ArgA complexed with AceCoA and glutamate

Experimental Data Snapshot

  • Resolution: 2.04 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Crystal structure of l-glutamate N-acetyltransferase ArgA from Mycobacterium tuberculosis

Yang, X.Wu, L.Ran, Y.Xu, A.Zhang, B.Yang, X.Zhang, R.Rao, Z.Li, J.

(2017) Biochim Biophys Acta 1865: 1800-1807

  • DOI: https://doi.org/10.1016/j.bbapap.2017.09.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    l-arginine is used as a source of both carbon and nitrogen in Mycobacterium tuberculosis (Mtb) and its biosynthesis is essential for the pathogen's survival. MtbArgA (Rv2747) catalyzes the initial step in l-arginine biosynthesis by transferring an acetyl group from acetyl coenzyme A (AcCoA) to l-glutamate. MtbArgA is a class III N-acetylglutamate synthase (NAGS) with no structural information. Here, we solved the crystal structure of MtbArgA complexed with AcCoA and l-glutamate. The overall structure adopts a classic fold of the GCN5-related N-acetyltransferase (GNAT) family, characterized by a "V"-shaped cleft and β-bulge, but uses distinct residues for the binding and reaction of AcCoA. In particular, its activity depends on dimerization to form a deep, vast pocket for l-glutamate binding. Interestingly, in the structure, l-glutamate binds at a site far away from AcCoA, implying a mechanism of separate capture and catalysis. Additionally, based on a docking model of l-glutamate at the catalytic site, a one-step sequential mechanism was proposed for enzymatic catalysis. Important sites for substrate binding and catalysis were also evaluated by site-directed mutagenesis study and activity analysis. The unique features of the MtbArgA structure will provide useful insights for inhibitor design and anti-tuberculosis drug discovery.

  • Organizational Affiliation

    National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amino-acid acetyltransferase
A, B
174Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: argARv2747
Find proteins for O33289 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O33289 
Go to UniProtKB:  O33289
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO33289
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO (Subject of Investigation/LOI)
Query on ACO

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
C23 H38 N7 O17 P3 S
GLU (Subject of Investigation/LOI)
Query on GLU

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
C5 H9 N O4
Query on CAD

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B]
C2 H7 As O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.04 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.728α = 90
b = 73.728β = 90
c = 187.231γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references