1ZSQ

Crystal Structure of MTMR2 in complex with phosphatidylinositol 3-phosphate

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)
A	d1zsqa1	All beta proteins	PH domain-like barrel	PH domain-like	GRAM domain	Myotubularin-related protein 2, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1zsqa2	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Myotubularin-like phosphatases	Myotubularin-related protein 2, C-terminal domain	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	SCOP2 Family	GRAM domain	8023855	4000903	SCOP2 (2022-06-29)
A	SCOP2 Family	Myotubularin-like phosphatases	8023856	4001084	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PH domain-like	8036235	3000134	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	(Phosphotyrosine protein) phosphatases II	8036236	3000304	SCOP2 (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	GRAM	e1zsqA1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: GRAM	ECOD (1.6)
A	Myotub-related	e1zsqA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: Myotub-related	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02893	GRAM domain (GRAM)	GRAM domain	The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Note the alignment is lacking the last two beta strands and alpha helix.	Domain
A	PF06602	Myotubularin-like phosphatase domain (Myotub-related)	Myotubularin-like phosphatase domain	This family represents the phosphatase domain within eukaryotic myotubularin-related proteins. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate [1]. M ...	This family represents the phosphatase domain within eukaryotic myotubularin-related proteins. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate [1]. Mutations in gene encoding myotubularin-related proteins have been associated with disease [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Myotubularin-related protein 2	phosphoric ester hydrolase activity phosphatidylinositol-3-phosphate phosphatase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity phosphatidylinositol phosphate phosphatase activity catalytic activity phosphatidylinositol monophosphate phosphatase activity phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity phosphatidylinositol bisphosphate phosphatase activity phosphatidylinositol-3,5-bisphosphate phosphatase activity identical protein binding protein binding binding	phosphatidylinositol metabolic process dephosphorylation cellular metabolic process glycerophospholipid metabolic process lipid modification primary metabolic process phospholipid metabolic process organophosphate metabolic process phosphatidylinositol dephosphorylation phospholipid dephosphorylation phosphate-containing compound metabolic process cellular lipid metabolic process metabolic process cellular process phosphatidylinositol metabolic process dephosphorylation cellular metabolic process glycerophospholipid metabolic process lipid modification primary metabolic process phospholipid metabolic process organophosphate metabolic process phosphatidylinositol dephosphorylation phospholipid dephosphorylation phosphate-containing compound metabolic process cellular lipid metabolic process metabolic process cellular process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process developmental process multicellular organismal process cellular component assembly involved in morphogenesis nervous system development myelin assembly cellular component organization cellular component biogenesis myelination anatomical structure morphogenesis multicellular organism development cellular anatomical entity morphogenesis cellular component assembly axon ensheathment ensheathment of neurons anatomical structure formation involved in morphogenesis anatomical structure development cellular component organization or biogenesis system development regulation of localization import into cell regulation of cellular process regulation of cellular component organization receptor internalization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis regulation of receptor internalization vesicle-mediated transport localization negative regulation of cellular process regulation of endocytosis regulation of biological process negative regulation of cellular component organization regulation of transport negative regulation of receptor-mediated endocytosis regulation of receptor-mediated endocytosis biological regulation regulation of vesicle-mediated transport establishment of localization endocytosis receptor-mediated endocytosis negative regulation of receptor internalization negative regulation of nervous system process system process regulation of developmental process regulation of myelination regulation of system process regulation of nervous system development regulation of multicellular organismal process regulation of multicellular organismal development nervous system process regulation of nervous system process negative regulation of myelination negative regulation of multicellular organismal process regulation of lipid metabolic process regulation of primary metabolic process regulation of phosphate metabolic process regulation of dephosphorylation regulation of phospholipid metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of phosphatidylinositol dephosphorylation regulation of phosphorus metabolic process macromolecule metabolic process regulation of metabolic process glycerophospholipid biosynthetic process cellular biosynthetic process lipid biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process biosynthetic process glycerolipid biosynthetic process organophosphate biosynthetic process dendritic spine maintenance dendritic spine organization postsynapse organization plasma membrane bounded cell projection organization cell projection organization cellular component maintenance cell junction organization neuron projection organization synapse organization positive regulation of early endosome to late endosome transport cellular localization positive regulation of biological process establishment of localization in cell positive regulation of intracellular transport positive regulation of cellular process regulation of intracellular transport intracellular transport endosomal transport vesicle-mediated transport between endosomal compartments regulation of early endosome to late endosome transport early endosome to late endosome transport positive regulation of transport regulation of cellular localization cellular response to stimulus regulation of postsynaptic membrane potential response to stimulus signaling modulation of chemical synaptic transmission regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication synaptic signaling modulation of excitatory postsynaptic potential signal transduction regulation of biological quality trans-synaptic signaling regulation of signaling cell surface receptor signaling pathway cell-cell signaling chemical synaptic transmission regulation of trans-synaptic signaling regulation of response to stimulus negative regulation of excitatory postsynaptic potential anterograde trans-synaptic signaling regulation of cell communication excitatory postsynaptic potential regulation of membrane potential negative regulation of cellular catabolic process receptor catabolic process catabolic process macromolecule catabolic process negative regulation of cellular metabolic process cellular catabolic process receptor metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process negative regulation of receptor catabolic process negative regulation of metabolic process regulation of catabolic process regulation of receptor catabolic process regulation of cellular catabolic process cellular developmental process cell development generation of neurons neurogenesis neuron differentiation cell differentiation neuron development	membrane cellular anatomical entity cell periphery plasma membrane synapse cell junction plasma membrane region synaptic membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle membrane cellular anatomical entity cell periphery plasma membrane synapse cell junction plasma membrane region synaptic membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle intracellular membrane-bounded organelle somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection endosome membrane early endosome endosome intracellular vesicle early endosome membrane endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle membrane neuron spine dendritic spine postsynapse postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse perinuclear region of cytoplasm vacuolar membrane vacuole axon transport vesicle presynapse synaptic vesicle secretory vesicle exocytic vesicle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR004182	GRAM domain	Domain
A	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A	IPR010569	Myotubularin-like, phosphatase domain	Domain
A	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
A	IPR030564	Myotubularin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q13614	Charcot-Marie-Tooth disease type 4B1 Charcot-Marie-Tooth disease peripheral neuropathy brain glioma malignant ependymoma ovarian cancer psoriasis breast cancer intellectual disability motor peripheral neuropathy peripheral nervous system disease lung cancer neurodegenerative disease

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.