8K9T | pdb_00008k9t

Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07819	PGAP1-like alpha/beta domain (PGAP1)	PGAP1-like alpha/beta domain	This domain is found in GPI inositol-deacylase PGAP1 and related proteins. PGAP1 is an endoplasmic reticulum membrane protein with a catalytic serine containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacyla ...	This domain is found in GPI inositol-deacylase PGAP1 and related proteins. PGAP1 is an endoplasmic reticulum membrane protein with a catalytic serine containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacylase; this deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body [1]. This entry also includes Tgl2, a mitochondria protein that serves as a triacylglycerol lipase in budding yeasts [2]. The domain represented by this entry is found toward the N terminus and it is a lipase domain with a typical alpha/beta/alpha hydrolase architecture [3].	Domain
A	PF25141	GPI inositol-deacylase beta-sandwich domain (PGAP1_2nd)	GPI inositol-deacylase beta-sandwich domain	This domain is found in GPI inositol-deacylase (BST1 also known as PGAP1) and related proteins. PGAP1 is involved in inositol deacylation of GPI-anchored proteins. This deacylation is important for the efficient transport of GPI-anchored proteins fro ...	This domain is found in GPI inositol-deacylase (BST1 also known as PGAP1) and related proteins. PGAP1 is involved in inositol deacylation of GPI-anchored proteins. This deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body [1]. This entry represents a beta-sandwich domain which is located next to the PGAP1 alpha/beta domain. The function of this domain is unclear but it is not necessary for the deacylase activity [2].	Domain
A	PF25140	GPI inositol-deacylase transmembrane domain (PGAP1_TMD)	GPI inositol-deacylase transmembrane domain	This domain is found in GPI inositol-deacylase (BST1 also known as PGAP1) and related proteins. PGAP1 is involved in inositol deacylation of GPI-anchored proteins. This deacylation is important for the efficient transport of GPI-anchored proteins fro ...	This domain is found in GPI inositol-deacylase (BST1 also known as PGAP1) and related proteins. PGAP1 is involved in inositol deacylation of GPI-anchored proteins. This deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body [1]. This entry represents the transmembrane domain which consists of 10 transmembrane helices that are mostly perpendicular to the membrane, with the exception of a long TMH4 which crosses the membrane diagonally [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Green fluorescent protein,Complement decay-accelerating factor	protein binding binding virus receptor activity exogenous protein binding lipid binding	multicellular organismal process regulation of cellular process regulation of alpha-beta T cell activation regulation of leukocyte activation positive regulation of biological process regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of CD4-positive, alpha-beta T cell activation positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion multicellular organismal process regulation of cellular process regulation of alpha-beta T cell activation regulation of leukocyte activation positive regulation of biological process regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of CD4-positive, alpha-beta T cell activation positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation CD4-positive, alpha-beta T cell activation positive regulation of leukocyte activation alpha-beta T cell activation regulation of immune system process regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of cellular process regulation of biological process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation biological regulation regulation of T cell activation positive regulation of alpha-beta T cell activation regulation of CD4-positive, alpha-beta T cell activation immune system process regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process cellular process regulation of lymphocyte activation positive regulation of cytosolic calcium ion concentration regulation of biological quality adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity response to stimulus T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of immune response cytokine production leukocyte mediated immunity positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production regulation of T cell mediated immunity regulation of cytokine production involved in immune response immune response regulation of adaptive immune response immune effector process regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process regulation of response to stimulus positive regulation of production of molecular mediator of immune response regulation of immune response metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of response to stimulus regulation of T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of biosynthetic process regulation of cytokine production positive regulation of immune effector process cytokine production involved in immune response production of molecular mediator of immune response regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process adaptive immune response regulation of lymphocyte mediated immunity positive regulation of gene expression positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response humoral immune response complement activation humoral immune response mediated by circulating immunoglobulin complement activation, classical pathway immunoglobulin mediated immune response B cell mediated immunity