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Protein Engineering, Vol. 14, No. 10, 717-721, October 2001
© 2001 Oxford University Press

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Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY–YIG superfamily member, using NMR restraints and Monte Carlo dynamics

Janusz M. Bujnicki1,2, Piotr Rotkiewicz3, Andrzej Kolinski3 and Leszek Rychlewski1,4

1 Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, 3 Laboratory of Theory of Biopolymers, Department of Chemistry, Warsaw University, ul. Pasteura 1, 02-093 Warsaw and 4 BioInfoBank Institute, ul. Limanowskiego 24A,60-744 Poznan, Poland

Using a recent version of the SICHO algorithm for in silico protein folding, we made a blind prediction of the tertiary structure of the N-terminal, independently folded, catalytic domain (CD) of the I-TevI homing endonuclease, a representative of the GIY–YIG superfamily of homing endonucleases. The secondary structure of the I-TevI CD has been determined using NMR spectroscopy, but computational sequence analysis failed to detect any protein of known tertiary structure related to the GIY–YIG nucleases (Kowalski et al., Nucleic Acids Res., 1999, 27, 2115–2125). To provide further insight into the structure–function relationships of all GIY–YIG superfamily members, including the recently described subfamily of type II restriction enzymes (Bujnicki et al., Trends Biochem. Sci., 2000, 26, 9–11), we incorporated the experimentally determined and predicted secondary and tertiary restraints in a reduced (side chain only) protein model, which was minimized by Monte Carlo dynamics and simulated annealing. The subsequently elaborated full atomic model of the I-TevI CD allows the available experimental data to be put into a structural context and suggests that the GIY–YIG domain may dimerize in order to bring together the conserved residues of the active site.


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