PDBsum entry 3d2m

Transferase

PDB id: 3d2m

Contents

Protein chain

424 a.a. *

Ligands

COA

GLU

Waters ×81

* Residue conservation analysis

PDB id:

3d2m

Name:

Transferase

Title:

Crystal structure of n-acetylglutamate synthase from neisseria gonorrhoeae complexed with coenzyme a and l-glutamate

Structure:

Putative acetylglutamate synthase. Chain: a. Engineered: yes. Mutation: yes

Source:

Neisseria gonorrhoeae. Strain: atcc53420. Gene: arga. Expressed in: escherichia coli.

Resolution:

2.21Å R-factor: 0.231 R-free: 0.280

Authors:

D.Shi,L.Min,Z.Jin,N.M.Allewell,M.Tuchman

Key ref:

L.Min et al. (2009). Mechanism of allosteric inhibition of N-acetyl-L-glutamate synthase by L-arginine. J Biol Chem, 284, 4873-4880. PubMed id: 19095660 DOI: 10.1074/jbc.M805348200

Date:

08-May-08 Release date: 23-Dec-08

Protein chain

Q5FAK7  (Q5FAK7_NEIG1) -  Amino-acid acetyltransferase from Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)

Seq: 436 a.a.

Struc: 424 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.3.1.1 - amino-acid N-acetyltransferase.
• Pathway: Ornithine Biosynthesis
• Reaction: L-glutamate + acetyl-CoA = N-acetyl-L-glutamate + CoA + H⁺

L-glutamate + acetyl-CoA (Bound ligand (Het Group name = GLU) corresponds exactly) = N-acetyl-L-glutamate (Bound ligand (Het Group name = COA) corresponds exactly) + CoA + H(+)

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

reference

DOI no: 10.1074/jbc.M805348200

J Biol Chem 284:4873-4880 (2009)

PubMed id: 19095660

Mechanism of allosteric inhibition of N-acetyl-L-glutamate synthase by L-arginine.

L.Min, Z.Jin, L.Caldovic, H.Morizono, N.M.Allewell, M.Tuchman, D.Shi.

ABSTRACT

N-Acetylglutamate synthase (NAGS) catalyzes the first committed step in l-arginine biosynthesis in plants and micro-organisms and is subject to feedback inhibition by l-arginine. This study compares the crystal structures of NAGS from Neisseria gonorrhoeae (ngNAGS) in the inactive T-state with l-arginine bound and in the active R-state complexed with CoA and l-glutamate. Under all of the conditions examined, the enzyme consists of two stacked trimers. Each monomer has two domains: an amino acid kinase (AAK) domain with an AAK-like fold but lacking kinase activity and an N-acetyltransferase (NAT) domain homologous to other GCN5-related transferases. Binding of l-arginine to the AAK domain induces a global conformational change that increases the diameter of the hexamer by approximately 10 A and decreases its height by approximately 20A(.) AAK dimers move 5A outward along their 2-fold axes, and their tilt relative to the plane of the hexamer decreases by approximately 4 degrees . The NAT domains rotate approximately 109 degrees relative to AAK domains enabling new interdomain interactions. Interactions between AAK and NAT domains on different subunits also change. Local motions of several loops at the l-arginine-binding site enable the protein to close around the bound ligand, whereas several loops at the NAT active site become disordered, markedly reducing enzymatic specific activity.

Selected figure(s)

Figure 2.
The l-arginine-binding site in the T-state structure (A), CoA and l-glutamate binding sites in the R-state structure (B), and amino acid sequences around l-arginine-binding site (C). A and B, electron density maps (2F[o] – F[c]) are shown as a blue cage contoured at 1.0 σ. Carbon atoms of CoA, l-glutamate, and l-arginine are shown as pink, yellow, and green sticks, respectively. Carbon atoms of the protein are shown as light blue sticks. Hydrogen bonds between bound ligands and protein are indicated by red dashed lines. C, sequence alignment around l-arginine-binding site for NAGS sequences from N. gonorrhoeae, P. aeruginosa, zebrafish, and human; NAGK sequences from Pseudomonas aeruginosa and Arabidopsis thaliana; and bifunctional NAGS/K sequences from X. campestris and Maricaulis maris. Fully conserved residues are highlighted in green, and partially conserved residues are in blue.

Figure 5.
l-Arginine-induced quaternary structure changes of hexamer. A and B, simplified model showing the molecular hexamer in two different orientations. Different subunits are shown in different colors. K and S refer to AAK and NAT domains, respectively, and the numbers are used to distinguish subunits. The two types of AAK interfaces that link the trimers are illustrated by the interactions between K1 and K4 and between K1 and K5. In addition, monomers within trimers interact via interactions between AAK and NAT domains of adjacent subunits, for example K2 and S1. C, detailed view of interactions between AAK domain K2 and NAT domain S1 for R-state (left panel) and T-state (right panel).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 4873-4880) copyright 2009.

Figures were selected by an automated process.