3D2P

Crystal structure of N-acetylglutamate synthase from Neisseria gonorrhoeae complexed with coenzyme A and L-arginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of Allosteric Inhibition of N-Acetyl-L-glutamate Synthase by L-Arginine.

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

(2009) J.Biol.Chem. 284: 4873-4880

  • DOI: 10.1074/jbc.M805348200
  • Primary Citation of Related Structures:  3D2M

  • PubMed 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 gonor ...

    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.


    Organizational Affiliation

    Research Center for Genetic Medicine, Children's National Medical Center, The George Washington University, Washington, D. C. 20010, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative acetylglutamate synthase
A, B
456Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)Gene Names: argA
EC: 2.3.1.1
Find proteins for Q5FAK7 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Go to UniProtKB:  Q5FAK7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
A, B
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
ARG
Query on ARG

Download SDF File 
Download CCD File 
A, B
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 
  • Space Group: P 3 1 2
Unit Cell:
Length (Å)Angle (°)
a = 107.054α = 90.00
b = 107.054β = 90.00
c = 185.466γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
CBASSdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance