The conserved crown bridge loop at the catalytic centre of enzymes of the haloacid dehalogenase superfamily

The crown bridge loop is hexapeptide motif in which the backbone carbonyl group at position 1 is hydrogen bonded to the backbone imino groups of positions 4 and 6. Residues at positions 1 and 4–6 are held in a tight substructure, but different orientations of the plane of the peptide bond between positions 2 and 3 result in two conformers: the 2,3-α(R)α(R) crown bridge loop — found in approximately 7% of proteins — and the 2,3-β(R)α(L) crown bridge loop, found in approximately 1–2% of proteins. We constructed a relational database in which we identified 60 instances of the 2,3-β(R)α(L) conformer, and find that about half occur in enzymes of the haloacid dehalogenase (HAD) superfamily, where they are located next to the catalytic aspartate residue. Analysis of additional enzymes of the HAD superfamily in the extensive SCOPe dataset showed this crown bridge loop to be a conserved feature. Examination of available structures showed that the 2,3-β(R)α(L) conformation — but not the 2,3-α(R)α(R) conformation — allows the backbone carbonyl group at position 2 to interact with the essential Mg(2+) ion. The possibility of interconversion between the 2,3-β(R)α(L) and 2,3-α(R)α(R) conformations during catalysis is discussed.