3O91

High resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into catalytic mechanism and inhibition by aldehydes

3O91 の概要

• エントリーDOI: 10.2210/pdb3o91/pdb
• 関連するPDBエントリー: 3O90 3O92 3O93 3O94
• 分子名称: nicotinamidase, ZINC ION (3 entities in total)
• 機能のキーワード: nicotinamidase, hydrolase
• 由来する生物種: Streptococcus pneumoniae
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 95191.86

構造登録者

French, J.B.,Cen, Y.,Sauve, A.A.,Ealick, S.E. (登録日: 2010-08-03, 公開日: 2011-01-12, 最終更新日: 2025-03-26)

主引用文献

French, J.B.,Cen, Y.,Sauve, A.A.,Ealick, S.E.
High-resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into the catalytic mechanism and inhibition by aldehydes .
Biochemistry, 49:8803-8812, 2010

PubMed Abstract: Nicotinamidases are salvage enzymes that convert nicotinamide to nicotinic acid. These enzymes are essential for the recycling of nicotinamide into NAD(+) in most prokaryotes and most single-cell and multicellular eukaryotes, but not in mammals. The significance of these enzymes for nicotinamide salvage and for NAD(+) homeostasis has stimulated interest in nicotinamidases as possible antibiotic targets. Nicotinamidases are also regulators of intracellular nicotinamide concentrations, thereby regulating signaling of downstream NAD(+)-consuming enzymes, such as the NAD(+)-dependent deacetylases (sirtuins). Here, we report several high-resolution crystal structures of the nicotinamidase from Streptococcus pneumoniae (SpNic) in unliganded and ligand-bound forms. The structure of the C136S mutant in complex with nicotinamide provides details about substrate binding, while a trapped nicotinoyl thioester in a complex with SpNic reveals the structure of the proposed thioester reaction intermediate. Examination of the active site of SpNic reveals several important features, including a metal ion that coordinates the substrate and the catalytically relevant water molecule and an oxyanion hole that both orients the substrate and offsets the negative charge that builds up during catalysis. Structures of this enzyme with bound nicotinaldehyde inhibitors elucidate the mechanism of inhibition and provide further details about the catalytic mechanism. In addition, we provide a biochemical analysis of the identity and role of the metal ion that orients the ligand in the active site and activates the water molecule responsible for hydrolysis of the substrate. These data provide structural evidence of several proposed reaction intermediates and allow for a more complete understanding of the catalytic mechanism of this enzyme.

PubMed: 20853856
DOI: 10.1021/bi1012436

実験手法

X-RAY DIFFRACTION (1.63 Å)