activation of immune response regulation of humoral immune response negative regulation of biological process negative regulation of complement activation negative regulation of response to stimulus negative regulation of immune response negative regulation of immune effector process negative regulation of humoral immune response negative regulation of immune system process regulation of complement activation biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus regulation of lipopolysaccharide-mediated signaling pathway cellular response to stimulus regulation of response to biotic stimulus response to lipid regulation of response to external stimulus signaling cellular response to lipopolysaccharide regulation of signal transduction cell communication lipopolysaccharide-mediated signaling pathway cellular response to biotic stimulus response to bacterium signal transduction regulation of signaling cell surface receptor signaling pathway response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to lipid regulation of cell communication response to molecule of bacterial origin regulation of complement-dependent cytotoxicity regulation of cell killing complement-dependent cytotoxicity cell killing positive regulation of cell population proliferation positive regulation of alpha-beta T cell proliferation positive regulation of CD4-positive, alpha-beta T cell proliferation alpha-beta T cell proliferation lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation regulation of CD4-positive, alpha-beta T cell proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation leukocyte proliferation regulation of alpha-beta T cell proliferation positive regulation of mononuclear cell proliferation T cell proliferation regulation of lymphocyte proliferation CD4-positive, alpha-beta T cell proliferation regulation of T cell proliferation regulation of mononuclear cell proliferation respiratory burst	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell surface cell periphery plasma membrane membrane extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell surface cell periphery plasma membrane membrane membrane microdomain membrane raft intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle cytoplasm side of membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane secretory granule secretory vesicle organelle membrane secretory granule membrane Golgi membrane Golgi apparatus endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment ficolin-1-rich granule membrane ficolin-1-rich granule tertiary granule
A	GPI inositol-deacylase,MCherry protein	hydrolase activity, acting on ester bonds phosphatidylinositol deacylase activity carboxylic ester hydrolase activity hydrolase activity catalytic activity	localization cellular localization transport establishment of localization in cell intracellular transport cellular process endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization Golgi vesicle transport vesicle-mediated transport phosphatidylinositol metabolic process glycolipid metabolic process glycerophospholipid metabolic process liposaccharide metabolic process localization cellular localization transport establishment of localization in cell intracellular transport cellular process endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization Golgi vesicle transport vesicle-mediated transport phosphatidylinositol metabolic process glycolipid metabolic process glycerophospholipid metabolic process liposaccharide metabolic process carbohydrate derivative metabolic process primary metabolic process GPI anchor metabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process glycerolipid metabolic process metabolic process phosphorus metabolic process lipid metabolic process establishment of protein localization protein transport macromolecule localization intracellular protein localization	membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR000436	Sushi/SCR/CCP domain	Domain
B	IPR035976	Sushi/SCR/CCP superfamily	Homologous Superfamily
B	IPR050350	Complement & Cell Adhesion Regulators	Family
A	IPR056824	GPI inositol-deacylase, transmembrane domain	Domain
A	IPR012908	GPI inositol-deacylase PGAP1-like alpha/beta domain	Domain
A	IPR039529	GPI inositol-deacylase	Family
A	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P08174	protein-losing enteropathy endometriosis amphetamine abuse lung cancer malignant mesothelioma myopathy oligodendroglioma adrenal cortex carcinoma pancreatic intraductal papillary-mucinous carcinoma Amphetamine-Related Disorders Barrett esophagus tuberculosis gastric carcinoma interstitial lung disease lung carcinoma protein-losing enteropathy endometriosis amphetamine abuse lung cancer malignant mesothelioma myopathy oligodendroglioma adrenal cortex carcinoma pancreatic intraductal papillary-mucinous carcinoma Amphetamine-Related Disorders Barrett esophagus tuberculosis gastric carcinoma interstitial lung disease lung carcinoma malignant pancreatic neoplasm nasopharyngeal carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm astrocytic tumor proteinuria breast cancer ulcerative colitis dermatomyositis lung adenocarcinoma malignant glioma medulloblastoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia atopic eczema spina bifida common variable immunodeficiency Down syndrome esophageal adenocarcinoma interstitial cystitis

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	O-acyltransferases	GPI inositol-deacylase PGAP1 (also known as Bst1), apo form

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.

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