7Z16 | pdb_00007z16

E. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP and PhnK E171Q mutation

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	PhnH-like	8034005	3001133	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PhnH-like	8034005	3001133	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)
L	ABC_tran	e7z16L1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)
K	ABC_tran	e7z16K1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)
J	ABC_tran	e7z16J1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)
I	ABC_tran	e7z16I1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)
H	PhnJ_N	e7z16H1	A: a/b three-layered sandwiches	X: PhnH-like (From Topology)	H: PhnH-like (From Topology)	T: PhnH-like	F: PhnJ_N	ECOD (1.6)
H	PhnJ_C	e7z16H2	A: few secondary structure elements	X: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology)	H: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology)	T: C-P lyase subunit PhnJ C-terminal Zn-binding domain	F: PhnJ_C	ECOD (1.6)
D	PhnJ_N	e7z16D1	A: a/b three-layered sandwiches	X: PhnH-like (From Topology)	H: PhnH-like (From Topology)	T: PhnH-like	F: PhnJ_N	ECOD (1.6)
D	PhnJ_C	e7z16D2	A: few secondary structure elements	X: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology)	H: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology)	T: C-P lyase subunit PhnJ C-terminal Zn-binding domain	F: PhnJ_C	ECOD (1.6)
G	PhnI_N	e7z16G1	A: alpha arrays	X: RuvA-C	H: C-P lyase subunit PhnI N-terminal domain (From Topology)	T: C-P lyase subunit PhnI N-terminal domain	F: PhnI_N	ECOD (1.6)
G	PhnI_C	e7z16G2	A: a+b two layers	X: C-P lyase subunit PhnG (From Topology)	H: C-P lyase subunit PhnG (From Topology)	T: C-P lyase subunit PhnG	F: PhnI_C	ECOD (1.6)
C	PhnI_N	e7z16C2	A: alpha arrays	X: RuvA-C	H: C-P lyase subunit PhnI N-terminal domain (From Topology)	T: C-P lyase subunit PhnI N-terminal domain	F: PhnI_N	ECOD (1.6)
C	PhnI_C	e7z16C1	A: a+b two layers	X: C-P lyase subunit PhnG (From Topology)	H: C-P lyase subunit PhnG (From Topology)	T: C-P lyase subunit PhnG	F: PhnI_C	ECOD (1.6)
F	PhnH	e7z16F1	A: a/b three-layered sandwiches	X: PhnH-like (From Topology)	H: PhnH-like (From Topology)	T: PhnH-like	F: PhnH	ECOD (1.6)
B	PhnH	e7z16B1	A: a/b three-layered sandwiches	X: PhnH-like (From Topology)	H: PhnH-like (From Topology)	T: PhnH-like	F: PhnH	ECOD (1.6)
E	PhnG	e7z16E1	A: a+b two layers	X: C-P lyase subunit PhnG (From Topology)	H: C-P lyase subunit PhnG (From Topology)	T: C-P lyase subunit PhnG	F: PhnG	ECOD (1.6)
A	PhnG	e7z16A1	A: a+b two layers	X: C-P lyase subunit PhnG (From Topology)	H: C-P lyase subunit PhnG (From Topology)	T: C-P lyase subunit PhnG	F: PhnG	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.11310	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Bacterial phosphonate metabolism protein PhnH	CATH (utative)
B	3.40.50.11310	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Bacterial phosphonate metabolism protein PhnH	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
K, L	PF00005	ABC transporter (ABC_tran)	ABC transporter	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are comp ...	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain Pfam:PF00664. These four domains may belong to a single polypeptide as in Swiss:P13569, or belong in different polypeptide chains.	Domain
I, J	PF08352	Oligopeptide/dipeptide transporter, C-terminal region (oligo_HPY)	Oligopeptide/dipeptide transporter, C-terminal region	-	Family
I, J	PF00005	ABC transporter (ABC_tran)	ABC transporter	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are comp ...	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain Pfam:PF00664. These four domains may belong to a single polypeptide as in Swiss:P13569, or belong in different polypeptide chains.	Domain
D, H	PF06007	Phosphonate metabolism protein PhnJ (PhnJ)	Phosphonate metabolism protein PhnJ	-	Family
C, G	PF05861	Bacterial phosphonate metabolism protein (PhnI) (PhnI)	Bacterial phosphonate metabolism protein (PhnI)	-	Family
B, F	PF05845	Bacterial phosphonate metabolism protein (PhnH) (PhnH)	Bacterial phosphonate metabolism protein (PhnH)	-	Family
A, E	PF06754	Phosphonate metabolism protein PhnG (PhnG)	Phosphonate metabolism protein PhnG	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
K, L	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL	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 pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity transferase activity phosphotransferase activity, for other substituted phosphate groups transferase activity, transferring phosphorus-containing groups	localization transport organic phosphonate transport establishment of localization inorganic anion transport catabolic process organic phosphonate metabolic process oxoacid metabolic process organic phosphonate catabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process phosphorus metabolic process	protein-containing complex catalytic complex carbon phosphorus lyase complex transferase complex, transferring phosphorus-containing groups alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex transferase complex
