Crystal structure of ADL1, a plant-specific homologue of the universal diaminopimelate amino transferase enzyme of lysine biosynthesis
Vladimir Sobolev, Marvin Edelman, Orly Dym, Tamar Unger, Shira Albeck, and Gad Galili[1]
Molecular Tour
The Arabidopsis “Aberrant growth and death-2” (AGD2) protein was originally identified as a protein that is associated with pathogen resistance. The AGD2 protein was subsequently identified as the diaminopimelate amino transferase (DAPAT) enzyme. An Arabidopsis homologue of this protein was subsequently identified and originally named as the AGD2-like defense response protein 1 (ALD1). Both DAPAT and ALD1 require pyridoxal-5′-phosphate (PLP) for their activities. Here we report the structure of the ALD1 protein from Arabidopsis thaliana (AtALD1), to a resolution of 2.1 Å.
The structure of AtALD1 shows a to the structures described for PLP dependent DAPAT from Arabidopsis thaliana (AtDAPAT) (PDB entry 2z20), with an RMSD between structures of 0.64 Å over 324 Cα atoms. AtALD1 is in cyan and AtDAPAT is in yellow. The largest difference between the two structures can be seen at the carboxy terminal regions of two helices: helix α2 (residues 57-73) and helix α12 (residues 393-416). There is a difference of about 6 Å at the loop edge carboxy-terminal to helix α2, between the Cα atom of Asn69 in AtALD1 and the structurally aligned Cα atom of Asp55 in AtDAPAT. Helix α2 diverges between the two structures mainly because of differences in the dihedral angles of Gly56 and Tyr57 in AtALD1 loop 53-57 verses its AtDAPAT counterparts. On the other hand, differences in helix α12 occur because of non-dramatic changes in dihedral angles of all the residues of loop 390-393.
The in AtALD1 and AtDAPAT (RMSD following superimposition equals 0.48 Å over 13 Cα atoms). Carbon atoms of PLP complexed with AtALD1 are in green, carbon atoms of PLP complexed with AtDAPAT are in darkmagenta, nitrogen, oxygen, and phosphorus atoms are colored in blue, red, and orange, respectively. There are, however, two residues that are not conserved: . Lys129 and Tyr152 of AtDAPAT are labeled in yellow and Gln123 and Phe146 in AtALD1 are labeled in cyan. While PLP has contacts with the , it is likely that upon mutation to Gln does not significantly change the position of these atoms and their contacts . Furthermore, PLP has only minor contact with the side chain oxygen of (about 1 Å2). Therefore, at these positions should not affect PLP binding.
Can AtALD1 bind similar substrates as AtDAPAT? For this we: analyzed malate interactions in AtDAPAT (2z1z); compared the structure of the with the site formed by the corresponding residues in AtALD1; and speculated on malate interactions if it were placed at the same position in AtALD1 as it has in AtDAPAT. of the malate binding-site in AtDAPAT with the site formed by the corresponding residues of AtALD1 (RMSD equals 0.71 Å over 10 Cα atoms) revealed that in spite of some rearrangement in the binding site, most contacts are conserved. However, we can see that for the three binding site positions that differ in composition between the structures (, in AtDAPAT and AtALD1, respectively), malate loses some or all of its contacts in the AtALD1 structure. AtALD1 is in cyan, AtDAPAT is in magenta (2z1z), carbon atoms of PLP complexed with AtALD1 are in green, carbon atoms of PLP complexed with AtDAPAT are in yellow, and carbon atoms of malate are in salmon.
In spite of considerable structural similarity between AtALD1 and AtDAPAT, residue differences at the binding site and the resulting changes in putative interaction at the corresponding malate binding positions in AtALD1 lead us to conclude that substrate specificity of AtALD1 is essentially different from those of AtDAPAT.
The resolved structure of AtALD1 can be exploited for understanding the substrate specificity of this protein and may help elucidating the plant-specific structure/function evolution of ALD1 from DAPAT.
