Structural adaptation of serine hydroxymethyltransferase to extreme environments

Serine hydroxymethyltransferase (SHMT) catalyzes the reversible cleavage of serine, to form glycine and monocarbonic groups, essential in several biosynthetic pathways. SHMT utilizes pyridoxal-5’-phosphate (PLP) and tetrahydrofolate (THF) as cofactors, the latter employed as carrier of monocarbonic units. Recently, the crystallographic structures of SHMT from four mesophilic organisms were solved. The availability of sequential information produced by the genomic projects, prompted the analysis of the structural adaptation of SHMT to extreme environments, particularly to high temperatures, by exploitation of data from extremophilic organisms. The sequences of 10 thermophilic SHMTs obtained from the databanks were multiply aligned to 54 homologs from mesophilic organisms and analyzed to detect the net flow of preferred amino acidic exchanges in the direction mesophile -> thermophile. The structural bases of the observed exchanges were further investigated, through the systematic application of homology modelling to the 10 thermophilic SHMTs, using the structures of SHMT from E.coli, man and rabbit as templates. The results of the study suggested that, in SHMT, thermal stability can be achieved through three main strategies: - an increased number of electrostatically charged residues on protein surface; - a preference for beta-branched amino acids in parallel beta-strands; - substitution of thermolabile amino acids exposed to the solvent, especially aspartic acid. The latter data suggests that the structural changes, adopted by SHMT, are the result of the necessary compromise between the conservation of the distribution of electrostatic charge on the surface of the enzyme, necessary to the binding of THF, and changes necessary to avoid the denaturation due to the possible cleavage of the peptide bonds in correspondence of the aspartic acid residues at high temperatures. Application of homology modelling to the sequences available from the genomic projects allowed the analysis of the structural features possibly related to adaptation to extreme environments, which could not have been inferred solely by sequence analysis and posed the rational basis for the design of experiments to test such hypotheses. The analysis reported here can be applied to other enzyme systems for which suitable three-dimensional and sequential information is available.