4YWD | pdb_00004ywd

Structure of rat cytosolic pepck in complex with 2,3-Pyridine dicarboxylic acid

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4ywda2	Alpha and beta proteins (a/b)	PEP carboxykinase-like	PEP carboxykinase-like	PEP carboxykinase C-terminal domain	Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d4ywda1	Alpha and beta proteins (a/b)	PEP carboxykinase N-terminal domain	PEP carboxykinase N-terminal domain	PEP carboxykinase N-terminal domain	Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PEPCK/HprK-like	8056004	3001670	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PEP carboxykinase N-terminal domain	8056005	3001788	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		e4ywdA1	A: Piezo CTL2 domain	X: Piezo CTL2 domain	H: Nudix	T: Pkinase, Kdo	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.449.10	Alpha Beta	3-Layer(aba) Sandwich	Phosphoenolpyruvate Carboxykinase	domain 1	CATH (4.3.0)
A	2.170.8.10	Mainly Beta	Beta Complex	Phosphoenolpyruvate Carboxykinase	domain 2	CATH (4.3.0)
A	3.90.228.20	Alpha Beta	Alpha-Beta Complex	Phosphoenolpyruvate Carboxykinase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00821	Phosphoenolpyruvate carboxykinase C-terminal P-loop domain (PEPCK_GTP)	Phosphoenolpyruvate carboxykinase C-terminal P-loop domain	Catalyses the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate.	Domain
A	PF17297	Phosphoenolpyruvate carboxykinase N-terminal domain (PEPCK_N)	Phosphoenolpyruvate carboxykinase N-terminal domain	Catalyses the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Phosphoenolpyruvate carboxykinase, cytosolic [GTP]	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding organic acid binding anion binding carboxylic acid binding phosphoenolpyruvate carboxykinase activity carboxy-lyase activity lyase activity catalytic activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding organic acid binding anion binding carboxylic acid binding phosphoenolpyruvate carboxykinase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity nucleobase-containing compound kinase activity kinase activity transferase activity phosphotransferase activity, phosphate group as acceptor nucleoside diphosphate kinase activity transferase activity, transferring phosphorus-containing groups catalytic activity, acting on a protein protein serine kinase activity (using GTP as donor) protein kinase activity phosphotransferase activity, alcohol group as acceptor phosphoenolpyruvate carboxykinase (GTP) activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding magnesium ion binding GDP binding	tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus response to raffinose response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to raffinose cellular response to carbohydrate stimulus response to carbohydrate neutral lipid metabolic process neutral lipid biosynthetic process glycerol biosynthetic process lipid biosynthetic process alcohol metabolic process acylglycerol biosynthetic process triglyceride metabolic process triglyceride biosynthetic process polyol biosynthetic process pyruvate metabolic process carbohydrate metabolic process polyol metabolic process small molecule biosynthetic process carbohydrate biosynthetic process alditol biosynthetic process glycerol biosynthetic process from pyruvate primary metabolic process glycerol metabolic process biosynthetic process glycerolipid biosynthetic process alcohol biosynthetic process glycerolipid metabolic process monocarboxylic acid metabolic process acylglycerol metabolic process lipid metabolic process response to lipid response to retinoic acid cellular response to retinoic acid cellular response to lipid response to ketone cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to ketone cellular response to steroid hormone stimulus cellular response to hormone stimulus response to endogenous stimulus cellular response to dexamethasone stimulus response to glucocorticoid cellular response to glucocorticoid stimulus cellular response to corticosteroid stimulus response to corticosteroid response to dexamethasone response to osmotic stress cellular response to chemical stress cellular response to osmotic stress cellular response to environmental stimulus hyperosmotic response cellular hyperosmotic response cellular response to abiotic stimulus cellular hypotonic salinity response cellular response to salt stress cellular hypotonic response response to salt stress hypotonic response hypotonic salinity response response to alcohol response to phorbol 13-acetate 12-myristate cellular response to alcohol cellular response to phorbol 13-acetate 12-myristate monosaccharide metabolic process hexose metabolic process glucose metabolic process establishment of protein localization cellular localization NLS-bearing protein import into nucleus nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport developmental process multicellular organismal process epithelium development cellular developmental process gland development animal organ development tissue development liver development epithelial cell differentiation multicellular organism development cell differentiation hepaticobiliary system development anatomical structure development hepatocyte differentiation system development monosaccharide biosynthetic process gluconeogenesis hexose biosynthetic process protein phosphorylation phosphorylation peptidyl-serine modification peptidyl-serine phosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process response to acid chemical response to methionine response to nitrogen compound response to amino acid cellular hyperosmotic salinity response hyperosmotic salinity response response to nutrient levels carbohydrate derivative biosynthetic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process aldehyde biosynthetic process aldehyde metabolic process organophosphate metabolic process organophosphate biosynthetic process glyceraldehyde-3-phosphate biosynthetic process dicarboxylic acid metabolic process oxaloacetate metabolic process response to pH response to acidic pH regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process response