 |
PDBsum entry 3d2m
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Mechanism of allosteric inhibition of n-Acetyl-L-Glutamate synthase by l-Arginine.
|
|
|
Authors
|
|
L.Min,
Z.Jin,
L.Caldovic,
H.Morizono,
N.M.Allewell,
M.Tuchman,
D.Shi.
|
|
|
Ref.
|
|
J Biol Chem, 2009,
284,
4873-4880.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
Note: In the PDB file this reference is
annotated as "TO BE PUBLISHED". The citation details given above have
been manually determined.
|
|
|
|
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.
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
