NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution.Symersky, J., Devedjiev, Y., Moore, K., Brouillette, C., DeLucas, L.
(2002) Acta Crystallogr.,Sect.D 58: 1138-1146
- PubMed: 12077433
- PubMed Abstract:
- Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis
Devedjiev, Y.,Symersky, J.,Singh, R.,Jedrzejas, M.,Brouillette, C.,Brouillette, W.,Muccio, D.,Chattopadhyay, D.,DeLucas, L.
(2001) Acta Crystallogr.,Sect.D 57: 806
- A novel deamido-NAD+ binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure
Rizzi, M.,Bolognesi, M.,Coda, A.
(1998) Structure 6: 1129
- Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis
Rizzi, M.,Nessi, C.,Mattevi, A.,Coda, A.,Bolognesi, M.,Galizzi, A.
(1996) Embo J. 15: 5125
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 ...
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.
Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, 35294, USA.