Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis.
Bottom Line: Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally "zipped up" by additional binding interactions.Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme.A "movie" that reconstructs this entire process can be further extrapolated to catalysis.
Affiliation: CNRS, ISV, UPR2355, Gif-sur-Yvette, France.
For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally "zipped up" by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A "movie" that reconstructs this entire process can be further extrapolated to catalysis.
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Mentions: The closed final conformation was identical to that previously reported for PDF complexes obtained either with actinonin or with a product of the reaction ,,,, indicating that this structure is common for the ligands (compare Figures 1B and 2A, and Figure S4). Hydrogen bonding was also conserved, especially the bond between the backbone nitrogen of Ile42 (corresponding to Ile44 in EcPDF, see Figure 1B and Figure S5A) and the alkyl carbonyl chain of actinonin, which potently contributes to the formation of the super β-sheet (Movie S2 and Figure S1B, see also below). Between the open and closed states, the side chains of Ile42, Phe58, and Ile130 underwent significant structural changes (Figure 3A and D and Figure S6), corresponding to a hydophobic pocket rearrangement, with Ile42 being the most affected (Figure 3). Interestingly, Ile42 is the second residue of the conserved active-site motif G41IGLAAXG (motif 1) that was previously shown to be essential for activity .