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

Experimental Data Snapshot

  • Resolution: 2.21 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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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: https://doi.org/10.1074/jbc.M805348200
  • Primary Citation of Related Structures:  
    3D2M, 3D2P

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative acetylglutamate synthase456Neisseria gonorrhoeaeMutation(s): 3 
Gene Names: argA
Find proteins for Q5FAK7 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Explore Q5FAK7 
Go to UniProtKB:  Q5FAK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5FAK7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on COA

Download Ideal Coordinates CCD File 
C21 H36 N7 O16 P3 S
Query on GLU

Download Ideal Coordinates CCD File 
C5 H9 N O4
Experimental Data & Validation

Experimental Data

  • Resolution: 2.21 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 3 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.802α = 90
b = 98.802β = 90
c = 90.107γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description