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In Silico Study of the Structure and Ligand Preference of Pyruvate Kinases from Cyanobacterium Synechocystis sp. PCC 6803

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Abstract

Finding reliable cheap sources for producing chemicals and materials is always challenging. During recent decades, photosynthetic organisms such as cyanobacteria, which used CO2 as a carbon source for making products, have attracted a great deal of attention. Among cyanobacteria, Synechocystis sp. PCC 6803 has been considered as a model strain and has some desirable features that make it suitable for use as an industrial strain. Pyruvate kinase (PK) catalyzes the transformation of phosphoenolpyruvate (PEP) to pyruvate in the last step of glycolysis that is an essential enzyme to produce adenosine triphosphate (ATP) in all organisms. Therefore, it plays a critical role in regulating cell metabolism. However, active and allosteric sites of PK and allosteric mechanisms governing PK activity are poorly understood in many bacteria. This study was aimed to provide more insight into PKs of Synechocystis sp. PCC 6803, using in silico methods. The results indicated that predicted structures of PKs from Synechocystis sp. PCC 6803 are reliable and can be considered for further studies. Molecular docking studies suggested that for predicted structures of sll0587 and sll1275, respectively, there are three and two possible active or allosteric sites. Furthermore, molecular interaction analysis of modeled structures proposes that sll0587 is strongly inhibited by ATP and when ATP concentration is low, this isoenzyme is active.

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Data Availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

I wish to thank all my friends at the University of Isfahan and NIGEB for their support.

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  1. Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P. O. Box 14155-6343, Tehran, Iran

    Omid Haghighi

  2. Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran

    Omid Haghighi

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Haghighi, O. In Silico Study of the Structure and Ligand Preference of Pyruvate Kinases from Cyanobacterium Synechocystis sp. PCC 6803. Appl Biochem Biotechnol 193, 3651–3671 (2021). https://doi.org/10.1007/s12010-021-03630-9

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