle process neuron apoptotic process hippocampal neuron apoptotic process cellular process apoptotic process cell death programmed cell death mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division cell cycle mitotic cell cycle cell cycle process cellular response to stimulus regulation of cellular process small GTPase-mediated signal transduction response to stimulus signaling negative regulation of signaling regulation of small GTPase mediated signal transduction negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction regulation of Ras protein signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of biological process regulation of signaling negative regulation of response to stimulus Ras protein signal transduction negative regulation of small GTPase mediated signal transduction biological regulation negative regulation of signal transduction negative regulation of Ras protein signal transduction regulation of response to stimulus regulation of cell communication protein deubiquitination protein K63-linked deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of biological process positive regulation of cellular process cell surface receptor signaling pathway via STAT cell surface receptor signaling pathway cell surface receptor signaling pathway via JAK-STAT regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death regulation of hippocampal neuron apoptotic process negative regulation of apoptotic process negative regulation of hippocampal neuron apoptotic process regulation of neuron apoptotic process proteolysis	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane cell division site cleavage furrow plasma membrane region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen early endosome endosome intracellular vesicle endomembrane system cytoplasmic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G	IPR044098	STAMBP/STALP-like, MPN domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR015063	USP8 dimerisation domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR037518	MPN domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G	Pharos: O95630	microcephaly-capillary malformation syndrome microcephaly brain disease epilepsy osteosarcoma Severe Congenital Microcephaly cerebrovascular disorder intellectual disability ovarian cancer developmental disability malignant glioma microlissencephaly capillary malformation-arteriovenous malformation syndrome glioblastoma

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.