4DY6

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 2'-phosphate bis(adenosine)-5'-diphosphate

「2I2E」から置き換えられました

4DY6 の概要

• エントリーDOI: 10.2210/pdb4dy6/pdb
• 分子名称: inorganic polyphosphate/ATP-NAD kinase 1, [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE, CITRIC ACID, ... (4 entities in total)
• 機能のキーワード: lmnadk1, nad analog, inorganic polyphosphates, transferase
• 由来する生物種: Listeria monocytogenes
• 細胞内の位置: Cytoplasm (By similarity): Q8Y8D7
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 31993.81

構造登録者

Poncet-Montange, G.,Assairi, L.,Arold, S.,Pochet, S.,Labesse, G. (登録日: 2012-02-28, 公開日: 2012-03-07, 最終更新日: 2023-09-13)

主引用文献

Poncet-Montange, G.,Assairi, L.,Arold, S.,Pochet, S.,Labesse, G.
NAD kinases use substrate-assisted catalysis for specific recognition of NAD.
J.Biol.Chem., 282:33925-33934, 2007

PubMed Abstract: Here we describe the crystal structures of the NAD kinase (LmNADK1) from Listeria monocytogenes in complex with its substrate NAD, its product NADP, or two synthesized NAD mimics. We identified one of the NAD mimics, di-adenosine diphosphate, as a new substrate for LmNADK1, whereas we showed that the closely related compound di-5'-thioadenosine is a novel non-natural inhibitor for this enzyme. These structures suggest a mechanism involving substrate-assisted catalysis. Indeed, sequence/structure comparison and directed mutagenesis have previously shown that NAD kinases (NADKs) and the distantly related 6-phosphofructokinases share the same catalytically important GGDGT motif. However, in this study we have shown that these enzymes use the central aspartate of this motif differently. Although this acidic residue chelates the catalytic Mg(2+) ion in 6-phosphofructokinases, it activates the phospho-acceptor (NAD) in NADKs. Sequence/structure comparisons suggest that the role of this aspartate would be conserved in NADKs and the related sphingosine and diacylglycerol kinases.

PubMed: 17686780
DOI: 10.1074/jbc.M701394200

実験手法

X-RAY DIFFRACTION (2.2 Å)