Amongst 16 disease-related variants, two occur at metal-binding (METAL) and two at ligand-binding (BINDING) residues, which are directly responsible for the disease by inducing the loss of activity for the protein [35], [37], [38].
Thomas and coworkers reported that comparison of AHL lactonase with other superfamily members including glyoxalase II, phosphodiesterase-ZiPD, and methyl parathion hydrolase suggests possible zinc binding residues which are totally conserved in all known AHL lactonases: His104, His106, and His169 for the metal-1 site and Asp108, His109, and His235 for the metal-2 site [ 22].
In this study, we carried out site-directed mutagenesis on oxygen-binding residues, which are observed in the high-resolution crystal structure, in order to elucidate the amino acid residues responsible for the oxidase activity.
Zn2+-binding residues, which are known to be essential for enzyme catalytic activity and structure, and the Zn2+-binding consensuses were also found (Box I).
Despite its presence and the overall structural similarity of HNV-G to HN glycoproteins, only one of the seven sialic acid-binding residues which are conserved in the HNs are present in HNV-G.
In EcBirA, there is a biotin binding loop (BBL) 115 120 residues which is conserved and adenylate binding loop (ABL) consisting of residues 212 223 (25, 25).
The parasite protein, SAR1 (PF3D7_0416800), is a small GTP-binding protein of 192 amino acid residues, which is involved in the crucial step of budding reaction in vesicle-mediated secretory pathway.
Canonically, PDZs fold to modular structures that bind C-terminal ligands via 16 key binding pocket residues, which are dispersed over alpha-helix 2 and beta-sheets 2 and 3 (βB and βC) [10], [14], [17] (Fig. 2A).
This hydrophilic stretch is surface accessible inspite of being adjacent to binding site residues (which are buried in the hydrophobic core) and forms a loop away from the active site.
Level 1 residues are strict binding site residues, which are defined as residues that are in direct contact with the ligand, that is, at least one pair of nonhydrogen atoms an atom from the residue and an atom from the ligand is positioned with 4 Å distance.
