Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: mutational effects on hydride transfer rates.
Recently, the participation in catalysis of residues spatially removed from the enzyme's active site has received considerable attention. The influence of the distal Gly-121 residue on the chemical step of hydride transfer in dihydrofolate reductase (DHFR) catalysis had been demonstrated previously [Cameron, C. E., and Benkovic, S. J. (1997) Biochemistry 36, 15792-15800]. In our continuing effort to identify catalytically important residues that are distal from the active site, we used sequence conservation information, kinetic data on site-directed mutants, dynamic motion information from NMR methods, and correlated motions from MD simulations to identify a subset of residues. Among them, the region spanning positions 41-45 is distal to the active site and was chosen as the focus for the mutagenesis and kinetic studies reported here. Specifically, the highly conserved Met-42 was selected for site-directed mutagenesis. While the reaction kinetics for the M42F mutant enzyme did not deviate from wild-type behavior, a 41-fold reduction in the forward hydride transfer rate was found for the M42W mutant. Given the established role of Gly-121 in the hydride transfer process, double mutant enzymes involving positions 42 and 121 were constructed and characterized. These double mutant enzymes generally showed little changes in substrate and cofactor binding but synergistic decreases in forward hydride transfer rates, while the decreases in reverse rates were additive. Along with supporting information from mixed quantum/classical MD simulations [Agarwal, P. K., Billeter, S. R., Rajagopalan, P. T., Benkovic, S. J., and Hammes-Schiffer, S. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 2794-2799], the data suggest that a coupled dynamic motion of these distal residues enhances crossing of the chemical reaction barrier and imply an expanded nonstatic role for the protein fold in catalysis.
Rajagopalan
P T Ravi
PT
Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Lutz
Stefan
S
Benkovic
Stephen J
SJ
D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics*; D001665:Binding Sites / Q000235:genetics; D002384:Catalysis; D019295:Computational Biology; D017124:Conserved Sequence; D019143:Evolution, Molecular; D031541:Fluorescence Resonance Energy Transfer; D005998:Glycine / Q000737:chemistry; D006859:Hydrogen / Q000737:chemistry*; D007700:Kinetics; D008024:Ligands; D008715:Methionine / Q000737:chemistry; D016297:Mutagenesis, Site-Directed; D009249:NADP / Q000737:chemistry; D013329:Structure-Activity Relationship; D013379:Substrate Specificity / Q000235:genetics; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry* / Q000235:genetics* / Q000302:isolation & purification; D013816:Thermodynamics
D001426:Bacterial Proteins; D008024:Ligands; D009249:NADP; D006859:Hydrogen; D008715:Methionine; D013762:Tetrahydrofolate Dehydrogenase; D005998:Glycine