Structural Basis of Compound Recognition by Adenosine Deaminase

Abstract

Structural snapshots corresponding to various states enable elucidation of the molecular recognition mechanism of enzymes. Adenosine deaminase has two distinct conformations, an open form and a closed form, although it has so far been unclear what factors influence adaptation of the alternative conformations. Herein, we have determined the first nonligated structure as an initial state, which was the open form, and have thereby rationally deduced the molecular recognition mechanism. Inspection of the active site in the nonligated and ligated states indicated that occupancy at one of the water-binding positions in the nonligated state was highly significant in determining alternate conformations. When this position is empty, subsequent movement of Phe65 toward the space induces the closed form. On the other hand, while occupied, the overall conformation remains in the open form. This structural understanding should greatly assist structure-oriented drug design and enable control of the enzymatic activity.

Structural Basis for the Growth Factor Activity of Human Adenosine Deaminase ADA2

“…The resulting coordination geometry of the bound zinc is distorted trigonal bipyramidal with atoms N⑀2 of His-86 and His-88 and the O8 atom of CF occupying the equatorial positions and atoms N⑀2 of His-330 and O␦2 of Asp-415 occupying the axial positions (supplemental Table 2S). This binding geometry is very similar to that observed for the zinc coordination in ADA1 proteins (6,8,10) (Fig. 4B and supplemental Table 2S).…”

“…Side chains of other active site residues undergo only minor changes. This is in sharp contrast to the dramatic conformational changes in the structures of ADA1 proteins, which switch between open (ligand-free) and closed (complexed) conformations (8). Interestingly, superposition of 40 active site residues in ADA2 with corresponding residues in the open and closed conformations in ADA1 revealed significantly higher similarity to the open (r.m.s.d.…”

Sampling protein motion and solvent effect during ligand binding

“…A rational drug design is further complicated by the fact that in response to different inhibitors, ADA can assume either an open or a closed conformation by changing the position of the H3 α-helix (Thr57-Ala73). The open conformation corresponds to the apo-form (PDB ID code 3iar) and is preferred when a nonnucleoside inhibitor is bound (12,13). In this case, the active site presents a hydrophilic subsite S0 and three hydrophobic subsites F0, F1, and F2 ( Fig.…”

“…In this case, the active site presents a hydrophilic subsite S0 and three hydrophobic subsites F0, F1, and F2 ( Fig. 1A) (13). The S0 subsite is defined by the structural gate formed by a β-strand (Leu182-Asp185) and two leucine side chains attached to the H3 α-helix while the F0 site is formed by the hydrophobic side chains of the H3 α-helix.…”

“…The S0 subsite is defined by the structural gate formed by a β-strand (Leu182-Asp185) and two leucine side chains attached to the H3 α-helix while the F0 site is formed by the hydrophobic side chains of the H3 α-helix. In the open form the H3 α-helix assumes a conformation that exposes two additional hydrophobic subsites in the upper part the helix, namely F1 and F2 (13). The binding of a ground-state inhibitor, like the hydroxylated form of adenosine (HDPR) (V in Fig.…”