5LU4 | pdb_00005lu4

C4-type pyruvate phosphate dikinase: conformational intermediate of central domain in the swiveling mechanism

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)
B	d5lu4b3	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	d5lu4b2	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	d5lu4b1	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)
A	d5lu4a3	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	d5lu4a2	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	d5lu4a1	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)
B	PPDK_N	e5lu4B1	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: PPDK_N	ECOD (1.6)
B	PEP-utilizers_C	e5lu4B2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP-utilizers_C	ECOD (1.6)
B	PEP-utilizers	e5lu4B3	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: PEP-utilizers	ECOD (1.6)
A	PPDK_N	e5lu4A3	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: PPDK_N	ECOD (1.6)
A	PEP-utilizers_C	e5lu4A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PEP-utilizers_C	ECOD (1.6)
A	PEP-utilizers	e5lu4A2	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: PEP-utilizers	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.50.30.10	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (utative)
B	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (utative)
A	3.50.30.10	Alpha Beta	3-Layer(bba) Sandwich	Glucose Oxidase	domain 1	CATH (utative)
A	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01326	Pyruvate phosphate dikinase, AMP/ATP-binding domain (PPDK_N)	Pyruvate phosphate dikinase, AMP/ATP-binding domain	-	Family
A, B	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	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	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 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 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	photosynthesis metabolic process cellular process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A, B	IPR008279	PEP-utilising enzyme, mobile domain	Domain
A, B	IPR018274	PEP-utilising enzyme, active site	Active Site
A, B	IPR010121	Pyruvate, phosphate dikinase	Family
A, B	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B	IPR023151	PEP-utilising enzyme, conserved site	Conserved Site
A, B	IPR036637	Phosphohistidine domain superfamily	Homologous Superfamily
A, B	IPR002192	Pyruvate phosphate dikinase, AMP/ATP-binding	Domain
A, B	IPR040442	Pyruvate kinase-like domain superfamily	Homologous Superfamily
A, B	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 R01GM157729.