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Protein Engineering, Vol. 14, No. 9, 639-646, September 2001
© 2001 Oxford University Press

Structural analysis of free and enzyme-bound amaranth {alpha}-amylase inhibitor: classification within the knottin fold superfamily and analysis of its functional flexibility

Oliviero Carugo1,2, Shanyun Lu3, Jingchu Luo3, Xiaocheng Gu3, Songping Liang4, Stefan Strobl5 and Sándor Pongor1,6

1 International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste 2 Department of General Chemistry, University of Pavia, Pavia, Italy, 3 Peking University, Beijing, China, 4 Hunan Normal University, Hunan, China and 5 Proteros Biostructures GmbH, Planegg-Martinsried, Germany

The three-dimensional structure of the amaranth {alpha}-amylase inhibitor (AAI) adopts a knottin fold of abcabc topology. Upon binding to {alpha}-amylase, it adopts a more compact conformation characterized by an increased number of intramolecular hydrogen bonds, a decreased volume and in addition a trans to cis isomerization of Pro20. A systematic analysis of the 3-D structural databanks revealed that similar proteins and domains share with AAI the characteristic presence of proline residues, many of which are in a cis backbone conformation. As these proteins fulfil a variety of functional roles and are expressed in very different organisms, we conclude that the structure of the knottin fold, including the propensity of the cis bond, are the result of convergent evolution.


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