4RF8

Crystal structure of double-domain arginine kinase from Anthopleura japonicas in complex with ADP

4RF8 の概要

• エントリーDOI: 10.2210/pdb4rf8/pdb
• 関連するPDBエントリー: 4RF6 4RF7 4RF9
• 分子名称: Arginine kinase, ADENOSINE-5'-DIPHOSPHATE, NITRATE ION, ... (5 entities in total)
• 機能のキーワード: double domain, tandem domain, phsphagen kinase, transferase
• 由来する生物種: Anthopleura japonica (Sea anemone)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 163455.77

構造登録者

Wang, Z.,Qiao, Z.,Ye, S.,Zhang, R. (登録日: 2014-09-25, 公開日: 2015-04-08, 最終更新日: 2023-09-20)

主引用文献

Wang, Z.,Qiao, Z.,Ye, S.,Zhang, R.
Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains.
Acta Crystallogr.,Sect.D, 71:779-789, 2015

PubMed Abstract: Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.

PubMed: 25849389
DOI: 10.1107/S1399004715001169

実験手法

X-RAY DIFFRACTION (2.17 Å)