1XDP

Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP

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	d1xdpa1	All alpha proteins	Spectrin repeat-like	PPK N-terminal domain-like	PPK N-terminal domain-like	Polyphosphate kinase, PPK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1xdpa3	Alpha and beta proteins (a+b)	Phospholipase D/nuclease	Phospholipase D/nuclease	Polyphosphate kinase C-terminal domain	Polyphosphate kinase, PPK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1xdpa2	Alpha and beta proteins (a+b)	PHP14-like	PHP14-like	PPK middle domain-like	Polyphosphate kinase, PPK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1xdpb1	All alpha proteins	Spectrin repeat-like	PPK N-terminal domain-like	PPK N-terminal domain-like	Polyphosphate kinase, PPK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1xdpb3	Alpha and beta proteins (a+b)	Phospholipase D/nuclease	Phospholipase D/nuclease	Polyphosphate kinase C-terminal domain	Polyphosphate kinase, PPK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1xdpb2	Alpha and beta proteins (a+b)	PHP14-like	PHP14-like	PPK middle domain-like	Polyphosphate kinase, PPK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PPK N-terminal domain-like	8021318	4001177	SCOP2 (2022-06-29)
A	SCOP2 Family	PPK middle domain-like	8021322	4003942	SCOP2 (2022-06-29)
A	SCOP2 Family	Polyphosphate kinase C-terminal domain	8021323	4000402	SCOP2 (2022-06-29)
A	SCOP2 Family	Polyphosphate kinase C-terminal domain	8021325	4000402	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PPK N-terminal domain-like	8033698	3000992	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PHP14-like	8033702	3001869	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Phospholipase D/nuclease-like	8033703	3000664	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Phospholipase D/nuclease-like	8033705	3000664	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PHP14-like	8033702	3001869	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phospholipase D/nuclease-like	8033703	3000664	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phospholipase D/nuclease-like	8033705	3000664	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PPK N-terminal domain-like	8033698	3000992	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	PP_kinase_N	e1xdpA1	A: alpha bundles	X: Spectrin repeat-like	H: PPK N-terminal domain-like (From Topology)	T: PPK N-terminal domain-like	F: PP_kinase_N	ECOD (1.6)
A	PP_kinase	e1xdpA2	A: a+b two layers	X: PHP14-like (From Topology)	H: PHP14-like (From Topology)	T: PHP14-like	F: PP_kinase	ECOD (1.6)
A	PP_kinase_C_N	e1xdpA3	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: PP_kinase_C_N	ECOD (1.6)
A	PP_kinase_C_C	e1xdpA4	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: PP_kinase_C_C	ECOD (1.6)
B	PP_kinase_N	e1xdpB1	A: alpha bundles	X: Spectrin repeat-like	H: PPK N-terminal domain-like (From Topology)	T: PPK N-terminal domain-like	F: PP_kinase_N	ECOD (1.6)
B	PP_kinase	e1xdpB2	A: a+b two layers	X: PHP14-like (From Topology)	H: PHP14-like (From Topology)	T: PHP14-like	F: PP_kinase	ECOD (1.6)
B	PP_kinase_C_N	e1xdpB3	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: PP_kinase_C_N	ECOD (1.6)
B	PP_kinase_C_C	e1xdpB4	A: a+b three layers	X: Phospholipase D/nuclease (From Topology)	H: Phospholipase D/nuclease (From Topology)	T: Phospholipase D/nuclease	F: PP_kinase_C_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.58.310	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	3.30.1840.10	Alpha Beta	2-Layer Sandwich	polyphosphate kinase like	Polyphosphate kinase middle domain	CATH (4.3.0)
A	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)
B	1.20.58.310	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	3.30.1840.10	Alpha Beta	2-Layer Sandwich	polyphosphate kinase like	Polyphosphate kinase middle domain	CATH (4.3.0)
B	3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02503	Polyphosphate kinase middle domain (PP_kinase)	Polyphosphate kinase middle domain	Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules.	Domain
A, B	PF17941	Polyphosphate kinase C-terminal domain 1 (PP_kinase_C_1)	Polyphosphate kinase C-terminal domain 1	Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C1-terminal domain has a structure similar to phospholipase D. It is one of two closely relate ...	Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C1-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed beta-sheet flanked by five alpha-helices. However, the structural topology and relative orientations of the helices to the beta-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains [1].	Domain
A, B	PF13089	Polyphosphate kinase N-terminal domain (PP_kinase_N)	Polyphosphate kinase N-terminal domain	Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules.	Domain
A, B	PF13090	Polyphosphate kinase C-terminal domain 2 (PP_kinase_C)	Polyphosphate kinase C-terminal domain 2	Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C2-terminal domain has a structure similar to phospholipase D. It is one of two closely relate ...	Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C2-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed beta-sheet flanked by five alpha-helices. However, the structural topology and relative orientations of the helices to the beta-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Polyphosphate kinase	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 polyphosphate kinase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups identical protein binding protein binding protein homodimerization activity protein dimerization activity polyphosphate:AMP phosphotransferase activity diphosphotransferase activity cation binding metal ion binding	biosynthetic process polyphosphate biosynthetic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process phosphorus metabolic process polyphosphate metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex polyphosphate kinase complex transferase complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane cell outer membrane external encapsulating structure transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex polyphosphate kinase complex transferase complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane cell outer membrane external encapsulating structure cell envelope periplasmic side of cell outer membrane outer membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036830	Polyphosphate kinase middle domain superfamily	Homologous Superfamily
A, B	IPR036832	Polyphosphate kinase N-terminal domain superfamily	Homologous Superfamily
A, B	IPR041108	Polyphosphate kinase, C-terminal domain 1	Domain
A, B	IPR024953	Polyphosphate kinase middle domain	Domain
A, B	IPR001736	Phospholipase D/Transphosphatidylase	Domain
A, B	IPR003414	Polyphosphate kinase	Family
A, B	IPR025200	Polyphosphate kinase C-terminal domain 2	Domain
A, B	IPR025198	Polyphosphate kinase N-terminal domain	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.