2I2C

Crystal structure of LmNADK1

Summary for 2I2C

• Entry DOI: 10.2210/pdb2i2c/pdb
• Related: 2I1W 2I29 2I2A 2I2B 2I2D 2I2E 2I2F
• Descriptor: Probable inorganic polyphosphate/ATP-NAD kinase 1, (2S,3S,4R,5R,2'S,3'S,4'R,5'R)-2,2'-[DITHIOBIS(METHYLENE)]BIS[5-(6-AMINO-9H-PURIN-9-YL)TETRAHYDROFURAN-3,4-DIOL], TETRAETHYLENE GLYCOL, ... (4 entities in total)
• Functional Keywords: nadp bound crystal structure of lmnadk1, transferase
• Biological source: Listeria monocytogenes EGD-e
• Cellular location: Cytoplasm : Q8Y8D7
• Total number of polymer chains: 1
• Total formula weight: 31804.10

Authors

Poncet-Montange, G.,Labesse, G. (deposition date: 2006-08-16, release date: 2007-08-07, Last modification date: 2023-08-30)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.85 Å)