1KQP

NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION

1KQP の概要

• エントリーDOI: 10.2210/pdb1kqp/pdb
• 関連するPDBエントリー: 1EE1 1FYD 1IFX 1IH8 1NSY 2NSY
• 分子名称: NH(3)-dependent NAD(+) synthetase, MAGNESIUM ION, 1,2-ETHANEDIOL, ... (6 entities in total)
• 機能のキーワード: ligase, amidotransferase, atp pyrophosphatase, nad-adenylate
• 由来する生物種: Bacillus subtilis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 63701.44

構造登録者

Symersky, J.,Devedjiev, Y.,Moore, K.,Brouillette, C.,DeLucas, L. (登録日: 2002-01-07, 公開日: 2002-06-28, 最終更新日: 2023-08-16)

主引用文献

Symersky, J.,Devedjiev, Y.,Moore, K.,Brouillette, C.,DeLucas, L.
NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution.
Acta Crystallogr.,Sect.D, 58:1138-1146, 2002

PubMed Abstract: The final step of NAD+ biosynthesis includes an amide transfer to nicotinic acid adenine dinucleotide (NaAD) catalyzed by NAD+ synthetase. This enzyme was co-crystallized in microgravity with natural substrates NaAD and ATP at pH 8.5. The crystal was exposed to ammonium ions, synchrotron diffraction data were collected and the atomic model was refined anisotropically at 1 A resolution to R = 11.63%. Both binding sites are occupied by the NAD-adenylate intermediate, pyrophosphate and two magnesium ions. The atomic resolution of the structure allows better definition of non-planar peptide groups, reveals a low mean anisotropy of protein and substrate atoms and indicates the H-atom positions of the phosphoester group of the reaction intermediate. The phosphoester group is protonated at the carbonyl O atom O7N, suggesting a carbenium-ion structure stabilized by interactions with two solvent sites presumably occupied by ammonia and a water molecule. A mechanism is proposed for the second catalytic step, which includes a nucleophilic attack by the ammonia molecule on the intermediate.

PubMed: 12077433
DOI: 10.1107/S0907444902006698

実験手法

X-RAY DIFFRACTION (1.03 Å)