1GS5 | pdb_00001gs5

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.213 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.198 (DCC) 

Starting Model: experimental
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Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 27.91 kDa 
  • Atom Count: 2,189 
  • Modeled Residue Count: 258 
  • Deposited Residue Count: 258 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACETYLGLUTAMATE KINASE258Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 2.7.2.8
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.213 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.198 (DCC) 
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
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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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
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description