Biologia, Bratislava, 57/Suppl. 11: 43-57, 2002.

ISSN 0006-3088 (Biologia).

 

Full Paper

Independent folding of the A and B domains in the aa--amylase family.

 

Gerard Pujadas* & Jaume Palau

Unitat de Biotecnologia Computacional, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Plaça de la Imperial Tàrraco, 1. Tarragona 43005, Catalonia (Spain); tel.: ++ 34 977 55 95 65, fax: ++ 34 977 55 95 97, e-mail: pujadas@quimica.urv.es

* corresponding author

Received: October 29, 2001 / Accepted: February 12, 2002

 

AbstractBratislava, 57/Suppl. 10: xxx-xxx, 2002; ISSN 0006-3088 (Biologia). ISSN 1335-6399 (Biologia. Section Cellular and Molecular Biology).

 

 

Although the activities of the a-a-amylase family of enzymes are different, they have a common ancestor. Their polypeptide chain always has a multi-domain arrangement (though the number of domains usually depends on the enzyme activity). The domains that we call A and B are always found in these structures. The A domain, which is the catalytic domain, is always a TIM-barrel fold. The B domain varies in sequence length and fold, and lies between the third b-strand and the third a-helix of the A domain. Its function has not yet been fully established. To determine whether the variability of the B domain affects the folding of the A domain, we studied the geometrical characteristics of the eight-stranded b-sheet at the core of the A domain. Our results show that the geometry of the TIM barrel does not depend on the length or fold of the B domain and supports the idea of an independent folding pathway for the A and B domains in a-a-amylase enzymes. Unwanted mutations that produce a different barrel geometry may be recognised by molecular chaperones and discarded as functional molecules. Our results show that family 77 enzymes have the same barrel geometry as family 13 enzymes. This supports the hypothesis that they have a common origin.

 

Key words: b/a a/b barrel, TIM barrel, a-a-amylase family, family 13 glycoside hydrolases, family 77 glycoside hydrolases, clan GH-H, chaperones.