1YTM | pdb_00001ytm

Crystal structure of phosphoenolpyruvate carboxykinase of Anaerobiospirillum succiniciproducens complexed with ATP, oxalate, magnesium and manganese ions

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)
B	d1ytmb2	Alpha and beta proteins (a/b)	PEP carboxykinase-like	PEP carboxykinase-like	automated matches	automated matches	(Anaerobiospirillum succiniciproducens ) [TaxId: 13335 ],	SCOPe (2.08)
B	d1ytmb1	Alpha and beta proteins (a/b)	PEP carboxykinase N-terminal domain	PEP carboxykinase N-terminal domain	automated matches	automated matches	(Anaerobiospirillum succiniciproducens ) [TaxId: 13335 ],	SCOPe (2.08)
A	d1ytma2	Alpha and beta proteins (a/b)	PEP carboxykinase-like	PEP carboxykinase-like	automated matches	automated matches	(Anaerobiospirillum succiniciproducens ) [TaxId: 13335 ],	SCOPe (2.08)
A	d1ytma1	Alpha and beta proteins (a/b)	PEP carboxykinase N-terminal domain	PEP carboxykinase N-terminal domain	automated matches	automated matches	(Anaerobiospirillum succiniciproducens ) [TaxId: 13335 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PEPCK/HprK-like	8056001	3001670	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PEP carboxykinase N-terminal domain	8056002	3001788	SCOP2B (2022-06-29)
A	SCOP2 Family	PEPCK-like	8056000	4000841	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PEPCK/HprK-like	8056001	3001670	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PEP carboxykinase N-terminal domain	8056002	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)
B	PEPCK_ATP_C	e1ytmB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: PEP carboxykinase catalytic C-terminal domain	F: PEPCK_ATP_C	ECOD (1.6)
B	PEPCK_ATP_N	e1ytmB2	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: PEPCK_ATP_N	ECOD (1.6)
A	PEPCK_ATP_C	e1ytmA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: PEP carboxykinase catalytic C-terminal domain	F: PEPCK_ATP_C	ECOD (1.6)
A	PEPCK_ATP_N	e1ytmA1	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: PEPCK_ATP_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	PF01293	Phosphoenolpyruvate carboxykinase (PEPCK_ATP)	Phosphoenolpyruvate carboxykinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	phosphoenolpyruvate carboxykinase [ATP]	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding phosphoenolpyruvate carboxykinase activity carboxy-lyase activity lyase activity phosphoenolpyruvate carboxykinase (ATP) activity catalytic activity carbon-carbon lyase activity	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 biosynthetic process small molecule metabolic process metabolic process cellular process glucose metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR008210	Phosphoenolpyruvate carboxykinase, N-terminal	Homologous Superfamily
A, B	IPR013035	Phosphoenolpyruvate carboxykinase, C-terminal	Homologous Superfamily
A, B	IPR001272	Phosphoenolpyruvate carboxykinase, ATP-utilising	Family
A, B	IPR015994	Phosphoenolpyruvate carboxykinase (ATP), 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.