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	Nucleotide- and metalloid-driven conformational changes in the arsenite efflux ATPase ArsA.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 122, Issue 35, Page e2506440122, Year 2025
Publish date	Sep 2, 2025
Authors	Shivansh Mahajan / Ashley E Pall / Yancheng E Li / Timothy L Stemmler / Douglas C Rees / William M Clemons /
PubMed Abstract	Arsenite (As) is toxic to all organisms due to its ability to tightly bind exposed thiols within cells. An important As resistance mechanism in prokaryotes involves proteins encoded by the operon. A ...Arsenite (As) is toxic to all organisms due to its ability to tightly bind exposed thiols within cells. An important As resistance mechanism in prokaryotes involves proteins encoded by the operon. A central component of the operon in many bacteria is the cytoplasmic ATPase, ArsA, which orchestrates a series of nucleotide-dependent handoffs, starting with the capture of As by the ArsD metallochaperone and culminating in its removal from the cell by the ArsB efflux pump. Although the mechanism of ArsA has been widely studied, the molecular details of how nucleotide hydrolysis modulates these events remain unclear. ArsA is an archetypal member of the intradimeric Walker A (IWA) family of ATPases, implicated in a diversity of complex biological functions. Conformational changes typical of IWA ATPases have been postulated to drive these molecular events but have not been demonstrated. We report cryogenic electron microscopy (cryo-EM) structures of ArsA in MgADP-bound and MgATP-bound states, as well as a distinct MgATP-bound state liganded to As. X-ray absorption spectroscopy (XAS) confirmed three-coordinate binding of As to the conserved cysteines at the metalloid-binding site of the closed state. Coupled with biochemical characterization, our cryo-EM structures reveal key conformational changes in the ArsA catalytic cycle consistent with other IWA ATPases and provide the structural basis for allosteric activation of nucleotide hydrolysis by As. This work establishes how the nucleotide state of ArsA transiently creates a high-affinity binding site that can sequester metalloid within the cell, followed by a nucleotide-driven handoff to ArsB for efflux.
External links	Proc Natl Acad Sci U S A / PubMed:40880530 / PubMed Central
Methods	EM (single particle)
Resolution	3.0 - 6.6 Å
Structure data	49231 9nbl EMDB-49231, PDB-9nbl: Open conformation of ArsA from L. ferriphilum in complex with MgADP determined in the presence of arsenite Method: EM (single particle) / Resolution: 3.4 Å 49232 9nbm EMDB-49232, PDB-9nbm: Open conformation of ArsA from L. ferriphilum in complex with MgADP determined in absence of arsenite Method: EM (single particle) / Resolution: 3.8 Å EMDB-49233: Open conformation of ArsA from L. ferriphilum in presence of MgATP Method: EM (single particle) / Resolution: 6.6 Å 49234 9nbo EMDB-49234, PDB-9nbo: Closed conformation of ArsA from L. ferriphilum in complex with MgATP and arsenite Method: EM (single particle) / Resolution: 3.0 Å 49237 9nbw EMDB-49237, PDB-9nbw: Closed conformation of ArsA from L. ferriphilum in complex with MgATP and arsenite at 1.5 minute time point Method: EM (single particle) / Resolution: 3.0 Å
Chemicals	ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-ARS: ARSENIC ChemComp-HOH: WATER
Source	leptospirillum ferriphilum (bacteria) leptospirillum ferriphilum ml-04 (bacteria)
Keywords	HYDROLASE / ATPase / open conformation / arsenite / arsenic / ADP / Intradimeric Walker A / closed conformation / closed state / ATP