2ZCI

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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00821	e2zciA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: PEP carboxykinase catalytic C-terminal domain	F: PF00821	ECOD (1.6)
A	PF17297	e2zciA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: PEP carboxykinase N-terminal domain (From Topology)	T: PEP carboxykinase N-terminal domain	F: PF17297	ECOD (1.6)
B	PF00821	e2zciB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: PEP carboxykinase catalytic C-terminal domain	F: PF00821	ECOD (1.6)
B	PF17297	e2zciB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: PEP carboxykinase N-terminal domain (From Topology)	T: PEP carboxykinase N-terminal domain	F: PF17297	ECOD (1.6)
C	PF00821	e2zciC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: PEP carboxykinase catalytic C-terminal domain	F: PF00821	ECOD (1.6)
C	PF17297	e2zciC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: PEP carboxykinase N-terminal domain (From Topology)	T: PEP carboxykinase N-terminal domain	F: PF17297	ECOD (1.6)
D	PF00821	e2zciD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: PEP carboxykinase catalytic C-terminal domain	F: PF00821	ECOD (1.6)
D	PF17297	e2zciD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: PEP carboxykinase N-terminal domain (From Topology)	T: PEP carboxykinase N-terminal domain	F: PF17297	ECOD (1.6)

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)
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)
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)
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)

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 organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding	monosaccharide metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process primary metabolic process monosaccharide biosynthetic process gluconeogenesis hexose biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process small molecule metabolic process metabolic process monosaccharide metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process primary metabolic process monosaccharide biosynthetic process gluconeogenesis hexose biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process small molecule metabolic process metabolic process glucose metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR035077	Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain	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 R01GM133198.