1NSY

CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS

Summary for 1NSY

• Entry DOI: 10.2210/pdb1nsy/pdb
• Descriptor: NAD SYNTHETASE, MAGNESIUM ION, ADENOSINE-5'-TRIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: lyase, amidotransferase, nh3 dependent, atp pyrophosphatase
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 62717.32

Authors

Rizzi, M.,Nessi, C.,Bolognesi, M.,Galizzi, A.,Coda, A. (deposition date: 1996-07-22, release date: 1997-07-23, Last modification date: 2024-02-14)

Primary citation

Rizzi, M.,Nessi, C.,Mattevi, A.,Coda, A.,Bolognesi, M.,Galizzi, A.
Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis.
EMBO J., 15:5125-5134, 1996

PubMed Abstract: NAD+ synthetase catalyzes the last step in the biosynthesis of nicotinamide adenine dinucleotide. The three-dimensional structure of NH3-dependent NAD+ synthetase from Bacillus subtilis, in its free form and in complex with ATP, has been solved by X-ray crystallography (at 2.6 and 2.0 angstroms resolution, respectively) using a combination of multiple isomorphous replacement and density modification techniques. The enzyme consists of a tight homodimer with alpha/beta subunit topology. The catalytic site is located at the parallel beta-sheet topological switch point, where one AMP molecule, one pyrophosphate and one Mg2+ ion are observed. Residue Ser46, part of the neighboring 'P-loop', is hydrogen bonded to the pyrophosphate group, and may play a role in promoting the adenylation of deamido-NAD+ during the first step of the catalyzed reaction. The deamido-NAD+ binding site, located at the subunit interface, is occupied by one ATP molecule, pointing towards the catalytic center. A conserved structural fingerprint of the catalytic site, comprising Ser46, is very reminiscent of a related protein region observed in glutamine-dependent GMP synthetase, supporting the hypothesis that NAD+ synthetase belongs to the newly discovered family of 'N-type' ATP pyrophosphatases.

PubMed: 8895556

Experimental method

X-RAY DIFFRACTION (2 Å)