Structure of L-isoaspartyl (D-aspartyl) methyltransferase

The structure of Pyrococcus furiosus L-isoaspartyl (D-aspartyl) methyltransferase has been determined to 1.2 Å with a working R-value of 0.15 and a free R-value of 0.20. The structural model was built using x-ray diffraction data from a native crystal and experimental phases from a single samarium crystal. This structure provides independent confirmation of the unique topological rearrangement found in S-adenosylmethionine dependent L-isoaspartyl methyltransferases. In addition to the S-adenosylhomocysteine (AdoHcy) and P. furiosus enzyme complex, the P. furiosus enzyme structure has been determined in complex with S-adenosylmethionine (AdoMet), in complex with adenosine, and in a ternary complex with adenosine and the VYP-L-isoAsp-HA polypeptide substrate. The human homolog structure has also been determined using the P. furiosus AdoHcy structure for initial phasing by molecular replacement.; Comparisons of the various forms of the L-isoaspartyl methyltransferases have shown major conformational change in the loop region near amino acids 190–195 as the protein shifts from the inhibited AdoHcy bound form to the fully active AdoMet bound form. This backbone and residue rearrangement of atoms may play a role in catalysis, cofactor exchange or in both.; The substrate in the active site of the enzyme shows how the enzyme meets its uniquely challenging stereo-specificity requirements. The protein uses protein-substrate contacts to stabilize an unfolded polypeptide conformation at the accepting aspartyl residue. The substrate-enzyme contacts and the enforced intermolecular substrate torsion angles insure that only L-isoaspartyl and D-aspartyl containing polypeptides can be substrates. This mechanism represents the discovery of a new method utilized by enzymes to recognize and repair age related protein damage.