5X9H

Crystal structure of the Mg2+ channel MgtE in complex with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.598 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

ATP-dependent modulation of MgtE in Mg(2+) homeostasis

Tomita, A.Zhang, M.Jin, F.Zhuang, W.Takeda, H.Maruyama, T.Osawa, M.Hashimoto, K.I.Kawasaki, H.Ito, K.Dohmae, N.Ishitani, R.Shimada, I.Yan, Z.Hattori, M.Nureki, O.

(2017) Nat Commun 8: 148-148

  • DOI: 10.1038/s41467-017-00082-w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Magnesium is an essential ion for numerous physiological processes. MgtE is a Mg <sup>2+ </sup> selective channel involved in the maintenance of intracellular Mg <sup>2+ </sup> homeostasis, whose gating is regulated by intracellular Mg <sup>2+ </sup> ...

    Magnesium is an essential ion for numerous physiological processes. MgtE is a Mg 2+ selective channel involved in the maintenance of intracellular Mg 2+ homeostasis, whose gating is regulated by intracellular Mg 2+ levels. Here, we report that ATP binds to MgtE, regulating its Mg 2+ -dependent gating. Crystal structures of MgtE-ATP complex show that ATP binds to the intracellular CBS domain of MgtE. Functional studies support that ATP binding to MgtE enhances the intracellular domain affinity for Mg 2+ within physiological concentrations of this divalent cation, enabling MgtE to function as an in vivo Mg 2+ sensor. ATP dissociation from MgtE upregulates Mg 2+ influx at both high and low intracellular Mg 2+ concentrations. Using site-directed mutagenesis and structure based-electrophysiological and biochemical analyses, we identify key residues and main structural changes involved in the process. This work provides the molecular basis of ATP-dependent modulation of MgtE in Mg 2+ homeostasis.MgtE is an Mg 2+ transporter involved in Mg 2+ homeostasis. Here, the authors report that ATP regulates the Mg +2 -dependent gating of MgtE and use X-ray crystallography combined with functional studies to propose the molecular mechanisms involved in this process.


    Organizational Affiliation

    Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan.,State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center of Genetics and Development, Institute of Brain Science, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai, 200438, China. zqyan@fudan.edu.cn.,Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Department of Green and Sustainable Chemistry, Tokyo Denki University, 5 Asahi-cho, Senju, Adachi-ku, Tokyo, 120-8551, Japan.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai, 200438, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai, 200438, China. hattorim@fudan.edu.cn.,Faculty of Life Science, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.,Department of Human Anatomy, School of Basic Medicine Sciences, Southwest Medical University, Luzhou, Sichuan, 646000, China. zqyan@fudan.edu.cn.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.,State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center of Genetics and Development, Institute of Brain Science, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai, 200438, China.,Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan. nureki@bs.s.u-tokyo.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Magnesium transporter MgtE
A, B
473Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Find proteins for Q5SMG8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SMG8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.598 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.250 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.330α = 90.00
b = 85.651β = 100.02
c = 156.558γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology of ChinaChina2016YFA0502800

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Database references