3DI1

Crystal structure of the Staphylococcus aureus Dihydrodipicolinate synthase-pyruvate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase

Girish, T.S.Sharma, E.Gopal, B.

(2008) FEBS Lett 582: 2923-2930

  • DOI: 10.1016/j.febslet.2008.07.035
  • Primary Citation of Related Structures:  
    3DI0, 3DI1

  • PubMed Abstract: 
  • Lysine biosynthesis is crucial for cell-wall formation in bacteria. Enzymes involved in lysine biosynthesis are thus potential targets for anti-microbial therapeutics. Dihydrodipicolinate synthase (DHDPS) catalyzes the first step of this pathway. Unlike its homologues, Staphylococcus aureus DHDPS is a dimer both in solution and in the crystal and is not feedback inhibited by lysine ...

    Lysine biosynthesis is crucial for cell-wall formation in bacteria. Enzymes involved in lysine biosynthesis are thus potential targets for anti-microbial therapeutics. Dihydrodipicolinate synthase (DHDPS) catalyzes the first step of this pathway. Unlike its homologues, Staphylococcus aureus DHDPS is a dimer both in solution and in the crystal and is not feedback inhibited by lysine. The crystal structure of S. aureus DHDPS in the free and substrate bound forms provides a structural rationale for its catalytic mechanism. The structure also reveals unique conformational features of the S. aureus enzyme that could be crucial for the design of specific non-competitive inhibitors.


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydrodipicolinate synthase AB295Staphylococcus aureus subsp. aureus COLMutation(s): 0 
Gene Names: DHDPSdapASACOL1430
EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
Find proteins for Q5HG25 (Staphylococcus aureus (strain COL))
Explore Q5HG25 
Go to UniProtKB:  Q5HG25
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYR
Query on PYR

Download Ideal Coordinates CCD File 
A, B
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.44α = 90
b = 117.44β = 90
c = 182.616γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-06-19 
  • Released Date: 2008-08-12 
  • Deposition Author(s): Tavarekere, G.S.

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance