1Z0Z

Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with NAD

Summary for 1Z0Z

• Entry DOI: 10.2210/pdb1z0z/pdb
• Descriptor: Probable inorganic polyphosphate/ATP-NAD kinase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE (3 entities in total)
• Functional Keywords: nad kinase, nad, atp, nadp, structural genomics, psi, protein structure initiative, berkeley structural genomics center, bsgc, transferase
• Biological source: Archaeoglobus fulgidus
• Cellular location: Cytoplasm (By similarity): O30297
• Total number of polymer chains: 4
• Total formula weight: 126812.54

Authors

Liu, J.,Lou, Y.,Yokota, H.,Adams, P.D.,Kim, R.,Kim, S.H.,Berkeley Structural Genomics Center (BSGC) (deposition date: 2005-03-02, release date: 2005-04-26, Last modification date: 2024-02-14)

Primary citation

Liu, J.,Lou, Y.,Yokota, H.,Adams, P.D.,Kim, R.,Kim, S.H.
Crystal Structures of an NAD Kinase from Archaeoglobus fulgidus in Complex with ATP, NAD, or NADP
J.Mol.Biol., 354:289-303, 2005

PubMed Abstract: NAD kinase is a ubiquitous enzyme that catalyzes the phosphorylation of NAD to NADP using ATP or inorganic polyphosphate (poly(P)) as phosphate donor, and is regarded as the only enzyme responsible for the synthesis of NADP. We present here the crystal structures of an NAD kinase from the archaeal organism Archaeoglobus fulgidus in complex with its phosphate donor ATP at 1.7 A resolution, with its substrate NAD at 3.05 A resolution, and with the product NADP in two different crystal forms at 2.45 A and 2.0 A resolution, respectively. In the ATP bound structure, the AMP portion of the ATP molecule is found to use the same binding site as the nicotinamide ribose portion of NAD/NADP in the NAD/NADP bound structures. A magnesium ion is found to be coordinated to the phosphate tail of ATP as well as to a pyrophosphate group. The conserved GGDG loop forms hydrogen bonds with the pyrophosphate group in the ATP-bound structure and the 2' phosphate group of the NADP in the NADP-bound structures. A possible phosphate transfer mechanism is proposed on the basis of the structures presented.

PubMed: 16242716
DOI: 10.1016/j.jmb.2005.09.026

Experimental method

X-RAY DIFFRACTION (2.85 Å)