5JVL

C4-type pyruvate phospate dikinase: nucleotide binding domain with bound ATP analogue

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d5jvla3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)
A	d5jvla2	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	Phosphohistidine domain	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)
A	d5jvla1	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)
B	d5jvlb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)
B	d5jvlb3	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	Phosphohistidine domain	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)
B	d5jvlb2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)
C	d5jvlc3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)
C	d5jvlc2	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	Phosphohistidine domain	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)
C	d5jvlc1	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)
D	d5jvld3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Phosphoenolpyruvate/pyruvate domain	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)
D	d5jvld2	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	Phosphohistidine domain	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)
D	d5jvld1	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	automated matches	automated matches	Clustered yellowtops (Flaveria trinervia ) [TaxId: 4227 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF01326	e5jvlA2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: PF01326	ECOD (1.6)
A	PF02896	e5jvlA3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02896	ECOD (1.6)
A	PF00391	e5jvlA1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF00391	ECOD (1.6)
C	PF01326	e5jvlC3	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: PF01326	ECOD (1.6)
C	PF02896	e5jvlC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02896	ECOD (1.6)
C	PF00391	e5jvlC2	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF00391	ECOD (1.6)
D	PF01326	e5jvlD1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: PF01326	ECOD (1.6)
D	PF02896	e5jvlD3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02896	ECOD (1.6)
D	PF00391	e5jvlD2	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: PF00391	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	1.20.80.30	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein		CATH (4.3.0)
A	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	1.10.189.10	Mainly Alpha	Orthogonal Bundle	Pyruvate Phosphate di-kinase	domain 2	CATH (4.3.0)
A	3.50.30.10	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
A	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
C	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
C	1.20.80.30	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein		CATH (4.3.0)
C	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
C	1.10.189.10	Mainly Alpha	Orthogonal Bundle	Pyruvate Phosphate di-kinase	domain 2	CATH (4.3.0)
C	3.50.30.10	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
C	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
D	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
D	1.10.189.10	Mainly Alpha	Orthogonal Bundle	Pyruvate Phosphate di-kinase	domain 2	CATH (4.3.0)
D	3.50.30.10	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (4.3.0)
D	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01326	Pyruvate phosphate dikinase, AMP/ATP-binding domain (PPDK_N)	Pyruvate phosphate dikinase, AMP/ATP-binding domain	-	Family
A, B, C, D	PF00391	PEP-utilising enzyme, mobile domain (PEP-utilizers)	PEP-utilising enzyme, mobile domain	This domain is a "swivelling" beta/beta/alpha domain which is thought to be mobile in all proteins known to contain it.	Domain
A, B, C, D	PF02896	PEP-utilising enzyme, PEP-binding domain (PEP-utilizers_C)	PEP-utilising enzyme, PEP-binding domain	This entry represents a TIM barrel domain found at the C terminus of a number of PEP (phosphoenolpyruvate)-utilising proteins. In PPDK (Pyruvate phosphate dikinase) this C-terminal domain has been shown to be a PEP-binding domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Pyruvate, phosphate dikinase, chloroplastic	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups pyruvate, phosphate dikinase activity phosphotransferase activity, paired acceptors cation binding metal ion binding	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process pyruvate metabolic process organic substance metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process photosynthesis	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR008279	PEP-utilising enzyme, mobile domain	Domain
A, B, C, D	IPR018274	PEP-utilising enzyme, active site	Active Site
A, B, C, D	IPR010121	Pyruvate, phosphate dikinase	Family
A, B, C, D	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B, C, D	IPR023151	PEP-utilising enzyme, conserved site	Conserved Site
A, B, C, D	IPR036637	Phosphohistidine domain superfamily	Homologous Superfamily
A, B, C, D	IPR002192	Pyruvate phosphate dikinase, AMP/ATP-binding	Domain
A, B, C, D	IPR040442	Pyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR000121	PEP-utilising enzyme, C-terminal	Domain

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.