In Silico Study of the Structure and Ligand Interactions of Alcohol Dehydrogenase from Cyanobacterium Synechocystis Sp. PCC 6803 as a Key Enzyme for Biofuel Production

Appl Biochem Biotechnol. 2020 Dec;192(4):1346-1367. doi: 10.1007/s12010-020-03400-z. Epub 2020 Aug 7.

Abstract

Alcohol dehydrogenase is one of the most critical enzymes in the production of ethanol and butanol. Synechocystis sp. PCC 6803 is a model cyanobacterium organism that is able to produce alcohols through its autotrophic energy production system. In spite of the high potential for biofuel production by this bacteria, the structure of its alcohol dehydrogenase has not been subjected to in-depth studies. The current study was aimed to analyze the molecular model for alcohol dehydrogenase of Synechocystis sp. PCC 6803 and scrutinize the interactions of different chemicals, including substrates and coenzymes. Also, the phylogenetic tree was provided to investigate the relation between different sources. The results indicated that alcohol dehydrogenase of Synechocystis sp. PCC 6803 has a different sequence compared with other Alcohol dehydrogenases (ADHs) of cyanobacterial family members. Verification of the homology model using Ramachandran plot by PROCHECK indicated that all of the residues are in favored or allowed regions of the plot. This enzyme has two Zn ions in its structure which is very similar to the other Zn-dependent ADHs. Docking studies suggest that this enzyme could have more active sites for different substrates. In addition, this enzyme has more affinity to NADH as a cofactor and sinapaldehyde as a substrate compared with the other cofactor and substrates.

Keywords: Alcohol dehydrogenase; Ethanol; Molecular docking; Molecular modeling; Synechocystis.

MeSH terms

  • Alcohol Dehydrogenase / chemistry*
  • Alcohol Dehydrogenase / metabolism*
  • Biofuels*
  • Computer Simulation*
  • Ligands
  • Molecular Docking Simulation
  • Protein Binding
  • Protein Conformation
  • Synechocystis / enzymology*

Substances

  • Biofuels
  • Ligands
  • Alcohol Dehydrogenase