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Node 35 structural features implicated in a proposed induced-fit mechanism.

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posted on 2016-12-21, 18:29 authored by Andrew F. Neuwald, Stephen F. Altschul

A-C. Conformational changes that involve two conserved residues and that mediate opening and closing of the substrate binding pocket of a putative acetylase from Salmonella typhimurium with and without bound acetyl-CoA (pdb_id: 3dr8 and 3dr6). A. (top) Surface view of the open conformation when CoA is bound to both subunits (pdb_id: 3dr8). The surface of Glu82 is shown in red, of Arg72 in yellow and of the rest of the substrate binding pocket (SBP) in green. (bottom) Close up view of Glu82 and Arg72 at the dimeric interface (pdb_id: 3dr8); the SBP is indicated. B. (top) Surface view of the closed conformation when neither subunit is bound to CoA (pdb_id: 3dr6). Note that the substrate binding pocket appears inaccessible. (bottom) Close up of the Glu82-Arg72 salt bridge formed at the subunit interface. C. (top left) Surface side view of the acetyl-CoA bound form (pdb_id: 3dr8) showing the locations of a cluster of Set42-specific residues (shaded yellow). CoA is shown in cyan. (bottom) The same view of 3dr8 as in A but rotated by 90 degrees to show a side view. The expanded box shows the node-42 pattern residue interactions forming a bridge between adjacent loop regions. (top right) A similar view of C. Elegans Gna1 (pdb_id: 4ag9) showing the adjacent locations of the CoA and substrate within a channel rather than a pocket as in (A). D-F. Differences between node 40 and node 36 pattern residues. Residues with red sidechains correspond to node 35 pattern residues. See S3 Fig for the contrast alignment showing pattern residues. D. Node 40 pattern residues (orange sidechains) within 3dr6 (an acetylase assigned to node 42). E. Node 40 pattern residues (orange sidechains) within 1vhs (an acetylase assigned to node 41). F. Node 36 pattern residues (light green sidechains) within 4jxr (an acetylase assigned to node 39).