5X9G | pdb_00005x9g

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

PDB DOI: https://doi.org/10.2210/pdb5X9G/pdb

Classification: METAL TRANSPORT
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2017-03-07 Released: 2017-08-16
Deposition Author(s): Tomita, A., Hattori, M., Nureki, O.
Funding Organization(s): Ministry of Science and Technology of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.298 (Depositor), 0.299 (DCC)
R-Value Work:
0.240 (Depositor), 0.246 (DCC)
R-Value Observed:
0.243 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 28747715 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-017-00082-w
Primary Citation Related Structures:
5X9G, 5X9H

PubMed Abstract:
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 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.

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.

Faculty of Life Science, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.

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.

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.

Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, 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. nureki@bs.s.u-tokyo.ac.jp.

Macromolecule Content

Total Structure Weight: 128.62 kDa
Atom Count: 8,088
Modeled Residue Count: 991
Deposited Residue Count: 1,112
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnesium transporter MgtE	A, B, C, D	278	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: TTHA1060 Membrane Entity: Yes
UniProt
Find proteins for Q5SMG8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SMG8 Go to UniProtKB: Q5SMG8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SMG8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], N [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]