Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase.
Journal, issue, pages	Nat Commun, Vol. 14, Issue 1, Page 1001, Year 2023
Publish date	Feb 22, 2023
Authors	Søren K Amstrup / Sui Ching Ong / Nicholas Sofos / Jesper L Karlsen / Ragnhild B Skjerning / Thomas Boesen / Jan J Enghild / Bjarne Hove-Jensen / Ditlev E Brodersen /
PubMed Abstract	In Escherichia coli, the 14-cistron phn operon encoding carbon-phosphorus lyase allows for utilisation of phosphorus from a wide range of stable phosphonate compounds containing a C-P bond. As part ...In Escherichia coli, the 14-cistron phn operon encoding carbon-phosphorus lyase allows for utilisation of phosphorus from a wide range of stable phosphonate compounds containing a C-P bond. As part of a complex, multi-step pathway, the PhnJ subunit was shown to cleave the C-P bond via a radical mechanism, however, the details of the reaction could not immediately be reconciled with the crystal structure of a 220 kDa PhnGHIJ C-P lyase core complex, leaving a significant gap in our understanding of phosphonate breakdown in bacteria. Here, we show using single-particle cryogenic electron microscopy that PhnJ mediates binding of a double dimer of the ATP-binding cassette proteins, PhnK and PhnL, to the core complex. ATP hydrolysis induces drastic structural remodelling leading to opening of the core complex and reconfiguration of a metal-binding and putative active site located at the interface between the PhnI and PhnJ subunits.
External links	Nat Commun / PubMed:36813778 / PubMed Central
Methods	EM (single particle)
Resolution	1.93 - 2.57 Å
Structure data	14441 7z15 EMDB-14441, PDB-7z15: E. coli C-P lyase bound to a PhnK/PhnL dual ABC dimer and ADP + Pi Method: EM (single particle) / Resolution: 1.93 Å 14442 7z16 EMDB-14442, PDB-7z16: E. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP and PhnK E171Q mutation Method: EM (single particle) / Resolution: 2.09 Å 14443 7z17 EMDB-14443, PDB-7z17: E. coli C-P lyase bound to a PhnK ABC dimer in an open conformation Method: EM (single particle) / Resolution: 2.57 Å 14444 7z18 EMDB-14444, PDB-7z18: E. coli C-P lyase bound to a PhnK ABC dimer and ATP Method: EM (single particle) / Resolution: 1.98 Å 14445 7z19 EMDB-14445, PDB-7z19: E. coli C-P lyase bound to a single PhnK ABC domain Method: EM (single particle) / Resolution: 2.57 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-I9X: alpha-D-ribose-1,2-cyclic-phosphate-5-phosphate ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-PO4: PHOSPHATE ION / Phosphate ChemComp-MG: Unknown entry ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate ChemComp-HOH: WATER / Water ChemComp-ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM
Source	escherichia coli (E. coli)
Keywords	TRANSFERASE / protein complex / ABC / hydrolase / lyase / carbon phosphorus / carbon-phosphorus / SAM