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L,L-Diaminopimelate Aminotransferase from Chlamydomonas reinhardtii: A Target for Algaecide Development

By Renwick C. J. Dobson, Irma Girón and André O. Hudson

Abstract

In some bacterial species and photosynthetic cohorts, including algae, the enzyme l,l-diaminopimelate aminotransferase (DapL) (E.C. 2.6.1.83) is involved in the anabolism of the essential amino acid L-lysine. DapL catalyzes the conversion of tetrahydrodipicolinate (THDPA) to l,l-diaminopimelate (l,l-DAP), in one step bypassing the DapD, DapC and DapE enzymatic reactions present in the acyl DAP pathways. Here we present an in vivo and in vitro characterization of the DapL ortholog from the alga Chlamydomonas reinhardtii (Cr-DapL). The in vivo analysis illustrated that the enzyme is able to functionally complement the E. coli dap auxotrophs and was essential for plant development in Arabidopsis. In vitro, the enzyme was able to inter-convert THDPA and l,l-DAP, showing strong substrate specificity. Cr-DapL was dimeric in both solution and when crystallized. The structure of Cr-DapL was solved in its apo form, showing an overall architecture of a α/β protein with each monomer in the dimer adopting a pyridoxal phosphate-dependent transferase-like fold in a V-shaped conformation. The active site comprises residues from both monomers in the dimer and shows some rearrangement when compared to the apo-DapL structure from Arabidopsis. Since animals do not possess the enzymatic machinery necessary for the de novo synthesis of the amino acid l-lysine, enzymes involved in this pathway are attractive targets for the development of antibiotics, herbicides and algaecides

Topics: Research Article
Publisher: Public Library of Science
OAI identifier: oai:pubmedcentral.nih.gov:3102117
Provided by: PubMed Central

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Citations

  1. (1999). A prokaryotic gene cluster involved in synthesis of lysine through the amino adipate pathway: a key to the evolution of amino acid biosynthesis.
  2. (2006). An LL-diaminopimelate aminotransferase defines a novel variant of the lysine biosynthesis pathway in plants.
  3. (1988). Analogs of diaminopimelic acid as inhibitors of meso-diaminopimelate dehydrogenase and LL-diaminopimelate epimerase.
  4. (1999). Analyzing protein circular dichroism spectra for accurate secondary structures.
  5. (2000). Antibacterial activity of synthetic analogues based on the disaccharide structure of moenomycin, an inhibitor of bacterial transglycosylase.
  6. (2008). Biochemical and phylogenetic characterization of a novel diaminopimelate biosynthesis pathway in prokaryotes identifies a diverged form of LL-diaminopimelate aminotransferase.
  7. (2010). Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology.
  8. (2005). Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways.
  9. (1992). Computer-aided interpretation of analytical sedimentation data for proteins. Cambridge: The Royal Society of Chemistry.
  10. (2008). Conformationally constrained diketopimelic acid analogues as inhibitors of dihydrodipicolinate synthase.
  11. (2004). Coot: model-building tools for molecular graphics.
  12. (2008). Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis.
  13. (2007). Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia.
  14. (2011). Crystallization and preliminary X-ray diffraction analysis of L,L-diaminopimelate aminotransferase (DapL) from Chlamydomonas reinhardtii.
  15. (2010). Dali server: conservation mapping in 3D.
  16. (2004). Divergent roles in Arabidopsis thaliana development and defense of two homologous genes, aberrant growth and death2 and AGD2-LIKE DEFENSE RESPONSE PROTEIN1, encoding novel aminotransferases.
  17. (2000). Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set.
  18. (2008). Evolution of quaternary structure in a homotetrameric enzyme.
  19. (1999). Expanding the model: anisotropic displacement parameters in protein structure refinement.
  20. (2010). Exploration of inhibitors for diaminopimelate aminotransferase.
  21. (2007). Genetic dissection of histidine biosynthesis in Arabidopsis.
  22. (2008). Inhibiting dihydrodipicolinate synthase across species: towards specificity for pathogens?
  23. (2007). Inhibition of lysine biosynthesis: an evolving antibiotic strategy.
  24. (2001). Insertional mutagenesis of genes required for seed development in Arabidopsis thaliana.
  25. (2008). Irreversible inhibition of dihydrodipicolinate synthase by 4-oxo-heptenedioic acid analogues.
  26. (2003). KISS for STRAP: user extensions for a protein alignment editor.
  27. (2006). L,LDiaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine.
  28. (2002). Lazcano A
  29. (2008). Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana.JM o l
  30. (2010). Methanococci use the diaminopimelate aminotransferase (DapL) pathway for lysine biosynthesis.
  31. (2010). MolProbity: all-atom structure validation for macromolecular crystallography.
  32. (1976). Occurrence of meso-alpha, epsilon-diaminopimelate dehydrogenase in Bacillus sphaericus.
  33. (2007). Phaser crystallographic software.
  34. (2010). PHENIX: a comprehensive Python-based system for macromolecular structure solution.
  35. (1992). Recent changes to the MOSFLM package for processing film and image plate data.
  36. (2000). Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling.
  37. (2002). Sizedistribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems.
  38. (2008). Structure and evolution of a novel dimeric enzyme from a clinically important bacterial pathogen.
  39. (1986). Studies on the active site of succinyl-CoA:tetrahydrodipicolinate N-succinyltransferase. Characterization using analogs of tetrahydrodipicolinate.
  40. (2010). Substrate-mediated stabilization of a tetrameric drug target reveals Achilles heel in anthrax.
  41. (2004). The crystal structure of three sitedirected mutants of Escherichia coli dihydrodipicolinate synthase: further evidence for a catalytic triad.
  42. (2005). The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance.
  43. (1996). The DAP pathway to lysine as a target for antimicrobial agents.
  44. (2000). The manifold of vitamin B6 dependent enzymes.
  45. (2007). The three-dimensional structure of Nsuccinyldiaminopimelate aminotransferase from Mycobacterium tuberculosis.
  46. (2005). Two new irreversible inhibitors of dihydrodipicolinate synthase: diethyl (E,E)-4-oxo-2,5-heptadienedioate and diethyl (E)-4-oxo-2-heptenedioate.