2J5R

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

Summary for 2J5R

• Entry DOI: 10.2210/pdb2j5r/pdb
• Related: 1D3A 1GT2 1HLP 1O6Z 2HLP 2J5K 2J5Q
• Descriptor: MALATE DEHYDROGENASE, CHLORIDE ION (3 entities in total)
• Functional Keywords: nad, halophile, oxidoreductase, radiation damage, malate dehydrogenase, tricarboxylic acid cycle
• Biological source: HALOARCULA MARISMORTUI
• Total number of polymer chains: 4
• Total formula weight: 131634.53

Authors

Fioravanti, E.,Vellieux, F.M.D.,Amara, P.,Madern, D.,Weik, M. (deposition date: 2006-09-19, release date: 2006-09-25, Last modification date: 2023-12-13)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.25 Å)