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closeFurther support for Ty1 protease putative substrate grooves
Posted by GaryLaco on 21 Feb 2020 at 18:30 GMT
In regards to the absence of substrate grooves (S-groove) in the Ty1 PR the authors stated, "Therefore, we propose that Ty1 PR surface residues may have only weak interaction with the substrate at these sites" (Results/Enzymatic assays using recombinant protein substrates/pg 13/line 14) and "we presumed that the binding surface for P10-P6 and P6’-P10’ substrate residues in Ty1 PR is absent or has a different structure than that of the substrate-groove of HIV-1 protease (Results/In silico structural analysis/pg 17/line 4). However, given the support I found for a Ty1 PR substrate groove in their Results (see first comment) I asked for their Ty1 protease model, and they generously shared it with me. When I looked at that model of Ty1 PR I found that it was remarkably similar to that of the HIV-1 PR and the Ty1 PR putative S-grooves were similarly lined with charged/polar residues including: Arg41; Asp76; Lys86; Thr87; Ser88; Lys90; and Asp111. Furthermore, when I aligned my model of HIV-1 PR with bound 24-mer substrate (S-groove, Laco GS, Biochimie, 2015, 118, 90-103, https://doi.org/10.1016/j...) with the Ty1 PR model, I found the 24-mer substrate fit into the putative Ty1 PR S-grooves with only a couple of minor steric clashes. Mutation of the HIV-1 PR 24-mer substrate to the Ty1 PR PR/IN substrate, followed by minimization, revealed that the PR/IN cleavage site residues outside of P5-P5' were able to make direct contact with Ty1 PR putative S-groove residues including the PR/IN P9' Arg which H-bonded to the Ty1 PR putative S-groove Asp76. So the more I look into the Ty1 PR putative S-grooves, the more support I find for functional S-grooves in the Ty1 PR. Future experiments could potentially extend the retroviral protease S-groove hypothesis to retrotransposon proteases. Note: I did share this information with the authors via Dr. Janos A. Motyan.