PDBsum entry: 1wxe

Ligase

PDB id: 1wxe

Contents

Protein chain

258 a.a. *

Ligands

AMP ×2

Metals

_MG

Waters ×257

* Residue conservation analysis

PDB id:

1wxe

Name:

Ligase

Title:

E.Coli NAD synthetase, amp

Structure:

Nh(3)-dependent NAD(+) synthetase. Chain: a. Synonym: NAD synthetase, nitrogen-regulatory protein. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.191 R-free: 0.211

Authors:

R.Jauch,A.Humm,R.Huber,M.C.Wahl

Key ref:

R.Jauch et al. (2005). Structures of Escherichia coli NAD synthetase with substrates and products reveal mechanistic rearrangements. J Biol Chem, 280, 15131-15140. PubMed id: 15699042 DOI: 10.1074/jbc.M413195200

Date:

23-Jan-05 Release date: 15-Feb-05

Protein chain

P18843  (NADE_ECOLI) -  NH(3)-dependent NAD(+) synthetase

Seq: 275 a.a.

Struc: 258 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.1.5 - NAD(+) synthase.
• Reaction: ATP + deamido-NAD⁺ + NH₃ = AMP + diphosphate + NAD⁺

ATP + deamido-NAD(+) + NH(3) = AMP (Bound ligand (Het Group name = AMP) corresponds exactly) + diphosphate + NAD(+)

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

 Gene Ontology (GO) functional annotation 

• Biological process: NAD biosynthetic process (3 terms)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1074/jbc.M413195200

J Biol Chem 280:15131-15140 (2005)

PubMed id: 15699042

Structures of Escherichia coli NAD synthetase with substrates and products reveal mechanistic rearrangements.

R.Jauch, A.Humm, R.Huber, M.C.Wahl.

ABSTRACT

Nicotinamide adenine dinucleotide synthetases (NADS) catalyze the amidation of nicotinic acid adenine dinucleotide (NAAD) to yield the enzyme cofactor nicotinamide adenine dinucleotide (NAD). Here we describe the crystal structures of the ammonia-dependent homodimeric NADS from Escherichia coli alone and in complex with natural substrates and with the reaction product NAD. The structures disclosed two NAAD/NAD binding sites at the dimer interface and an adenosine triphosphate (ATP) binding site within each subunit. Comparison with the Bacillus subtilis NADS showed pronounced chemical differences in the NAAD/NAD binding sites and less prominent differences in the ATP binding pockets. In addition, the E. coli NADS structures revealed unexpected dynamical rearrangements in the NAAD/NAD binding pocket upon NAAD-to-NAD conversion, which define a catalysis state and a substrate/product exchange state. The two states are adopted by concerted movement of the nicotinysyl moieties of NAAD and NAD, Phe-170, and residues 224-228, which may be triggered by differential coordination of a magnesium ion to NAAD and NAD. Phylogenetic structure comparisons suggest that the present results are relevant for designing species-specific antibiotics.

Selected figure(s)

Figure 1.
FIG. 1. Chemical structures. A, structure of the reaction substrate (NAAD) and product (NAD). B, structure of the reaction intermediate NAD-adenylate.

Figure 5.
FIG. 5. Structural rearrangements. A, close-up stereo view of the ATP binding pocket of the ecoNADS apoenzyme (carbon atoms are in brown, and other atoms are colored as described in the legend to Fig. 4) superimposed onto the same region of the AMP complex structure (carbons in light blue). Residues lining the binding pocket are labeled in single letter style, and Arg-82 (R82) is highlighted. The arrow indicates repositioning of the Arg-82 side chain upon nucleotide binding. The dashed lines indicate hydrogen bonds of Arg-82 and of Gln-88 to the adenine base of AMP. B, F[o] - F[c] difference omit map contoured at the 2.5 level with a radius of 3 Å around NAAD (top) and NAD (bottom). The cofactors are shown as sticks. Arrows around NAAD bonds indicate the main rotations necessary to produce the NAD conformation. The arrow in NAD indicates the nitrogen of the amide group introduced in the course of the reaction. C, comparison of the NAAD/NAD binding pocket when complexed with NAD (carbon atoms and backbones traces in light blue) and when complexed with NAAD (carbon atoms and backbones traces in brown) after global superpositioning of the enzyme structures. Other atoms are color-coded as above. Mg2+-I is indicated as a green sphere coordinated to the Asp-51 and Glu-165 carboxylate groups and to water molecules (small red spheres). One water molecule also hydrogen bonds to the carboxylate of NAAD (dashed line). The different conformations of regions 224-228, C-terminal of the disordered loop P2, are indicated by the backbone traces with side chains.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 15131-15140) copyright 2005.

Figures were selected by an automated process.