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1KQP

NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION

Summary for 1KQP
Entry DOI10.2210/pdb1kqp/pdb
Related1EE1 1FYD 1IFX 1IH8 1NSY 2NSY
DescriptorNH(3)-dependent NAD(+) synthetase, MAGNESIUM ION, 1,2-ETHANEDIOL, ... (6 entities in total)
Functional Keywordsligase, amidotransferase, atp pyrophosphatase, nad-adenylate
Biological sourceBacillus subtilis
Total number of polymer chains2
Total formula weight63701.44
Authors
Symersky, J.,Devedjiev, Y.,Moore, K.,Brouillette, C.,DeLucas, L. (deposition date: 2002-01-07, release date: 2002-06-28, Last modification date: 2023-08-16)
Primary citationSymersky, J.,Devedjiev, Y.,Moore, K.,Brouillette, C.,DeLucas, L.
NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution.
Acta Crystallogr.,Sect.D, 58:1138-1146, 2002
Cited by
PubMed Abstract: 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.
PubMed: 12077433
DOI: 10.1107/S0907444902006698
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.03 Å)
Structure validation

237735

数据于2025-06-18公开中

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