4XPD | pdb_00004xpd

Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a bisubstrate

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8101495	3000403	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		e4xpdA1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: ubiquitin	F:	ECOD (20:10:01)
B		e4xpdB1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: ubiquitin	F:	ECOD (20:10:01)
C		e4xpdC1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: ubiquitin	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.630.30	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Gcn5-related N-acetyltransferase (GNAT)	CATH (4.3.0)
C	3.40.630.30	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Gcn5-related N-acetyltransferase (GNAT)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF12569	N-terminal acetyltransferase A, auxiliary subunit (NatA_aux_su)	N-terminal acetyltransferase A, auxiliary subunit	-	Repeat
B	PF00583	Acetyltransferase (GNAT) family (Acetyltransf_1)	Acetyltransferase (GNAT) family	-	Family
C	PF00583	Acetyltransferase (GNAT) family (Acetyltransf_1)	Acetyltransferase (GNAT) family	-	Family
D [auth F]	PF00976	Corticotropin ACTH domain (ACTH_domain)	Corticotropin ACTH domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	N-terminal acetyltransferase A complex subunit NAT1	enzyme regulator activity enzyme activator activity molecular function activator activity acetyltransferase activator activity molecular function regulator activity ribonucleoprotein complex binding protein-containing complex binding binding ribosome binding	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex NatA complex catalytic complex N-terminal protein acetyltransferase complex transferase complex acetyltransferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex NatA complex catalytic complex N-terminal protein acetyltransferase complex transferase complex acetyltransferase complex protein acetyltransferase complex intracellular protein-containing complex
B	N-terminal acetyltransferase A complex catalytic subunit ARD1	protein N-acetyltransferase activity catalytic activity, acting on a protein acyltransferase activity N-acetyltransferase activity transferase activity protein-N-terminal-alanine acetyltransferase activity protein N-acyltransferase activity protein-N-terminal amino-acid acetyltransferase activity acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity protein N-terminal-serine acetyltransferase activity protein-N-terminal-glutamate acetyltransferase activity protein N-acetyltransferase activity catalytic activity, acting on a protein acyltransferase activity N-acetyltransferase activity transferase activity protein-N-terminal-alanine acetyltransferase activity protein N-acyltransferase activity protein-N-terminal amino-acid acetyltransferase activity acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity protein N-terminal-serine acetyltransferase activity protein-N-terminal-glutamate acetyltransferase activity identical protein binding protein binding binding	-	protein-containing complex intracellular anatomical structure NatA complex catalytic complex N-terminal protein acetyltransferase complex transferase complex acetyltransferase complex cellular anatomical structure protein acetyltransferase complex cytoplasm intracellular protein-containing complex
C	N-terminal acetyltransferase A complex subunit NAT5	protein N-acetyltransferase activity catalytic activity, acting on a protein acyltransferase activity N-acetyltransferase activity protein N-terminal-methionine acetyltransferase activity transferase activity protein N-acyltransferase activity protein-N-terminal amino-acid acetyltransferase activity acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity	cellular component organization organelle organization mitotic sister chromatid cohesion chromosome organization sister chromatid cohesion cellular process cellular component organization or biogenesis cell cycle cell cycle process	protein-containing complex intracellular anatomical structure NatA complex catalytic complex N-terminal protein acetyltransferase complex transferase complex acetyltransferase complex cellular anatomical structure protein acetyltransferase complex cytoplasm intracellular protein-containing complex
D [auth F]	human ACTH8	protein binding binding signaling receptor binding melanocortin receptor binding G protein-coupled receptor binding neuropeptide receptor binding type 1 melanocortin receptor binding type 3 melanocortin receptor binding type 4 melanocortin receptor binding hormone activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity protein binding binding signaling receptor binding melanocortin receptor binding G protein-coupled receptor binding neuropeptide receptor binding type 1 melanocortin receptor binding type 3 melanocortin receptor binding type 4 melanocortin receptor binding hormone activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway multicellular organismal process system process circulatory system process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway multicellular organismal process system process circulatory system process regulation of blood pressure regulation of biological quality blood circulation regulation of tumor necrosis factor production negative regulation of biological process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process tumor necrosis factor superfamily cytokine production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process regulation of localization corticosterone secretion regulation of system process regulation of glucocorticoid secretion localization regulation of steroid hormone secretion regulation of hormone levels lipid transport regulation of corticosteroid hormone secretion establishment of localization regulation of secretion endocrine hormone secretion lipid export from cell glucocorticoid secretion regulation of endocrine process corticosteroid hormone secretion regulation of corticosterone secretion regulation of hormone secretion transport steroid hormone secretion regulation of lipid transport organic hydroxy compound