to peptide cellular response to interleukin-1 response to cytokine cellular response to cytokine stimulus response to interleukin-1 chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis response to starvation fatty acid metabolic process short-chain fatty acid catabolic process lipid catabolic process catabolic process short-chain fatty acid metabolic process organic acid catabolic process fatty acid catabolic process propionate catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule catabolic process propionate metabolic process cellular response to glucose stimulus intracellular glucose homeostasis response to hexose cellular homeostasis response to monosaccharide response to glucose cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus cellular response to nitrogen compound response to peptide hormone cellular response to peptide hormone stimulus response to glucagon cellular response to glucagon stimulus response to activity regulation of steroid biosynthetic process regulation of cholesterol biosynthetic process regulation of cholesterol metabolic process steroid metabolic process regulation of lipid metabolic process sterol metabolic process cholesterol metabolic process regulation of small molecule metabolic process positive regulation of lipid metabolic process steroid biosynthetic process secondary alcohol biosynthetic process regulation of alcohol biosynthetic process regulation of steroid metabolic process cholesterol biosynthetic process positive regulation of cholesterol biosynthetic process secondary alcohol metabolic process positive regulation of steroid biosynthetic process sterol biosynthetic process positive regulation of lipid biosynthetic process regulation of sterol biosynthetic process positive regulation of cholesterol metabolic process positive regulation of steroid metabolic process regulation of lipid biosynthetic process positive regulation of small molecule metabolic process positive regulation of alcohol biosynthetic process positive regulation of sterol biosynthetic process response to interleukin-6 response to organophosphorus response to purine-containing compound response to cAMP cellular response to cAMP regulation of cellular response to stress negative regulation of biological process regulation of signal transduction intracellular signal transduction cell communication maintenance of protein localization in endoplasmic reticulum ER-nucleus signaling pathway cellular response to sterol signal transduction protein localization to endoplasmic reticulum cellular response to sterol depletion regulation of SREBP signaling pathway maintenance of location regulation of response to stimulus maintenance of protein location signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of cell communication maintenance of location in cell negative regulation of SREBP signaling pathway regulation of intracellular signal transduction regulation of response to stress maintenance of protein location in cell negative regulation of cellular process regulation of signaling response to sterol negative regulation of response to stimulus negative regulation of signal transduction response to sterol depletion SREBP signaling pathway SREBP-SCAP complex retention in endoplasmic reticulum regulation of cell communication maintenance of protein localization in organelle cellular response to tumor necrosis factor response to tumor necrosis factor biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus response to insulin cellular response to fructose stimulus response to fructose protein maturation cellular response to insulin stimulus cellular response to potassium ion starvation cellular response to nutrient levels cellular response to starvation immunological memory formation process regulation of immune effector process regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation cell activation involved in immune response positive regulation of T cell differentiation regulation of cell development positive regulation of developmental process positive regulation of cell activation positive regulation of immune response T cell activation positive regulation of leukocyte activation regulation of immune system process T cell differentiation positive regulation of immune system process positive regulation of memory T cell differentiation positive regulation of T cell activation immune response positive regulation of cell development immune effector process regulation of leukocyte cell-cell adhesion regulation of immune response positive regulation of multicellular organismal process leukocyte differentiation regulation of developmental process cell development positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of response to stimulus memory T cell differentiation positive regulation of lymphocyte activation cell adhesion cell-cell adhesion T cell activation involved in immune response positive regulation of hemopoiesis positive regulation of cell differentiation leukocyte activation involved in immune response positive regulation of immune effector process regulation of multicellular organismal process regulation of cell-cell adhesion lymphocyte activation involved in immune response regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation T cell differentiation involved in immune response regulation of memory T cell differentiation immune system process regulation of hemopoiesis immunological memory process positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of lymphocyte activation response to lipopolysaccharide response to molecule of bacterial origin	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008209	Phosphoenolpyruvate carboxykinase, GTP-utilising	Family
A	IPR008210	Phosphoenolpyruvate carboxykinase, N-terminal	Homologous Superfamily
A	IPR035078	Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal	Domain
A	IPR035077	Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain	Domain
A	IPR013035	Phosphoenolpyruvate carboxykinase, C-terminal	Homologous Superfamily
A	IPR018091	Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site	Conserved Site

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.