In Silico Study of the Structure and Ligand Interactions of Alcohol Dehydrogenase from Cyanobacterium Synechocystis Sp.
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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 Omid Haghighi 1,2 & Mohammad Moradi 2 Received: 2 June 2020 / Accepted: 16 July 2020/ # Springer Science+Business Media, LLC, part of Springer Nature 2020
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 . Molecular modeling . Molecular docking . Synechocystis . Ethanol
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12010-02003400-z) contains supplementary material, which is available to authorized users.
* Omid Haghighi [email protected]; [email protected] * Mohammad Moradi [email protected]; [email protected] Extended author information available on the last page of the article
Applied Biochemistry and Biotechnology
Introduction Cyanobacteria have considerable potential for producing biofuel because of their accelerated growth rate, carbon dioxide gas fixation, and tractability of their genetic material. Moreover, they do not need carbon sources, such as biomass or arable condition to grow, which provides them with an advantage for alcohol production [1]. Regarding the use of CO2 as a source for carbon, it could be concluded that they provide many advantages, but they still suffer from a big drawback, which is the low yield of alcohol production [2]. Recent breakthroughs in the synthetic biology and genetic engineering have made it possible to manipulate the cyanobacteria to provide a higher yield of producing the desired compounds [3–5]. Accordingly, any information about their metabolism and involved enzymes in a
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