transport hormone secretion secretion by cell regulation of secretion by cell signal release regulation of signaling secretion regulation of transport lipid localization export from cell cell-cell signaling endocrine process regulation of lipid localization macromolecule localization hormone transport regulation of cell communication carbohydrate metabolic process energy derivation by oxidation of organic compounds glycogen metabolic process primary metabolic process regulation of generation of precursor metabolites and energy generation of precursor metabolites and energy regulation of polysaccharide metabolic process regulation of primary metabolic process glucan metabolic process polysaccharide metabolic process energy reserve metabolic process regulation of glycogen metabolic process regulation of carbohydrate metabolic process intracellular signal transduction calcium-mediated signaling intracellular signaling cassette positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction positive regulation of response to stimulus positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway regulation of G protein-coupled receptor signaling pathway positive regulation of cellular process adenylate cyclase-activating G protein-coupled receptor signaling pathway positive regulation of G protein-coupled receptor signaling pathway regulation of response to stimulus adenylate cyclase-modulating G protein-coupled receptor signaling pathway regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway positive regulation of signaling pigmentation cellular pigmentation response to nutrient levels regulation of appetite response to hormone response to chemical response to endogenous stimulus response to peptide hormone response to oxygen-containing compound response to nitrogen compound response to melanocyte-stimulating hormone oxytocin production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of oxytocin production positive regulation of gene expression positive regulation of oxytocin production positive regulation of DNA-templated transcription RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis	membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle extracellular region membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle extracellular region vesicle lumen membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular organelle lumen organelle lumen extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR021183	N-terminal acetyltransferase A, auxiliary subunit	Family
A	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A	IPR019734	Tetratricopeptide repeat	Repeat
B	IPR045047	N-acetyltransferase Ard1-like	Family
B	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
B	IPR000182	GNAT domain	Domain
C	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
C	IPR000182	GNAT domain	Domain
C	IPR051556	N-terminal and lysine N-acetyltransferase	Family
D [auth F]	IPR013531	Pro-opiomelanocortin/corticotropin, ACTH, central region	Domain
D [auth F]	IPR050878	Pro-opiomelanocortin-derived peptides	Family
D [auth F]	IPR013532	Opiodes neuropeptide	Domain
D [auth F]	IPR013593	Pro-opiomelanocortin N-terminal	Domain
D [auth F]	IPR001941	Pro-opiomelanocortin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth F]	Pharos: P01189	obesity disorder obesity due to pro-opiomelanocortin deficiency ACTH-dependent Cushing syndrome sick sinus syndrome nephrocalcinosis hypertensive disorder renal cell carcinoma synovitis early myoclonic encephalopathy hypertrophic cardiomyopathy diabetes insipidus myasthenia gravis glomerulonephritis potassium deficiency disease long QT syndrome obesity disorder obesity due to pro-opiomelanocortin deficiency ACTH-dependent Cushing syndrome sick sinus syndrome nephrocalcinosis hypertensive disorder renal cell carcinoma synovitis early myoclonic encephalopathy hypertrophic cardiomyopathy diabetes insipidus myasthenia gravis glomerulonephritis potassium deficiency disease long QT syndrome cardiomyopathy melanoma fatty liver disease osteoporosis diabetes mellitus sarcomatoid renal cell carcinoma chondrocalcinosis Pain monogenic obesity cocaine abuse multiple sclerosis gout visual epilepsy collecting duct carcinoma ectopic ACTH secretion syndrome bipolar disorder epilepsy spastic quadriplegia proteinuria subvalvular aortic stenosis facial paralysis chromophobe renal cell carcinoma dissociative amnesia cocaine dependence congestive heart failure penile disease pneumonia epilepsy with generalized tonic-clonic seizures calcinosis acute kidney tubular necrosis cystitis restless legs syndrome melancholia opsoclonus-myoclonus syndrome cholestasis papillary renal cell carcinoma West syndrome endogenous depression heroin dependence kidney disease spastic monoplegia hyperaldosteronism acute liver failure substance withdrawal syndrome Cushing syndrome adrenal cortex disease eye disease cerebral palsy rhabdomyoma hypotensive disorder athetoid cerebral palsy urinary tract infection Dravet syndrome autism pancreas disease heart failure inherited lipid metabolism disorder breast carcinoma constipation disorder pituitary cancer acquired metabolic disease sleep-wake disorder acute kidney failure spastic cerebral palsy Addison disease cutaneous melanoma alcohol abuse hypoglycemia familial infantile myoclonic epilepsy hypopituitarism developmental and epileptic encephalopathy hypothyroidism anxiety disorder type 2 diabetes mellitus pain agnosia immune system disease inborn carbohydrate metabolic disorder myocardial ischemia intracerebral hemorrhage X-linked adrenal hypoplasia congenita acromegaly coronary artery disease spastic diplegia cancer hyperglycemia Cushing disease due to pituitary adenoma psychiatric disorder adenoma malignant glioma hypogonadism depressive disorder amnestic disorder digestive system disease mixed cerebral palsy clear cell renal carcinoma mood disorder eating disorder pituitary apoplexy acquired hyperprolactinemia burn pneumonitis Spasmus nutans Nelson syndrome neurotic disorder renal carcinoma amenorrhea familial avascular necrosis of femoral head

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.