2RJH

Crystal structure of biosynthetic alaine racemase in D-cycloserine-bound form from Escherichia coli

2RJH の概要

• エントリーDOI: 10.2210/pdb2rjh/pdb
• 関連するPDBエントリー: 2RJG
• 分子名称: Alanine racemase, SULFATE ION, D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE, ... (4 entities in total)
• 機能のキーワード: alpha/beta barrel, cell shape, cell wall biogenesis/degradation, isomerase, peptidoglycan synthesis, pyridoxal phosphate
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 167574.25

構造登録者

Wu, D.,Hu, T.,Zhang, L.,Jiang, H.,Shen, X. (登録日: 2007-10-15, 公開日: 2008-07-08, 最終更新日: 2023-11-15)

主引用文献

Wu, D.,Hu, T.,Zhang, L.,Chen, J.,Du, J.,Ding, J.,Jiang, H.,Shen, X.
Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis
Protein Sci., 17:1066-1076, 2008

PubMed Abstract: Alanine racemase (Alr) is an important enzyme that catalyzes the interconversion of L-alanine and D-alanine, an essential building block in the peptidoglycan biosynthesis. For the small size of the Alr active site, its conserved substrate entryway has been proposed as a potential choice for drug design. In this work, we fully analyzed the crystal structures of the native, the D-cycloserine-bound, and four mutants (P219A, E221A, E221K, and E221P) of biosynthetic Alr from Escherichia coli (EcAlr) and studied the potential roles in substrate orientation for the key residues involved in the substrate entryway in conjunction with the enzymatic assays. Structurally, it was discovered that EcAlr is similar to the Pseudomonas aeruginosa catabolic Alr in both overall and active site geometries. Mutation of the conserved negatively charged residue aspartate 164 or glutamate 165 at the substrate entryway could obviously reduce the binding affinity of enzyme against the substrate and decrease the turnover numbers in both D- to L-Ala and L- to D-Ala directions, especially when mutated to lysine with the opposite charge. However, mutation of Pro219 or Glu221 had only negligible or a small influence on the enzymatic activity. Together with the enzymatic and structural investigation results, we thus proposed that the negatively charged residues Asp164 and Glu165 around the substrate entryway play an important role in substrate orientation with cooperation of the positively charged Arg280 and Arg300 on the opposite monomer. Our findings are expected to provide some useful structural information for inhibitor design targeting the substrate entryway of Alr.

PubMed: 18434499
DOI: 10.1110/ps.083495908

実験手法

X-RAY DIFFRACTION (2.4 Å)