2YA7

Crystal structure of Streptococcus pneumoniae NanA (TIGR4) in complex with Zanamivir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Streptococcus Pneumoniae Nana Inhibition by Influenza Antivirals Zanamivir and Oseltamivir Carboxylate.

Gut, H.Xu, G.Taylor, G.L.Walsh, M.A.

(2011) J.Mol.Biol. 409: 496

  • DOI: 10.1016/j.jmb.2011.04.016
  • Primary Citation of Related Structures:  2YA4, 2YA5, 2YA6, 2YA8

  • PubMed Abstract: 
  • The human pathogen Streptococcus pneumoniae is the major cause of bacterial meningitis, respiratory tract infection, septicemia, and otitis media. The bacterium expresses neuraminidase (NA) proteins that contribute to pathogenesis by cleaving sialic ...

    The human pathogen Streptococcus pneumoniae is the major cause of bacterial meningitis, respiratory tract infection, septicemia, and otitis media. The bacterium expresses neuraminidase (NA) proteins that contribute to pathogenesis by cleaving sialic acids from host glycoconjugates, thereby enhancing biofilm formation and colonization. Recent in vivo experiments have shown that antiviral compounds, widely used in clinics and designed to inhibit influenza NA, significantly reduce biofilm formation and nasopharyngeal colonization of S. pneumoniae in mice. Here, we present the structural basis for the beneficial effect of these compounds against pneumococcal infection. Crystal structures of pneumococcal NanA in complex with zanamivir and oseltamivir carboxylate are discussed, correlated with measured inhibitory constants K(i), and compared with the binding modes of the inhibitors in the viral enzyme. Inhibitor structures show for the first time how clinically approved anti-influenza compounds interact with an NA of the human pathogen S. pneumoniae and give a rational explanation for their antibacterial effects.


    Organizational Affiliation

    MRC France, BM14 c/o ESRF, 6 rue Jules Horowitz, BP220, 38043 Grenoble, France. heinz.gut@fmi.ch




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEURAMINIDASE A
A, B, C, D
493Streptococcus pneumoniaeGene Names: nanA
EC: 3.2.1.18
Find proteins for P62575 (Streptococcus pneumoniae)
Go to UniProtKB:  P62575
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ZMR
Query on ZMR

Download SDF File 
Download CCD File 
A, B, C, D
ZANAMIVIR
MODIFIED SIALIC ACID
C12 H20 N4 O7
ARAIBEBZBOPLMB-UFGQHTETSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZMRKi: 720000 nM BINDINGMOAD
ZMRKi: 720000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.856α = 104.06
b = 87.161β = 91.04
c = 126.410γ = 106.68
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-06-02
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance