4GYJ

Crystal structure of mutant (D318N) bacillus subtilis family 3 glycoside hydrolase (nagz) in complex with glcnac-murnac (space group P1)

4GYJ の概要

• エントリーDOI: 10.2210/pdb4gyj/pdb
• 関連するPDBエントリー: 4GYK
• 分子名称: Uncharacterized lipoprotein ybbD, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• 機能のキーワード: tim-barrel, hydrolase, hydrolase-substrate complex, hydrolase/substrate
• 由来する生物種: Bacillus subtilis subsp. subtilis
• 細胞内の位置: Cell membrane ; Lipid-anchor : P40406
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 143896.62

構造登録者

Bacik, J.P.,Mark, B.L. (登録日: 2012-09-05, 公開日: 2012-12-19, 最終更新日: 2023-09-13)

主引用文献

Bacik, J.P.,Whitworth, G.E.,Stubbs, K.A.,Vocadlo, D.J.,Mark, B.L.
Active Site Plasticity within the Glycoside Hydrolase NagZ Underlies a Dynamic Mechanism of Substrate Distortion.
Chem.Biol., 19:1471-1482, 2012

PubMed Abstract: NagZ is a glycoside hydrolase that participates in peptidoglycan (PG) recycling by removing β-N-acetylglucosamine from PG fragments that are excised from the bacterial cell wall during growth. Notably, the products formed by NagZ, 1,6-anhydroMurNAc-peptides, activate β-lactam resistance in many Gram-negative bacteria, making this enzyme of interest as a potential therapeutic target. Crystal structure determinations of NagZ from Salmonella typhimurium and Bacillus subtilis in complex with natural substrate, trapped as a glycosyl-enzyme intermediate, and bound to product, define the reaction coordinate of the NagZ family of enzymes. The structures, combined with kinetic studies, reveal an uncommon degree of structural plasticity within the active site of a glycoside hydrolase, and unveil how NagZ drives substrate distortion using a highly mobile loop that contains a conserved histidine that has been proposed as the general acid/base.

PubMed: 23177201
DOI: 10.1016/j.chembiol.2012.09.016

実験手法

X-RAY DIFFRACTION (1.65 Å)