PDBsum entry 1kqp

Ligase

PDB id: 1kqp

Contents

Protein chains

271 a.a. *

Ligands

EDO ×10

ADJ ×2

POP ×2

Metals

_MG ×5

Waters ×714

* Residue conservation analysis

PDB id:

1kqp

Name:

Ligase

Title:

Nh3-dependent NAD+ synthetase from bacillus subtilis at 1 a resolution

Structure:

Nh(3)-dependent NAD(+) synthetase. Chain: a, b. Synonym: nh3-dependent NAD+ synthetase. NAD+ synthase. Sporulation protein outb. Spore outgrowth factor b. General stress protein 38. Gsp38. Engineered: yes. Other_details: complexed with a reaction intermediate NAD-a, residue adj

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: outb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.03Å R-factor: 0.118 R-free: 0.147

Authors:

J.Symersky,Y.Devedjiev,K.Moore,C.Brouillette,L.Delucas

Key ref:

J.Symersky et al. (2002). NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution. Acta Crystallogr D Biol Crystallogr, 58, 1138-1146. PubMed id: 12077433 DOI: 10.1107/S0907444902006698

Date:

07-Jan-02 Release date: 28-Jun-02

Protein chains

P08164  (NADE_BACSU) -  NH(3)-dependent NAD(+) synthetase from Bacillus subtilis (strain 168)

Seq: 272 a.a.

Struc: 271 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.1.5 - NAD(+) synthase.
• Reaction: deamido-NAD⁺ + NH4⁺ + ATP = AMP + diphosphate + NAD⁺ + H⁺

deamido-NAD(+) + NH4(+) + ATP = AMP + diphosphate (Bound ligand (Het Group name = POP) corresponds exactly) + NAD(+) + H(+) (Bound ligand (Het Group name = ADJ) matches with 64.18% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444902006698

Acta Crystallogr D Biol Crystallogr 58:1138-1146 (2002)

PubMed id: 12077433

NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution.

J.Symersky, Y.Devedjiev, K.Moore, C.Brouillette, L.DeLucas.

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.

Selected figure(s)

Figure 5.
Figure 5 Spatial relationship between the intermediate protonated at O7N and cation-binding sites M+(I) and M+(II). Distances are shown in Å for subunit A. C atoms are in green, N atoms in blue, O atoms in red, P atoms in magenta and H atoms in cyan. Hydrophobic residues are all in gray, magnesium ions in black and the monovalent cation-binding sites M+(I) and M+(II) are shown as golden spheres. Rendered using RIBBONS (Carson, 1997[Carson, M. (1997). Methods Enzymol. 277, 493-505.]).

Figure 6.
Figure 6 (a) Stabilization of the protonated intermediate by the hydrogen bond with ammonia positioned in the cation-binding site M+(I) and a hypothetical hydrogen bond with water molecule in the cation-binding site M+(II) releasing the ammonia molecule for nucleophilic attack. (b) Reaction scheme for the second catalytic step of NAD^+ synthetase. The NAD-adenylate intermediate reacts with ammonia to form NAD^+ and AMP and two protons are released. R[1] represents the ADP-nicotinosyl moiety and R[2] represents the AMP moiety.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1138-1146) copyright 2002.

Figures were selected by an automated process.