The CDR1 of the human λVI light chains adopts a new canonical structure.

We performed a comparative analysis of the conformation of the CDR1 of the human λVI variable domains JTO and WIL and the equivalent loop of the λI light chains RHE and KOL, which are representative of the type I canonical structure for λ light chains. On the basis of the differences found in the main chain conformation, as well as the identity of the residues at key positions, we showed that the L1 of some λVI light chains adopts a conformation that represents a new type of canonical structure. The conformation of the L1 of those λVI light chains, is primarily determined by the presence of an Arg residue at position 25. The analysis of the λVI light chain sequences so far reported, showed that near 25% of those proteins have Gly at position 25 instead of Arg, which represents an allotypic variant of the λVI variable locus. The presence of Gly at position 25 in the L1 of λVI light chains would imply a different conformation for this loop. Additionally, the position 68 in λVI light chains, which is at the top of the FR3 loop, showed such spatial orientation and variability that suggested its participation in the conformation of the antigen recognition surface in this subgroup of λ chains. Proteins 2006. © 2005 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]