6PAE

Dickeya chrysanthemi complex with L-Asp at pH 5.6

6PAE の概要

• エントリーDOI: 10.2210/pdb6pae/pdb
• 分子名称: L-asparaginase, ASPARTIC ACID, 1,2-ETHANEDIOL, ... (5 entities in total)
• 機能のキーワード: inactive mutant, hydrolysis of l-asparagine, hydrolase
• 由来する生物種: Dickeya chrysanthemi (Pectobacterium chrysanthemi)
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 141426.93

構造登録者

Lubkowski, J.,Wlodawer, A. (登録日: 2019-06-11, 公開日: 2019-09-04, 最終更新日: 2024-03-13)

主引用文献

Lubkowski, J.,Wlodawer, A.
Geometric considerations support the double-displacement catalytic mechanism of l-asparaginase.
Protein Sci., 28:1850-1864, 2019

PubMed Abstract: Twenty crystal structures of the complexes of l-asparaginase with l-Asn, l-Asp, and succinic acid that are currently available in the Protein Data Bank, as well as 11 additional structures determined in the course of this project, were analyzed in order to establish the level of conservation of the geometric parameters describing interactions between the substrates and the active site of the enzymes. We found that such stereochemical relationships are highly conserved, regardless of the organism from which the enzyme was isolated, specific crystallization conditions, or the nature of the ligands. Analysis of the geometry of the interactions, including Bürgi-Dunitz and Flippin-Lodge angles, indicated that Thr12 (Escherichia coli asparaginase II numbering) is optimally placed to be the primary nucleophile in the most likely scenario utilizing a double-displacement mechanism, whereas catalysis through a single-displacement mechanism appears to be the least likely.

PubMed: 31423681
DOI: 10.1002/pro.3709

実験手法

X-RAY DIFFRACTION (1.6 Å)