PEDS Advance Access published online on October 3, 2009
Protein Engineering Design and Selection, doi:10.1093/protein/gzp056
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The V119I polymorphism in protein L-isoaspartate O-methyltransferase alters the substrate-binding interface
1Department of Biochemistry, University of Washington, Box 355013, Seattle, WA 98195-5013, USA 2Department of Bioengineering, University of Washington, Box 355013, Seattle, WA 98195-5013, USA 3Present address: Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
4 To whom correspondence should be addressed. E-mail: daggett{at}u.washington.edu
Protein L-isoaspartate O-methyltransferase (PIMT) repairs isoaspartate residues in damaged proteins, and it contains a Val–Ile polymorphismin in 
5, 
13 Å from its active site. Val119 has lower activity and thermal stability but increased affinity for endogenous substrates. Studies suggest that heterozygosity for Val/Ile favors efficient isoaspartate repair. We have performed multiple molecular dynamics simulations of 119I and 119V PIMT. Both V119 and I119 interact with the same residues throughout all of the simulations. However, the larger Ile altered the orientations of 5 and β5, both of which have co-substrate binding residues on their distal ends. I119 increases the flexibility of several residues, loosening up the S-adenosylmethionine (SAM)-binding site. These subtle changes are propagated towards the isoaspartate-docking site via residues common to both active sites. The increased mobility in 119I PIMT reorients 3, resulting in a salt-bridge network at the substrate-binding interface that disrupts several key side-chain interactions in the isoaspartate site. In contrast, 119V PIMT remains quite rigid with little change to the co-substrate binding site, which could hinder SAM's binding and release, accounting for the decreased activity. These results shed light on the molecular basis behind the decreased activity and increased specificity for endogenous substrates of 119V PIMT relative to the 119I variant. 119I PIMT catalyzes the methylation reaction but may have difficulties recognizing and orienting specific substrates due to its distorted substrate-binding site. Heterozygosity for both the Ile and Val alleles may provide the best of both worlds, allowing the fast and specific methylation of damaged proteins.
Keywords: aging/molecular dynamics/polymorphisms/protein isoaspartate O-methyltransferase/protein repair
Received August 25, 2009; revised August 25, 2009; accepted August 26, 2009.