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Molecular Biology and Evolution 18:38-54 (2001)
© 2001 Society for Molecular Biology and Evolution

ARTICLE

Evolution of {alpha}-Amylases: Architectural Features and Key Residues in the Stabilization of the (ß/{alpha})8 Scaffold

Gerard Pujadas, and Jaume Palau

Unitat de Biotecnologia Computacional, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Catalonia, Spain

We provide a comprehensive analysis of the current enzymes with {alpha}-amylase activity (AAMYs) that belong to family 13 glycoside hydrolase (GH-13; 144 Archaea, Bacteria, and Eukaryota sequences from 87 different species). This study aims to further knowledge of the evolutionary molecular relationships among the sequences of their A and B domains with special emphasis on the correlation between what is observed in the structures and protein evolution. Multialignments for the A domain distinguish two clusters for sequences from Archaea organisms, eight for sequences from Bacteria organisms, and three for sequences from Eukaryota organisms. The clusters for Bacteria do not follow any strict taxonomic pathway; in fact, they are rather scattered. When we compared the A domains of sequences belonging to different kingdoms, we found that various pairs of clusters were significantly similar. Using either sequence similarity with crystallized structures or secondary-structure prediction methods, we identified in all AAMYs the eight putative ß-strands that constitute the ß-sheet in the TIM barrel of the A domain and studied the packing in its interior. We also discovered a "hidden homology" in the TIM barrel, an invariant Gly located upstream in the sequence before the conserved Asp in ß-strand 3. This Gly precedes an {alpha}-helix and is actively involved in capping its N-terminal end with a capping box. In all cases, a Schellman motif caps the C-terminal end of this helix.


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