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Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis.

Fieulaine S, Boularot A, Artaud I, Desmadril M, Dardel F, Meinnel T, Giglione C - PLoS Biol. (2011)

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.

View Article: PubMed Central - PubMed

Affiliation: CNRS, ISV, UPR2355, Gif-sur-Yvette, France.

ABSTRACT
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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Related in: MedlinePlus

Effect of actinonin binding on the conformation of key residues in PDF.Conformation of key residues Ile42, Phe58, and Ile130 in the different complexes: (A) in unbound WT AtPDF, (B and C) in the structure of G41Q and G41M actinonin-bound variants, respectively, and (D) of actinonin-bound WT protein. In the final complex (D), a hydrogen bond is formed between actinonin and the peptidic bond, which links Gly41 and Ile42. During the deformylation reaction, which is catalyzed by the PDF enzyme, the N-terminal formyl-methionine fits into the S1' pocket. The solvent-accessible surface of this pocket is represented here, and only the aliphatic chain of actinonin is shown, mimicking the N-terminal methionine. (E) Free WT enzyme with the S1' pocket shown open in two orientations (top and bottom). (F and G) S1' pocket in the G41Q and G41M variant structures, respectively, shown in two orientations (top and bottom). (H) After the complete conformational modifications of actinonin-bound WT protein induced by actinonin binding, the S1' pocket is shown closed in two orientations (top and bottom). (I) The four models are superimposed; the ligand-binding site is magnified: unbound WT AtPDF; G41Q and G41M actinonin-bound enzyme; and WT actinonin-bound enzyme are indicated in brown, red, orange, and yellow, respectively. Actinonin is indicated by lines. (J) A detailed view of the AtPDF ligand-binding site for all the complexes, which are superimposed, as indicated in the same colors. Arrows indicate the direction of the closing movement within the enzyme, from the open, unbound state to the closed, bound state.
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pbio-1001066-g003: Effect of actinonin binding on the conformation of key residues in PDF.Conformation of key residues Ile42, Phe58, and Ile130 in the different complexes: (A) in unbound WT AtPDF, (B and C) in the structure of G41Q and G41M actinonin-bound variants, respectively, and (D) of actinonin-bound WT protein. In the final complex (D), a hydrogen bond is formed between actinonin and the peptidic bond, which links Gly41 and Ile42. During the deformylation reaction, which is catalyzed by the PDF enzyme, the N-terminal formyl-methionine fits into the S1' pocket. The solvent-accessible surface of this pocket is represented here, and only the aliphatic chain of actinonin is shown, mimicking the N-terminal methionine. (E) Free WT enzyme with the S1' pocket shown open in two orientations (top and bottom). (F and G) S1' pocket in the G41Q and G41M variant structures, respectively, shown in two orientations (top and bottom). (H) After the complete conformational modifications of actinonin-bound WT protein induced by actinonin binding, the S1' pocket is shown closed in two orientations (top and bottom). (I) The four models are superimposed; the ligand-binding site is magnified: unbound WT AtPDF; G41Q and G41M actinonin-bound enzyme; and WT actinonin-bound enzyme are indicated in brown, red, orange, and yellow, respectively. Actinonin is indicated by lines. (J) A detailed view of the AtPDF ligand-binding site for all the complexes, which are superimposed, as indicated in the same colors. Arrows indicate the direction of the closing movement within the enzyme, from the open, unbound state to the closed, bound state.

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 [34],[35],[44],[50], 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 [51].


Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis.

Fieulaine S, Boularot A, Artaud I, Desmadril M, Dardel F, Meinnel T, Giglione C - PLoS Biol. (2011)

Effect of actinonin binding on the conformation of key residues in PDF.Conformation of key residues Ile42, Phe58, and Ile130 in the different complexes: (A) in unbound WT AtPDF, (B and C) in the structure of G41Q and G41M actinonin-bound variants, respectively, and (D) of actinonin-bound WT protein. In the final complex (D), a hydrogen bond is formed between actinonin and the peptidic bond, which links Gly41 and Ile42. During the deformylation reaction, which is catalyzed by the PDF enzyme, the N-terminal formyl-methionine fits into the S1' pocket. The solvent-accessible surface of this pocket is represented here, and only the aliphatic chain of actinonin is shown, mimicking the N-terminal methionine. (E) Free WT enzyme with the S1' pocket shown open in two orientations (top and bottom). (F and G) S1' pocket in the G41Q and G41M variant structures, respectively, shown in two orientations (top and bottom). (H) After the complete conformational modifications of actinonin-bound WT protein induced by actinonin binding, the S1' pocket is shown closed in two orientations (top and bottom). (I) The four models are superimposed; the ligand-binding site is magnified: unbound WT AtPDF; G41Q and G41M actinonin-bound enzyme; and WT actinonin-bound enzyme are indicated in brown, red, orange, and yellow, respectively. Actinonin is indicated by lines. (J) A detailed view of the AtPDF ligand-binding site for all the complexes, which are superimposed, as indicated in the same colors. Arrows indicate the direction of the closing movement within the enzyme, from the open, unbound state to the closed, bound state.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3101196&req=5

pbio-1001066-g003: Effect of actinonin binding on the conformation of key residues in PDF.Conformation of key residues Ile42, Phe58, and Ile130 in the different complexes: (A) in unbound WT AtPDF, (B and C) in the structure of G41Q and G41M actinonin-bound variants, respectively, and (D) of actinonin-bound WT protein. In the final complex (D), a hydrogen bond is formed between actinonin and the peptidic bond, which links Gly41 and Ile42. During the deformylation reaction, which is catalyzed by the PDF enzyme, the N-terminal formyl-methionine fits into the S1' pocket. The solvent-accessible surface of this pocket is represented here, and only the aliphatic chain of actinonin is shown, mimicking the N-terminal methionine. (E) Free WT enzyme with the S1' pocket shown open in two orientations (top and bottom). (F and G) S1' pocket in the G41Q and G41M variant structures, respectively, shown in two orientations (top and bottom). (H) After the complete conformational modifications of actinonin-bound WT protein induced by actinonin binding, the S1' pocket is shown closed in two orientations (top and bottom). (I) The four models are superimposed; the ligand-binding site is magnified: unbound WT AtPDF; G41Q and G41M actinonin-bound enzyme; and WT actinonin-bound enzyme are indicated in brown, red, orange, and yellow, respectively. Actinonin is indicated by lines. (J) A detailed view of the AtPDF ligand-binding site for all the complexes, which are superimposed, as indicated in the same colors. Arrows indicate the direction of the closing movement within the enzyme, from the open, unbound state to the closed, bound state.
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 [34],[35],[44],[50], 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 [51].

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.

View Article: PubMed Central - PubMed

Affiliation: CNRS, ISV, UPR2355, Gif-sur-Yvette, France.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus