2ZCI | pdb_00002zci

Structure of a GTP-dependent bacterial PEP-carboxykinase from Corynebacterium glutamicum

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)
D	d2zcid2	Alpha and beta proteins (a/b)	PEP carboxykinase-like	PEP carboxykinase-like	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)
D	d2zcid1	Alpha and beta proteins (a/b)	PEP carboxykinase N-terminal domain	PEP carboxykinase N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)
C	d2zcic2	Alpha and beta proteins (a/b)	PEP carboxykinase-like	PEP carboxykinase-like	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)
C	d2zcic1	Alpha and beta proteins (a/b)	PEP carboxykinase N-terminal domain	PEP carboxykinase N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)
B	d2zcib2	Alpha and beta proteins (a/b)	PEP carboxykinase-like	PEP carboxykinase-like	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)
B	d2zcib1	Alpha and beta proteins (a/b)	PEP carboxykinase N-terminal domain	PEP carboxykinase N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)
A	d2zcia2	Alpha and beta proteins (a/b)	PEP carboxykinase-like	PEP carboxykinase-like	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)
A	d2zcia1	Alpha and beta proteins (a/b)	PEP carboxykinase N-terminal domain	PEP carboxykinase N-terminal domain	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PEPCK/HprK-like	8056007	3001670	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PEP carboxykinase N-terminal domain	8056008	3001788	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PEPCK/HprK-like	8056007	3001670	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PEP carboxykinase N-terminal domain	8056008	3001788	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PEPCK/HprK-like	8056007	3001670	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PEP carboxykinase N-terminal domain	8056008	3001788	SCOP2B (2022-06-29)
A	SCOP2 Family	PEPCK-like	8056006	4000841	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PEPCK/HprK-like	8056007	3001670	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PEP carboxykinase N-terminal domain	8056008	3001788	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)
D	Redoxin	e2zciD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Redoxin	ECOD (v294.1)
C	Redoxin	e2zciC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Redoxin	ECOD (v294.1)
B	Redoxin	e2zciB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Redoxin	ECOD (v294.1)
A	Redoxin	e2zciA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Redoxin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.449.10	Alpha Beta	3-Layer(aba) Sandwich	Phosphoenolpyruvate Carboxykinase	domain 1	CATH (4.3.0)
D	2.170.8.10	Mainly Beta	Beta Complex	Phosphoenolpyruvate Carboxykinase	domain 2	CATH (4.3.0)
D	3.90.228.20	Alpha Beta	Alpha-Beta Complex	Phosphoenolpyruvate Carboxykinase	domain 3	CATH (4.3.0)
C	3.40.449.10	Alpha Beta	3-Layer(aba) Sandwich	Phosphoenolpyruvate Carboxykinase	domain 1	CATH (4.3.0)
C	2.170.8.10	Mainly Beta	Beta Complex	Phosphoenolpyruvate Carboxykinase	domain 2	CATH (4.3.0)
C	3.90.228.20	Alpha Beta	Alpha-Beta Complex	Phosphoenolpyruvate Carboxykinase	domain 3	CATH (4.3.0)
B	3.40.449.10	Alpha Beta	3-Layer(aba) Sandwich	Phosphoenolpyruvate Carboxykinase	domain 1	CATH (4.3.0)
B	2.170.8.10	Mainly Beta	Beta Complex	Phosphoenolpyruvate Carboxykinase	domain 2	CATH (4.3.0)
B	3.90.228.20	Alpha Beta	Alpha-Beta Complex	Phosphoenolpyruvate Carboxykinase	domain 3	CATH (4.3.0)
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, B, C, D	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, B, C, D	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, B, C, D	Phosphoenolpyruvate carboxykinase [GTP]	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding phosphoenolpyruvate carboxykinase activity phosphoenolpyruvate carboxykinase (GTP) activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity guanyl nucleotide binding cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding phosphoenolpyruvate carboxykinase activity phosphoenolpyruvate carboxykinase (GTP) activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding	fatty acid metabolic process short-chain fatty acid catabolic process lipid catabolic process catabolic process oxoacid metabolic process short-chain fatty acid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process organic acid catabolic process fatty acid catabolic process propionate catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process fatty acid metabolic process short-chain fatty acid catabolic process lipid catabolic process catabolic process oxoacid metabolic process short-chain fatty acid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process organic acid catabolic process fatty acid catabolic process propionate catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process small molecule catabolic process lipid metabolic process propionate metabolic process monosaccharide metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process gluconeogenesis hexose biosynthetic process biosynthetic process glucose metabolic process cellular response to stimulus response to stimulus homeostatic process response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular response to chemical stimulus cellular homeostasis response to monosaccharide response to carbohydrate chemical homeostasis response to glucose response to chemical glucose homeostasis carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus 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 polyol metabolic process alditol biosynthetic process glycerol biosynthetic process from pyruvate glycerol metabolic process glycerolipid biosynthetic process alcohol biosynthetic process glycerolipid metabolic process acylglycerol metabolic process response to lipid dicarboxylic acid metabolic process oxaloacetate metabolic process response to nutrient levels response to stress response to starvation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR035077	Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain	Domain
A, B, C, D	IPR008209	Phosphoenolpyruvate carboxykinase, GTP-utilising	Family
A, B, C, D	IPR008210	Phosphoenolpyruvate carboxykinase, N-terminal	Homologous Superfamily
A, B, C, D	IPR013035	Phosphoenolpyruvate carboxykinase, C-terminal	Homologous Superfamily
A, B, C, D	IPR035078	Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal	Domain
A, B, C, D	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.