I, J	Putative phosphonates utilization ATP-binding protein PhnK	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 pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity	localization transport organic phosphonate transport establishment of localization inorganic anion transport peptide transport nitrogen compound transport amide transport catabolic process organic phosphonate metabolic process oxoacid metabolic process organic phosphonate catabolic process metabolic process cellular process localization transport organic phosphonate transport establishment of localization inorganic anion transport peptide transport nitrogen compound transport amide transport catabolic process organic phosphonate metabolic process oxoacid metabolic process organic phosphonate catabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process phosphorus metabolic process	protein-containing complex catalytic complex carbon phosphorus lyase complex transferase complex, transferring phosphorus-containing groups alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex transferase complex
D, H	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase	lyase activity catalytic activity carbon phosphorus lyase activity alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	organic phosphonate metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process phosphorus metabolic process localization transport organic phosphonate transport establishment of localization inorganic anion transport catabolic process organic phosphonate catabolic process	protein-containing complex catalytic complex carbon phosphorus lyase complex transferase complex, transferring phosphorus-containing groups alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex transferase complex
C, G	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI	alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity transferase activity catalytic activity phosphotransferase activity, for other substituted phosphate groups transferase activity, transferring phosphorus-containing groups	organic phosphonate metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process phosphorus metabolic process localization transport organic phosphonate transport establishment of localization inorganic anion transport catabolic process organic phosphonate catabolic process	protein-containing complex catalytic complex carbon phosphorus lyase complex transferase complex, transferring phosphorus-containing groups alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex transferase complex
B, F	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity transferase activity catalytic activity phosphotransferase activity, for other substituted phosphate groups transferase activity, transferring phosphorus-containing groups	organic phosphonate metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process phosphorus metabolic process localization transport organic phosphonate transport establishment of localization inorganic anion transport catabolic process organic phosphonate catabolic process	protein-containing complex catalytic complex carbon phosphorus lyase complex transferase complex, transferring phosphorus-containing groups alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex transferase complex
A, E	Phosphonate C-P lyase system protein PhnG	alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity transferase activity catalytic activity phosphotransferase activity, for other substituted phosphate groups transferase activity, transferring phosphorus-containing groups	organic phosphonate metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process phosphorus metabolic process localization transport organic phosphonate transport establishment of localization inorganic anion transport catabolic process organic phosphonate catabolic process	protein-containing complex catalytic complex carbon phosphorus lyase complex transferase complex, transferring phosphorus-containing groups alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex transferase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
K, L	IPR017871	ABC transporter-like, conserved site	Conserved Site
K, L	IPR003439	ABC transporter-like, ATP-binding domain	Domain
K, L	IPR003593	AAA+ ATPase domain	Domain
K, L	IPR012701	Phosphonate C-P lyase system, PhnL	Family
K, L	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
I, J	IPR017871	ABC transporter-like, conserved site	Conserved Site
I, J	IPR013563	Oligopeptide/dipeptide ABC transporter, C-terminal	Domain
I, J	IPR003439	ABC transporter-like, ATP-binding domain	Domain
I, J	IPR003593	AAA+ ATPase domain	Domain
I, J	IPR012700	ATP-binding protein PhnK	Family
I, J	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D, H	IPR010306	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase	Family
C, G	IPR008773	Phosphonate metabolism protein PhnI	Family
B, F	IPR038058	PhnH-like superfamily	Homologous Superfamily
B, F	IPR008772	Bacterial phosphonate metabolism, PhnH	Family
A, E	IPR009609	Phosphonate metabolism PhnG	Family

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.