Heterodimeric interaction of the ADP-glucose pyrophosphorylase (AGPase) enzyme in <i>Hordeum vulgare</i>

Abstract

ADP-glucose pyrophosphorylase (E.C. 2.7.7.27; AGPase) is a key regulatory enzyme, constituting two small (SS) and two large (LS) subunits. The crystallographic structure of AGPase enzyme has not been reported yet for barley and its active site residues have also not been identified, which is restraining the complete understanding of structure-function relationships of this enzyme. In the present study, three-dimensional (3D) structures of LS and SS of barley AGPase were built through homology modeling and optimized using MD (molecular dynamics) simulations. Further evaluation resulted in about 74.8% residues of LS and 75.7% residues of SS falling in the favorable regions of Ramachandran Plot, demonstrating the stability and trustworthiness of the models. RMSD (root mean square deviation) of 1.1 Å and 1.2 Å was predicted on superimposition of the deduced LS and SS structure on the template 1YP2, implying the similarity between the structures. Protein-protein docking was carried out using ZDOCK and GRAMM-X server to obtain the stable heterodimer structure of barley AGPase. Interaction analysis using the Dimplot revealed six hydrogen-bonding interactions between HIS-359, GLN-322, SER-113, LEU-342, SER-324 and ASN-111 residues of LS, and ASN-341, SER-286, SER-8, ASP-261 and VAL-283 residues of SS. The structure-function relationship and substrate binding specificity of AGPase will provide better understanding for the role of specific amino acid accountable for allosteric regulation.