3H73

Crystal structure of Streptococcus pneumoniae D39 neuraminidase A precursor (NanA) in complex with DANA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of respiratory pathogen neuraminidases

Hsiao, Y.-S.Parker, D.Ratner, A.J.Prince, A.Tong, L.

(2009) Biochem.Biophys.Res.Commun. 380: 467-471

  • DOI: 10.1016/j.bbrc.2009.01.108
  • Primary Citation of Related Structures:  3H6J, 3H71, 3H72

  • PubMed Abstract: 
  • Currently there is pressing need to develop novel therapeutic agents for the treatment of infections by the human respiratory pathogens Pseudomonas aeruginosa and Streptococcus pneumoniae. The neuraminidases of these pathogens are important for host ...

    Currently there is pressing need to develop novel therapeutic agents for the treatment of infections by the human respiratory pathogens Pseudomonas aeruginosa and Streptococcus pneumoniae. The neuraminidases of these pathogens are important for host colonization in animal models of infection and are attractive targets for drug discovery. To aid in the development of inhibitors against these neuraminidases, we have determined the crystal structures of the P. aeruginosa enzyme NanPs and S. pneumoniae enzyme NanA at 1.6 and 1.7A resolution, respectively. In situ proteolysis with trypsin was essential for the crystallization of our recombinant NanA. The active site regions of the two enzymes are strikingly different. NanA contains a deep pocket that is similar to that in canonical neuraminidases, while the NanPs active site is much more open. The comparative studies suggest that NanPs may not be a classical neuraminidase, and may have distinct natural substrates and physiological functions. This work represents an important step in the development of drugs to prevent respiratory tract colonization by these two pathogens.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sialidase A
A, B
477Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Gene Names: nanA
EC: 3.2.1.18
Find proteins for P62576 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  P62576
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAN
Query on DAN

Download SDF File 
Download CCD File 
A, B
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 158.340α = 90.00
b = 47.400β = 116.45
c = 137.320γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
ADSCdata collection
CNSrefinement
COMOphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-04-24 
  • Released Date: 2009-05-12 
  • Deposition Author(s): Hsiao, Y.-S., Tong, L.

Revision History 

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance