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Insight into the 3D structure of ADP-glucose pyrophosphorylase from rice (Oryza sativa L.)

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Abstract

ADP-glucose pyrophosphorylase (E.C. 2.7.7.27; AGPase) is a key regulatory enzyme that catalyzes the rate-limiting step of starch biosynthesis in higher plants. AGPase consists of pair of small (SS) and large (LS) subunits thereby constituting a heterotetrameric structure. No crystal structure of the native heterotetrameric enzyme is available for any species, thus limiting the complete understanding of structure–function relationships of this enzyme. In this study, an attempt was made to deduce the heterotetrameric assembly of AGPase in rice. Homology modeling of the three-dimensional structure of the LS and SS was performed using the Swiss Model Server, and the models were evaluated and docked using GRAMM-X to obtain the stable heterodimer orientation (LS as receptor and SS as ligand) and then the heterotetrameric orientation. The initial heterotetrameric orientation was further refined using the RosettaDock Server. MD simulation of the representative heterodimer/tetramer was performed using NAMD, which indicated that the tail-to-tail interaction of LS and SS was more stable than the head-to-head orientation, and the heterotetramer energy was also minimized to −767,011 kcal mol−1. Subunit–subunit interaction studies were then carried out using the programs NACCESS and Dimplot. A total of 57 interface residues were listed in SS and 63 in LS. The residues plotted by Dimplot were similar to those listed by NACCESS. Multiple sequence alignment of the sequences of LS and SS from potato, maize and rice validated the interactions inferred in the study. RMSD of 1.093 Å was obtained on superimposition of the deduced heterotetramer on the template homo-tetramer (1YP2), showing the similarity between the two structures.

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Acknowledgments

The authors gratefully acknowledge the help rendered by Aytug Tuncel and Ibrahim Halil Kavakli, Department of Chemical and Biological Engineering, College of Engineering, Koc University, Rumeli Feneri Yolu, Istanbul, Turkey for MD simulations. The funding provided by the Department of Biotechnology, New Delhi and Indian Council of Agricultural Research, New Delhi for computing facilities is acknowledged.

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  1. Bioinformatics Section, CCS Haryana Agricultural University, Hisar, 125004, India

    Chhavi Dawar, Sunita Jain & Sudhir Kumar

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  1. Chhavi Dawar
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  2. Sunita Jain
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Correspondence to Sudhir Kumar.

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Dawar, C., Jain, S. & Kumar, S. Insight into the 3D structure of ADP-glucose pyrophosphorylase from rice (Oryza sativa L.). J Mol Model 19, 3351–3367 (2013). https://doi.org/10.1007/s00894-013-1851-7

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