Homology Modeling and Molecular Docking Studies of Glutamate Dehydrogenase (GDH) from Cyanobacterium Synechocystis sp. PCC 6803

Abstract

Glutamate dehydrogenase (GDH), which is present in most bacteria and eukaryotes’ mitochondria, plays an important role in amino acid metabolism. In general, GDH converts 2-oxoglutarate to l-glutamate using NAD(P)H as a cofactor, and vice versa. Acquiring more structural information about the GDH of Synechocystis sp. PCC 6803 could be helpful in many studies related to amino acid metabolism in cyanobacteria. In this study, homology modeling studies were conducted to achieve an acceptable structure of the GDH using recognized templates. To this end, a computational approach was used to demonstrate the coenzyme specificity of GDH for NADPH and NADH. The present study involved homology modeling of GDH and docking analyses of NADPH, NADH, 2-oxoglutarate, and l-glutamate into the predictive model of GDH. The results of this study suggest that GDH has similar coenzyme specificity for NADH and NADPH, while NADH has a better binding affinity than NADPH. Furthermore, the binding sites of 2-oxoglutarate and l-glutamate are similar to each other with differences in binding affinity.

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Acknowledgements

This investigation was financially supported by National Institute of Genetic Engineering and Biotechnology (NIGEB), Ministry of Science, Research and Technology, Tehran, Iran.

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Correspondence to Hossein Shahbani Zahiri or Hadi Maleki or Kambiz Akbari Noghabi.

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Haghighi, O., Davaeifar, S., Zahiri, H.S. et al. Homology Modeling and Molecular Docking Studies of Glutamate Dehydrogenase (GDH) from Cyanobacterium Synechocystis sp. PCC 6803. Int J Pept Res Ther 26, 783–793 (2020). https://doi.org/10.1007/s10989-019-09886-4

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Keywords

  • Glutamate dehydrogenase
  • Cyanobacteria
  • Homology modeling
  • Molecular docking