Crystal Structure of DapA (PA1010) at 1.6 A resolution

Experimental Data Snapshot

  • Resolution: 1.59 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.

Schnell, R.Oehlmann, W.Sandalova, T.Braun, Y.Huck, C.Maringer, M.Singh, M.Schneider, G.

(2012) PLoS One 7: e31133-e31133

  • DOI: https://doi.org/10.1371/journal.pone.0031133
  • Primary Citation of Related Structures:  
    3QZE, 3R5A, 3R5B, 3R5C, 3R5D

  • PubMed Abstract: 

    The diaminopimelic acid pathway of lysine biosynthesis has been suggested to provide attractive targets for the development of novel antibacterial drugs. Here we report the characterization of two enzymes from this pathway in the human pathogen Pseudomonas aeruginosa, utilizing structural biology, biochemistry and genetics. We show that tetrahydrodipicolinate N-succinyltransferase (DapD) from P. aeruginosa is specific for the L-stereoisomer of the amino substrate L-2-aminopimelate, and its D-enantiomer acts as a weak inhibitor. The crystal structures of this enzyme with L-2-aminopimelate and D-2-aminopimelate, respectively, reveal that both compounds bind at the same site of the enzyme. Comparison of the binding interactions of these ligands in the enzyme active site suggests misalignment of the amino group of D-2-aminopimelate for nucleophilic attack on the succinate moiety of the co-substrate succinyl-CoA as the structural basis of specificity and inhibition. P. aeruginosa mutants where the dapA gene had been deleted were viable and able to grow in a mouse lung infection model, suggesting that DapA is not an optimal target for drug development against this organism. Structure-based sequence alignments, based on the DapA crystal structure determined to 1.6 Å resolution revealed the presence of two homologues, PA0223 and PA4188, in P. aeruginosa that could substitute for DapA in the P. aeruginosa PAO1ΔdapA mutant. In vitro experiments using recombinant PA0223 protein could however not detect any DapA activity.

  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrodipicolinate synthase
A, B, C, D
314Pseudomonas aeruginosaMutation(s): 0 
Gene Names: dapAdapA (PA1010)PA1010
Find proteins for Q9I4W3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I4W3 
Go to UniProtKB:  Q9I4W3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I4W3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.59 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.11α = 95.7
b = 51.74β = 90.02
c = 140.35γ = 113.27
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: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-02-01
    Changes: Structure summary
  • Version 1.2: 2016-03-30
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description