8RJ4

E. coli adenylate kinase in complex with two ADP molecules and Mg2+ as a result of enzymatic AP4A hydrolysis

8RJ4 の概要

• エントリーDOI: 10.2210/pdb8rj4/pdb
• 分子名称: Adenylate kinase, ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: atp:amp phosphotransferase, energy metabolism, ap4a hydrolysis, potential moonlighting protein, transferase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 98017.24

構造登録者

Tischlik, S.,Ronge, P.,Wolf-Watz, M.,Sauer-Eriksson, A.E. (登録日: 2023-12-20, 公開日: 2024-07-10, 最終更新日: 2024-08-28)

主引用文献

Nam, K.,Thodika, A.R.A.,Tischlik, S.,Phoeurk, C.,Nagy, T.M.,Schierholz, L.,Aden, J.,Rogne, P.,Drescher, M.,Sauer-Eriksson, A.E.,Wolf-Watz, M.
Magnesium induced structural reorganization in the active site of adenylate kinase.
Sci Adv, 10:eado5504-eado5504, 2024

PubMed Abstract: Phosphoryl transfer is a fundamental reaction in cellular signaling and metabolism that requires Mg as an essential cofactor. While the primary function of Mg is electrostatic activation of substrates, such as ATP, the full spectrum of catalytic mechanisms exerted by Mg is not known. In this study, we integrate structural biology methods, molecular dynamic (MD) simulations, phylogeny, and enzymology assays to provide molecular insights into Mg-dependent structural reorganization in the active site of the metabolic enzyme adenylate kinase. Our results demonstrate that Mg induces a conformational rearrangement of the substrates (ATP and ADP), resulting in a 30° adjustment of the angle essential for reversible phosphoryl transfer, thereby optimizing it for catalysis. MD simulations revealed transitions between conformational substates that link the fluctuation of the angle to large-scale enzyme dynamics. The findings contribute detailed insight into Mg activation of enzymes and may be relevant for reversible and irreversible phosphoryl transfer reactions.

PubMed: 39121211
DOI: 10.1126/sciadv.ado5504

実験手法

X-RAY DIFFRACTION (2.11 Å)