The modular structure of alpha/beta-hydrolases: similarity of the N- and C-terminal domains to other proteins

To analyse the structural similarities of the N- and C-terminal domains, representative protein structures of each oxyanion hole type from the proteins of alpha/beta-hydrolase superfamilies 8 to 12 were selected from the Lipase Engineering Database (led.biocatnet.de/). The structures of the N- and C-terminal domains and the core domains were extracted and saved in separate .pdb files, which were then used to compare the domains by the "all against all" structure comparison tool on the Dali webserver (ekhidna2.biocenter.helsinki.fi/dali/).

In a second step, the PDB (Protein Data Bank) search tool on the Dali server was used to compare the N- and C-terminal domains against all structures in PDB25, a subset resulting from clustering the whole PDB database with an identity threshold of 25%. The Dali server has different measures to determine similarity between proteins. The Z-Score is a measure for structural similarity, where a Z-score >2 implies significant structural similarities and thus a similar fold.