4XB6 | pdb_00004xb6

Structure of the E. coli C-P lyase core complex

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4xb6b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PhnH-like	PhnH-like	automated matches	(Escherichia coli str. K-12 substr. MG1655 ) [TaxId: 511145 ],	SCOPe (2.08)
F	d4xb6f_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PhnH-like	PhnH-like	automated matches	(Escherichia coli str. K-12 substr. MG1655 ) [TaxId: 511145 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PhnH-like	8034005	3001133	SCOP2B (2022-06-29)
F	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)
A	Molybdopterin	e4xb6A1	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: Molybdopterin	ECOD (v294.1)
E	Mononeg_RNA_pol	e4xb6E1	A: a/b three-layered sandwiches	X: Cysteine proteinases-like	H: Cysteine proteinases	T: Cysteine proteinases	F: Mononeg_RNA_pol	ECOD (v294.1)
B	SSL_OB	e4xb6B1	A: a/b three-layered sandwiches	X: Sigma2 domain-like	H: Bacterial enterotoxins	T: Bacterial enterotoxins	F: SSL_OB	ECOD (v294.1)
F	SSL_OB	e4xb6F1	A: a/b three-layered sandwiches	X: Sigma2 domain-like	H: Bacterial enterotoxins	T: Bacterial enterotoxins	F: SSL_OB	ECOD (v294.1)
C	PhnI	e4xb6C1	A: a/b three-layered sandwiches	X: PhnH-like	H: C-P lyase subunit PhnG	T: C-P lyase subunit PhnG	F: PhnI	ECOD (v294.1)
C	PhnI	e4xb6C2	A: a/b three-layered sandwiches	X: PhnH-like	H: PhnH-like	T: PhnH-like	F: PhnI	ECOD (v294.1)
G	Molybdopterin	e4xb6G1	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: Molybdopterin	ECOD (v294.1)
D	PhnJ	e4xb6D1	A: a/b three-layered sandwiches	X: PhnH-like	H: PhnH-like	T: PhnH-like	F: PhnJ	ECOD (v294.1)
D	PhnJ	e4xb6D2	A: a/b three-layered sandwiches	X: Cysteine proteinases-like	H: Cysteine proteinases	T: Cysteine proteinases	F: PhnJ	ECOD (v294.1)
H	Molybdopterin	e4xb6H1	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: Molybdopterin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.11310	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Bacterial phosphonate metabolism protein PhnH	CATH (4.3.0)
F	3.40.50.11310	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Bacterial phosphonate metabolism protein PhnH	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E	PF06754	Phosphonate metabolism protein PhnG (PhnG)	Phosphonate metabolism protein PhnG	-	Family
B, F	PF05845	Bacterial phosphonate metabolism protein (PhnH) (PhnH)	Bacterial phosphonate metabolism protein (PhnH)	-	Family
C, G	PF05861	Bacterial phosphonate metabolism protein (PhnI) (PhnI)	Bacterial phosphonate metabolism protein (PhnI)	-	Family
D, H	PF06007	Phosphonate metabolism protein PhnJ (PhnJ)	Phosphonate metabolism protein PhnJ	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit 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
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
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
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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E	IPR009609	Phosphonate metabolism PhnG	Family
B, F	IPR038058	PhnH-like superfamily	Homologous Superfamily
B, F	IPR008772	Bacterial phosphonate metabolism, PhnH	Family
C, G	IPR008773	Phosphonate metabolism protein PhnI	Family
D, H	IPR010306	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
D	alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase M-CSA #949	This radical SAM (AdoMet) enzyme is part of the C-P lyase complex, which is responsible for processing phophonates into usable phosphate. The enzyme from the bacterium Escherichia coli can act on additional alpha-D-ribose phosphonate substrates with different substituents attached to the phosphonate phosphorus (e.g. alpha-D-ribose-1- (N-(phosphonomethyl)glycine)-5-phosphate and alpha-D-ribose-1-(2-N- acetamidomethylphosphonate)-5-phosphate).	Defined by 5 residues: GLY:D-32CYS:D-241CYS:D-244CYS:D-266CYS:D-272 \| Explore in 3D: M-CSA Motif Definition Extent of motif is too large to support Structure Motif searching. EC: 4.7.1.1 (PDB Primary Data)

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.