2J5R

2.25 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui after second radiation burn (radiation damage series)

2J5R の概要

• エントリーDOI: 10.2210/pdb2j5r/pdb
• 関連するPDBエントリー: 1D3A 1GT2 1HLP 1O6Z 2HLP 2J5K 2J5Q
• 分子名称: MALATE DEHYDROGENASE, CHLORIDE ION (3 entities in total)
• 機能のキーワード: nad, halophile, oxidoreductase, radiation damage, malate dehydrogenase, tricarboxylic acid cycle
• 由来する生物種: HALOARCULA MARISMORTUI
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 131634.53

構造登録者

Fioravanti, E.,Vellieux, F.M.D.,Amara, P.,Madern, D.,Weik, M. (登録日: 2006-09-19, 公開日: 2006-09-25, 最終更新日: 2023-12-13)

主引用文献

Fioravanti, E.,Vellieux, F.M.D.,Amara, P.,Madern, D.,Weik, M.
Specific Radiation Damage to Acidic Residues and its Relation to Their Chemical and Structural Environment.
J.Synchrotron Radiat., 14:84-, 2007

PubMed Abstract: Intense synchrotron radiation produces specific structural and chemical damage to crystalline proteins even at 100 K. Carboxyl groups of acidic residues (Glu, Asp) losing their definition is one of the major effects observed. Here, the susceptibilities to X-ray damage of acidic residues in tetrameric malate dehydrogenase from Haloarcula marismortui are investigated. The marked excess of acidic residues in this halophilic enzyme makes it an ideal target to determine how specific damage to acidic residues is related to their structural and chemical environment. Four conclusions are drawn. (i) Acidic residues interacting with the side-chains of lysine and arginine residues are less affected by radiation damage than those interacting with serine, threonine and tyrosine side-chains. This suggests that residues with higher pK(a) values are more vulnerable to damage than those with a lower pK(a). However, such a correlation was not found when calculated pK(a) values were inspected. (ii) Acidic side-chains located in the enzymatic active site are the most radiation-sensitive ones. (iii) Acidic residues in the internal cavity formed by the four monomers and those involved in crystal contacts appear to be particularly susceptible. (iv) No correlation was found between radiation susceptibility and solvent accessibility.

PubMed: 17211074
DOI: 10.1107/S0909049506038623

実験手法

X-RAY DIFFRACTION (2.25 Å)