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REVIEW: Role of a Structurally Equivalent Phenylalanine Residue in Catalysis and Thermal Stability of Formate Dehydrogenases from Different Sources

V. I. Tishkov1,2,3*, K. V. Goncharenko1,3, A. A. Alekseeva2,3, S. Yu. Kleymenov2,4, and S. S. Savin1,2

1Lomonosov Moscow State University, Faculty of Chemistry, 119991 Moscow, Russia; E-mail: vitishkov@gmail.com

2Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia

3Innovations and High Technologies MSU Ltd., 109451 Moscow, Russia

4Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia

* To whom correspondence should be addressed.

Received August 3, 2015; Revision received September 4, 2015
Comparison of amino acid sequences of NAD+-dependent formate dehydrogenases (FDH, EC from different sources and analysis of structures of holo-forms of FDH from bacterium Pseudomonas sp. 101 (PseFDH) and soya Glycine max (SoyFDH) as well as of structure of apo-form of FDH from yeast Candida boidinii (CboFDH) revealed the presence on the surface of protein globule of hydrophobic Phe residue in structurally equivalent position (SEP). The residue is placed in the coenzyme-binding domain and protects bound NAD+ from solvent. The effects of amino acid changes of the SEP on catalytic properties and thermal stability of PseFDH, SoyFDH, and CboFDH were compared. The strongest effect was observed for SoyFDH. All eight amino acid replacements resulted in increase in thermal stability, and in seven cases, increase in catalytic constant was achieved. Thermal stability of SoyFDH after mutations Phe290Asp and Phe290Glu increased 66- and 55-fold, respectively. KM values of the enzyme for substrate and coenzyme in different cases slightly increased or decreased. In case of one CboFDH, the mutein catalytic constant increased and thermal stability did not changed. In case of the second CboFDH mutant, results were the opposite. In one PseFDH mutant, amino acid change did not influence the catalytic constant, but in three others, the parameter was reduced. Two PseFDH mutants had higher and two mutants lower thermal stability in comparison with initial enzyme. Analysis of results of SEP mutagenesis in FDHs from bacterium, yeast, and plant shows that protein structure plays a key role for effect of the same amino acid changes in equivalent position in protein globule of formate dehydrogenases from different sources.
KEY WORDS: formate dehydrogenase, rational design, thermal stability, catalytic properties

DOI: 10.1134/S0006297915130052