Limits...
L,L-diaminopimelate aminotransferase from Chlamydomonas reinhardtii: a target for algaecide development.

Dobson RC, Girón I, Hudson AO - PLoS ONE (2011)

Bottom Line: Cr-DapL was dimeric in both solution and when crystallized.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.

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.

Show MeSH
The crystal structure of Cr-DapL.A) The dimer in the asymmetric unit. This view looks down the                            non-crystallographic two-fold axis. B) An overlay of the                                Cr-DapL dimer (magenta) with that of the                                apo-Ar-DapL (3EI7, yellow). The r.m.s.d. for the                            overlay was 0.67 Å for the α-carbon atoms. C) Monomer                            structure with the domains highlighted in the stereo image (D).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3102117&req=5

pone-0020439-g006: The crystal structure of Cr-DapL.A) The dimer in the asymmetric unit. This view looks down the non-crystallographic two-fold axis. B) An overlay of the Cr-DapL dimer (magenta) with that of the apo-Ar-DapL (3EI7, yellow). The r.m.s.d. for the overlay was 0.67 Å for the α-carbon atoms. C) Monomer structure with the domains highlighted in the stereo image (D).

Mentions: Consistent with our sedimentation velocity experiment, the two monomers in the asymmetric unit interact closely to form a dimeric species (Figure 6A) and are related by a non-crystallographic two-fold symmetry axis. The interface between the monomers in the dimer buries ∼21% of the surface accessible area of each monomer and is composed primarily of hydrogen bonds, but also includes four salt bridges between residues R314 and D170, and residues D311 and R39 of each monomer. An overlay with the apo-Arabidopsis DapL dimer (PDB id: 3EI7 [13]) shows close agreement with an r.m.s.d. of 0.67 Å for 688 α-carbon atoms (Figure 6B).


L,L-diaminopimelate aminotransferase from Chlamydomonas reinhardtii: a target for algaecide development.

Dobson RC, Girón I, Hudson AO - PLoS ONE (2011)

The crystal structure of Cr-DapL.A) The dimer in the asymmetric unit. This view looks down the                            non-crystallographic two-fold axis. B) An overlay of the                                Cr-DapL dimer (magenta) with that of the                                apo-Ar-DapL (3EI7, yellow). The r.m.s.d. for the                            overlay was 0.67 Å for the α-carbon atoms. C) Monomer                            structure with the domains highlighted in the stereo image (D).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102117&req=5

pone-0020439-g006: The crystal structure of Cr-DapL.A) The dimer in the asymmetric unit. This view looks down the non-crystallographic two-fold axis. B) An overlay of the Cr-DapL dimer (magenta) with that of the apo-Ar-DapL (3EI7, yellow). The r.m.s.d. for the overlay was 0.67 Å for the α-carbon atoms. C) Monomer structure with the domains highlighted in the stereo image (D).
Mentions: Consistent with our sedimentation velocity experiment, the two monomers in the asymmetric unit interact closely to form a dimeric species (Figure 6A) and are related by a non-crystallographic two-fold symmetry axis. The interface between the monomers in the dimer buries ∼21% of the surface accessible area of each monomer and is composed primarily of hydrogen bonds, but also includes four salt bridges between residues R314 and D170, and residues D311 and R39 of each monomer. An overlay with the apo-Arabidopsis DapL dimer (PDB id: 3EI7 [13]) shows close agreement with an r.m.s.d. of 0.67 Å for 688 α-carbon atoms (Figure 6B).

Bottom Line: Cr-DapL was dimeric in both solution and when crystallized.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.

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.

Show MeSH