4Y0X

Crystal structure of the S/T protein kinase PknG from Mycobacterium tuberculosis in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Molecular Basis of the Activity and the Regulation of the Eukaryotic-like S/T Protein Kinase PknG from Mycobacterium tuberculosis.

Lisa, M.N.Gil, M.Andre-Leroux, G.Barilone, N.Duran, R.Biondi, R.M.Alzari, P.M.

(2015) Structure 23: 1039-1048

  • DOI: https://doi.org/10.1016/j.str.2015.04.001
  • Primary Citation of Related Structures:  
    4Y0X, 4Y12

  • PubMed Abstract: 

    Tuberculosis remains one of the world's deadliest human diseases, with a high prevalence of antibiotic-resistant Mycobacterium tuberculosis (Mtb) strains. A molecular understanding of processes underlying regulation and adaptation of bacterial physiology may provide novel avenues for the development of antibiotics with unconventional modes of action. Here, we focus on the multidomain S/T protein kinase PknG, a soluble enzyme that controls central metabolism in Actinobacteria and has been linked to Mtb infectivity. Our biochemical and structural studies reveal how different motifs and domains flanking the catalytic core regulate substrate selectivity without significantly affecting the intrinsic kinase activity, whereas a rubredoxin-like domain is shown to downregulate catalysis through specific intramolecular interactions that modulate access to a profound substrate-binding site. Our findings provide the basis for the selective and specific inhibition of PknG, and open new questions about regulation of related bacterial and eukaryotic protein kinases.


  • Organizational Affiliation

    Institut Pasteur, Unité de Microbiologie Structurale, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France; CNRS UMR 3528, Biologie structurale des processus cellulaires et maladies infectieuses, Institut Pasteur, 75724 Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, Microbiologie structurale, 75724 Paris Cedex 15, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PknG375Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: pknGRv0410cMTCY22G10.06c
EC: 2.7.11.1
UniProt
Find proteins for P9WI73 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WI73 
Go to UniProtKB:  P9WI73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WI73
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.92α = 90
b = 37.25β = 97.74
c = 108.52γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description