Crystal structure of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 

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Structure and evolution of a novel dimeric enzyme from a clinically-important bacterial pathogen.

Burgess, B.R.Dobson, R.C.J.Bailey, M.F.Atkinson, S.C.Griffin, M.D.W.Jameson, G.B.Parker, M.W.Gerrard, J.A.Perugini, M.A.

(2008) J Biol Chem 

  • DOI: https://doi.org/10.1074/jbc.M804231200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step of the lysine biosynthetic pathway. The tetrameric structure of DHDPS is thought to be essential for enzymatic activity, as isolated dimeric mutants of Escherichia coli DHDPS possess less than 2.5% that of the activity of the wild-type tetramer. It has recently been proposed that the dimeric form lacks activity due to increased dynamics. Tetramerization, by buttressing two dimers together, reduces dynamics in the dimeric unit and explains why all active bacterial DHDPS enzymes to date have been shown to be homo-tetrameric. However, in this study we demonstrate for the first time that DHDPS from methicillin-resistant Staphylococcus aureus (MRSA) exists in a monomer-dimer equilibrium in solution. Fluorescence-detected analytical ultracentrifugation was employed to show that the dimerization dissociation constant of MRSA-DHDPS is 33 nm in the absence of substrates and 29 nm in the presence of (S)-aspartate semialdehyde (ASA), but is 20-fold tighter in the presence of the substrate pyruvate (1.6 nm). The MRSA-DHDPS dimer exhibits a ping-pong kinetic mechanism (k(cat)=70+/-2 s(-1), K(m)(Pyruvate)=0.11+/-0.01 mm, and K(m)(ASA)=0.22+/-0.02 mm) and shows ASA substrate inhibition with a K(si)(ASA) of 2.7+/-0.9 mm. We also demonstrate that unlike the E. coli tetramer, the MRSA-DHDPS dimer is insensitive to lysine inhibition. The near atomic resolution (1.45 A) crystal structure confirms the dimeric quaternary structure and reveals that the dimerization interface of the MRSA enzyme is more extensive in buried surface area and noncovalent contacts than the equivalent interface in tetrameric DHDPS enzymes from other bacterial species. These data provide a detailed mechanistic insight into DHDPS catalysis and the evolution of quaternary structure of this important bacterial enzyme.

  • Organizational Affiliation

    Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, VIC 3010, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, VIC 3010, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrodipicolinate synthase
A, B, C, D
292Staphylococcus aureus subsp. aureus MRSA252Mutation(s): 0 
Gene Names: dapASAR1407
Find proteins for Q6GH13 (Staphylococcus aureus (strain MRSA252))
Explore Q6GH13 
Go to UniProtKB:  Q6GH13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GH13
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
J [auth B]
L [auth C]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
N [auth C],
P [auth D],
Q [auth D]
C3 H8 O3
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
O [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.41α = 90.13
b = 67.573β = 68.85
c = 77.998γ = 72.29
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description