The crystal structure of Rv2747 from Mycobacterium tuberculosis in complex with CoA and NLQ

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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Structural insights into the substrate binding mechanism of novel ArgA from Mycobacterium tuberculosis

Das, U.Singh, E.Dharavath, S.Tiruttani Subhramanyam, U.K.Pal, R.K.Vijayan, R.Menon, S.Kumar, S.Gourinath, S.Srinivasan, A.

(2019) Int J Biol Macromol 125: 970-978

  • DOI: https://doi.org/10.1016/j.ijbiomac.2018.12.163
  • Primary Citation of Related Structures:  
    5YO2, 6ADD

  • PubMed Abstract: 

    The Mycobacterium tuberculosis (Mtb) Rv2747 gene encodes for a functional protein known as ArgA, which plays an important role in the first step of the l-arginine biosynthesis pathway. ArgA transfers the acetyl group from the acetyl-CoA to either l-glutamate or l-glutamine, which are the known substrates. Here, we present two crystal structures of ArgA: one complexed with CoA and product bound N-acetylglutamine and the other complexed with acetyl-CoA and the inhibitor l-arginine at 2.3 and 3.0 Å resolution respectively. The Mtb ArgA protomer was found to have a "V" cleft and a "β" bulge, archetypal of a classical GCN5-related N-acetyltransferase superfamily of proteins. The product bound form implies that ArgA can also acetylate l-glutamine like l-glutamate. The active site is strongly inhibited by l-arginine resulting in a closed conformation of ArgA and both l-arginine and N-acetylglutamine were found to occupy at the same active site. Together with structural analysis, molecular docking studies, microscale thermophoresis and enzyme inhibition assays, we conclude that l-glutamine, l-glutamate and l-arginine, all occupy at the same active site of ArgA. Furthermore in case of Mtb ArgA, l-arginine does not act as an allosteric inhibitor unlike other N-acetylglutamate synthase family of proteins.

  • Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India. Electronic address: uddipan.das@aiims.ac.in.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amino-acid acetyltransferase
A, B
182Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv2747
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
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.385α = 90
b = 82.385β = 90
c = 114.899γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description