3PYL

Crystal structure of aspartate beta-semialdehide dehydrogenase from Streptococcus pneumoniae with D-2,3-diaminopropionate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family.

Pavlovsky, A.G.Liu, X.Faehnle, C.R.Potente, N.Viola, R.E.

(2012) Chem.Biol.Drug Des. 79: 128-136

  • DOI: 10.1111/j.1747-0285.2011.01267.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The aspartate biosynthetic pathway provides essential metabolites for many important biological functions, including the production of four essential amino acids. As this critical pathway is only present in plants and microbes, any disruptions will b ...

    The aspartate biosynthetic pathway provides essential metabolites for many important biological functions, including the production of four essential amino acids. As this critical pathway is only present in plants and microbes, any disruptions will be fatal to these organisms. An early pathway enzyme, l-aspartate-β-semialdehyde dehydrogenase, produces a key intermediate at the first branch point of this pathway. Developing potent and selective inhibitors against several orthologs in the l-aspartate-β-semialdehyde dehydrogenase family can serve as lead compounds for antibiotic development. Kinetic studies of two small molecule fragment libraries have identified inhibitors that show good selectivity against l-aspartate-β-semialdehyde dehydrogenases from two different bacterial species, Streptococcus pneumoniae and Vibrio cholerae, despite the presence of an identical constellation of active site amino acids in this homologous enzyme family. Structural characterization of enzyme-inhibitor complexes have elucidated different modes of binding between these structurally related enzymes. This information provides the basis for a structure-guided approach to the development of more potent and more selective inhibitors.


    Organizational Affiliation

    Department of Chemistry, University of Toledo, Toledo, OH 43606, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate-semialdehyde dehydrogenase
A, B, C, D
366N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2RA
Query on 2RA

Download SDF File 
Download CCD File 
A, B, C
3-amino-D-alanine
diaminopropanoic acid
C3 H8 N2 O2
PECYZEOJVXMISF-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.115α = 90.00
b = 78.155β = 90.00
c = 246.061γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-04
    Type: Initial release
  • Version 1.1: 2014-05-14
    Type: Non-polymer description
  • Version 1.2: 2014-10-08
    Type: Database references
  • Version 1.3: 2014-10-15
    Type: Structure summary