Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential.

Azat Vadimovich Abdullatypov

doi:10.3390/ijms21010366

Abstract

Three-dimensional structures of six closely related hydrogenases from purple bacteria were modeled by combining the template-based and ab initio modeling approach. The results led to the conclusion that there should be a 4Fe3S cluster in the structure of these enzymes. Thus, these hydrogenases could draw interest for exploring their oxygen tolerance and practical applicability in hydrogen fuel cells. Analysis of the 4Fe3S cluster’s microenvironment showed intragroup heterogeneity. A possible function of the C-terminal part of the small subunit in membrane binding is discussed. Comparison of the built models with existing hydrogenases of the same subgroup (membrane-bound oxygen-tolerant hydrogenases) was carried out. Analysis of intramolecular interactions in the large subunits showed statistically reliable differences in the number of hydrophobic interactions and ionic interactions. Molecular tunnels were mapped in the models and compared with structures from the PDB. Protein–protein docking showed that these enzymes could exchange electrons in an oligomeric state, which is important for oxygen-tolerant hydrogenases. Molecular docking with model electrode compounds showed mostly the same results as with hydrogenases from E. coli, H. marinus, R. eutropha, and S. enterica; some interesting results were shown in case of HupSL from Rba. sphaeroides and Rvi. gelatinosus.

Highlights

Purple bacteria are widespread organisms possessing tremendous potential for practical application
Hyd-type hydrogenases from purple sulfur bacteria (Chromatium vinosum (Allochromatium vinosum) and Thiocapsa roseopersicina) have been used in hydrogen electrodes, which could act as components of fuel cells and hydrogen biosensors [8,9]
The sequences of six hydrogenases modeled in the current study (HupSL enzymes from Tca. roseopersicina, Rba. capsulatus, Rba. sphaeroides, Rps. palustris, Rvi. gelatinosus, and Rsp. rubrum) are listed in Appendix A

Summary

Introduction

Purple bacteria are widespread organisms possessing tremendous potential for practical application They are producers of many valuable compounds, such as photosynthetic pigments (carotenoids [1] and bacteriochlorophyll [2]), storage compounds (polyhydroxyalkanoates [3]), phytohormones [4], and molecular hydrogen [5]. Hyd-type hydrogenases from purple sulfur bacteria (Chromatium vinosum (Allochromatium vinosum) and Thiocapsa roseopersicina) have been used in hydrogen electrodes, which could act as components of fuel cells and hydrogen biosensors [8,9]. These enzymes are relatively oxygen-tolerant and thermostable. Since a fuel cell should be suitable for storage in air and operation in hydrogen, meaning that there could be steps of exposition of hydrogenase electrodes to hydrogen-oxygen mixture, this gives rise to some obstacles for the wide application of these enzymes in hydrogen electrodes

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