4JLD

Crystal Structures of adenylate kinase with 2 ADP's

4JLD の概要

• エントリーDOI: 10.2210/pdb4jld/pdb
• 関連するPDBエントリー: 4JL5 4JL8 4JLA 4JLB 4JLO 4JLP
• 分子名称: Adenylate kinase, ADENOSINE-5'-DIPHOSPHATE (3 entities in total)
• 機能のキーワード: transferase, adp binding, phosphoryl transfer reaction
• 由来する生物種: Aquifex aeolicus
• 細胞内の位置: Cytoplasm : O66490
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 47674.43

構造登録者

Cho, Y.-J.,Kern, D. (登録日: 2013-03-12, 公開日: 2014-06-25, 最終更新日: 2024-02-28)

主引用文献

Kerns, S.J.,Agafonov, R.V.,Cho, Y.J.,Pontiggia, F.,Otten, R.,Pachov, D.V.,Kutter, S.,Phung, L.A.,Murphy, P.N.,Thai, V.,Alber, T.,Hagan, M.F.,Kern, D.
The energy landscape of adenylate kinase during catalysis.
Nat.Struct.Mol.Biol., 22:124-131, 2015

PubMed Abstract: Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg(2+) cofactor activates two distinct molecular events: phosphoryl transfer (>10(5)-fold) and lid opening (10(3)-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 10(3)-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.

PubMed: 25580578
DOI: 10.1038/nsmb.2941

実験手法

X-RAY DIFFRACTION (1.552 Å)