Lipase engineering database - Understanding and exploiting sequence-structure-function relationships

The Lipase Engineering Database is a WWW-accessible resource on sequence-st ructure-function relationships of microbial lipases. Sequences of 92 microb ial lipases and homologous serine hydrolases were assigned to 32 homologous families and 15 superfamilies. Multisequence alignments of all homologous families and superfamilies are provided. Functionally relevant amino acids are annotated. The catalytic serine is part of the conserved nucleophilic e lbow and was identified in all sequences by its conserved signature GxSxG. The complete catalytic machinery (catalytic triad and two oxyanion hole res idues) could be annotated in 91% of LED sequence entries. Published mutants and their properties are provided. The X-ray structures of 22 lipases were superposed and consistently annotated. Sequence and structure data were ap plied to study the role of the first oxyanion hole residues. Although the b ackbone amides contribute to the oxyanion hole rather than side chains, the residues are well conserved. Two sequence signatures including the first o xyanion hole residue were identified: GX and GGGX. In the GX type, the posi tion of the first oxyanion hole residue X is stabilized by one or several a nchor residues. If X is hydrophilic, it is hydrogen bonded to hydrophilic a nchor residues, while hydrophobic oxyanion hole residues bind to hydrophobi c pockets. The GGGX type includes short chain length specific lipases and c arboxylesterases. The first oxyanion hole residue G is stabilized by intera ction of the dipeptide GX with the side chain of the second oxyanion hole r esidues, which is a conserved alanine as C-terminal neighbour of the cataly tic serine. Thus, short chain specific Lipases and carboxylesterase can be identified by combining the signatures GGGX and GxSAG. Consistently annotat ed aligned sequences and superimposed structures of microbial lipases help to understand the functional role of individual amino acids and thus the LE D is a useful tool for protein engineering. The Lipase Engineering Database is available at http: //www.led.uni-stuttgart.de/. (C) 2000 Elsevier Scien ce B.V. All rights reserved.