› 7z18

Electron Microscopy
1.98Å resolution

E. coli C-P lyase bound to a PhnK ABC dimer and ATP

Released:
DOI: 10.2210/pdb7z18/pdb
PDB entry 7z18 coloured by chain, front view.
PDB entry 7z18 coloured by chain, side view.
PDB entry 7z18 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase.
Amstrup SK, Ong SC, Sofos N, Karlsen JL, Skjerning RB, Boesen T, Enghild JJ, Hove-Jensen B, Brodersen DE
OpenAccess logo Nat Commun 14 1001 (2023)
PMID: 36813778
Related structures: EMD-14444

Function and Biology Details

Reactions catalysed: 
ATP + methylphosphonate = alpha-D-ribose 1-methylphosphonate 5-triphosphate + adenine
Alpha-D-ribose 1-methylphosphonate 5-phosphate + S-adenosyl-L-methionine + reduced electron acceptor = alpha-D-ribose 1,2-cyclic phosphate 5-phosphate + methane + L-methionine + 5'-deoxyadenosine + electron acceptor
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-147795 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG Chains: A, E
Molecule details ›
Chains: A, E
Length: 150 amino acids
Theoretical weight: 16.55 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P16685 (Residues: 1-150; Coverage: 100%)
Gene names: JW4062, b4101, phnG
Sequence domains: Phosphonate metabolism protein PhnG
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH Chains: B, F
Molecule details ›
Chains: B, F
Length: 194 amino acids
Theoretical weight: 21.05 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P16686 (Residues: 1-194; Coverage: 100%)
Gene names: JW4061, b4100, phnH
Sequence domains: Bacterial phosphonate metabolism protein (PhnH)
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI Chains: C, G
Molecule details ›
Chains: C, G
Length: 354 amino acids
Theoretical weight: 38.95 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P16687 (Residues: 1-354; Coverage: 100%)
Gene names: JW4060, b4099, phnI
Sequence domains: Bacterial phosphonate metabolism protein (PhnI)
Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase Chains: D, H
Molecule details ›
Chains: D, H
Length: 281 amino acids
Theoretical weight: 31.89 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P16688 (Residues: 1-281; Coverage: 100%)
Gene names: JW4059, b4098, phnJ
Sequence domains: Phosphonate metabolism protein PhnJ
Putative phosphonates utilization ATP-binding protein PhnK Chains: I, J
Molecule details ›
Chains: I, J
Length: 291 amino acids
Theoretical weight: 32 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P16678 (Residues: 1-252; Coverage: 100%)
Gene names: JW5727, b4097, phnK
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand ZN 4 x ZN
Ligand I9X 2 x I9X
Ligand ATP 2 x ATP
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 1.98Å
Relevant EMDB volumes: EMD-14444
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

1 review citation

The Microbial Degradation of Natural and Anthropogenic Phosphonates.
Ruffolo et al. (2023)
1 other article

1 mention without citation

Structure-Activity Relationship Target Prediction Studies of Clindamycin Derivatives with Broad-Spectrum Bacteriostatic Antibacterial Properties.
Jia et al. (2023)