Crystal structure and its proposed nucleolytic site of the single domain catalytic antibody 3D8-VH

Catalytic antibodies are monoclonal antibodies with catalytic activities. An anti-DNA antibody can bind DNA and hydrolyze it with modest catalytic activity. The monoclonal antibody 3D8 from the autoimmune-disease prone MRL-lpr/lpr mouse has been used to make a recombinant single-chain variable-fragment antibody (3D8 scFv) that hydrolyzes DNA. The catalytic site is composed of several hyper-variable loops. Two His residues from the variable domains of the heavy chain (VH) and the light chain (VL) are responsible for DNA hydrolysis. Interestingly, two single domain antibodies derived from 3D8 scFv, called 3D8-VH and 3D8-VL, also bind and hydrolyze DNA although their activities are significantly lower than those of 3D8 scFv. Here, we report the crystal structure of 3D8-VH, which revealed no significant difference compared to the VH domain from 3D8 scFv. The 3D8-VH antibody is also structurally very similar to 3D8-VL that has a catalytic metal ion on the newly exposed surface-curvature. The observed structural features of 3D8-VH, along with the fact that it retained catalytic activity when the His residue that was catalytic in the 3D8 scFv was replaced, suggest that 3D8-VH also has its DNA binding and cleavage activity on the newly exposed surface. These findings provide new insights into substrate recognition and catalysis by single domain anti-DNA antibodies.