8RJ4

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

Summary for 8RJ4

• Entry DOI: 10.2210/pdb8rj4/pdb
• Descriptor: Adenylate kinase, ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: atp:amp phosphotransferase, energy metabolism, ap4a hydrolysis, potential moonlighting protein, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 98017.24

Authors

Tischlik, S.,Ronge, P.,Wolf-Watz, M.,Sauer-Eriksson, A.E. (deposition date: 2023-12-20, release date: 2024-07-10, Last modification date: 2024-08-28)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.11 Å)