Inventory of interactions that participate in the proper positioning of the catalytic histidine next to the catalytic nucleophile in 40 ABH fold enzyme families.

The main-chain oxygen atom of residue XIV interacts with both the catalytic histidine and the catalytic nucleophile (column CA/Nucleophile–O/XIV), orienting the imidazole ring of the catalytic histidine with respect to the side-chain of the catalytic nucleophile. Residue XIV+1 also interacts with the catalytic nucleophile (column O/Nucleophile–CA/XIV+1) and thus, has an indirect influence on the optimal arrangement of the catalytic histidine-nucleophile pair. Unrelated to the coordination of the catalytic residues, an additional conserved contact (column Sc/(Nucleophile+4)–O/XIV+2) is formed between the residue that is located four positions after the catalytic nucleophile and the residue that is located two positions after residue XIV; this conserved contact is formed close to the catalytic nucleophile, residue XIV and residue XIV+1. In the second row of the table, the interactions from the carboxylesterase SshEstI (SCOP family #2, PDB ID:3WJ1_A) are listed, corresponding to the interactions that are illustrated in Fig 2. In four ABH fold families [SCOP families #12 (PDB ID:1MJ5_A), #23, #27 and #29], residue XIV is the catalytic acid residue. SCOP family #12 is represented by two structures in order to properly reflect the local structural variations in ABH fold enzymes that have their catalytic acid at the canonical position (i.e. at the turn that follows strand β7, e.g. structure PDB ID:1B6G_A) or at the alternate position (i.e. at the position of residue XIV, e.g. structure PDB ID:1MJ5_A). Alternative types of contacts to those described as conserved occur in a few representative structures, for example in ABH fold enzyme families of Epoxide hydrolase (SCOP family #18), Atu1826-like (SCOP family #36) and PHB depolymerase-like (SCOP family #37). Values in parentheses correspond to the distances of the hydrogen bond to the hydrogen atom.