N-acetyl-L-glutamate kinase from Escherichia coli complexed with its substrate N-acetylglutamate and its substrate analog AMPPNP

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.209 

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Structure of Acetylglutamate Kinase, a Key Enzyme for Arginine Biosynthesis and a Prototype for the Amino Acid Kinase Enzyme Family, During Catalysis

Ramon-Maiques, S.Marina, A.Gil-Ortiz, F.Fita, I.Rubio, V.

(2002) Structure 10: 329

  • DOI: https://doi.org/10.1016/s0969-2126(02)00721-9
  • Primary Citation of Related Structures:  
    1GS5, 1GSJ

  • PubMed Abstract: 

    N-Acetyl-L-glutamate kinase (NAGK), a member of the amino acid kinase family, catalyzes the second and frequently controlling step of arginine synthesis. The Escherichia coli NAGK crystal structure to 1.5 A resolution reveals a 258-residue subunit homodimer nucleated by a central 16-stranded molecular open beta sheet sandwiched between alpha helices. In each subunit, AMPPNP, as an alphabetagamma-phosphate-Mg2+ complex, binds along the sheet C edge, and N-acetyl-L-glutamate binds near the dyadic axis with its gamma-COO- aligned at short distance from the gamma-phosphoryl, indicating associative phosphoryl transfer assisted by: (1) Mg2+ complexation; (2) the positive charges on Lys8, Lys217, and on two helix dipoles; and (3) by hydrogen bonding with the y-phosphate. The structural resemblance with carbamate kinase and the alignment of the sequences suggest that NAGK is a structural and functional prototype for the amino acid kinase family, which differs from other acylphosphate-making devices represented by phosphoglycerate kinase, acetate kinase, and biotin carboxylase.

  • Organizational Affiliation

    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACETYLGLUTAMATE KINASE258Escherichia coli BL21(DE3)Mutation(s): 0 
Find proteins for P0A6C8 (Escherichia coli (strain K12))
Explore P0A6C8 
Go to UniProtKB:  P0A6C8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6C8
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.564α = 90
b = 72.332β = 90
c = 107.418γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata 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: 2002-05-16
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Data collection, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance