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Protein Engineering, Vol. 15, No. 12, 1005-1014, December 2002
© 2002 Oxford University Press

Structural basis of ICF-causing mutations in the methyltransferase domain of DNMT3B

Ilkka Lappalainen1,2 and Mauno Vihinen1,3,4

1 Institute of Medical Technology, FIN-33014 University of Tampere, 2 Department of Biosciences, Division of Biochemistry, P.O. Box 56, FIN-00014 University of Helsinki and 3 Research Unit, Tampere University Hospital, FIN-30520 Tampere, Finland

Mutations in the gene encoding for a de novo methyltransferase, DNMT3B, lead to an autosomal recessive Immunodeficiency, Centromeric instability and Facial anomalies (ICF) syndrome. To analyse the protein structure and consequences of ICF-causing mutations, we modelled the structure of the DNMT3B methyltransferase domain based on Haemophilus haemolyticus protein in complex with the cofactor AdoMet and the target DNA sequence. The structural model has a two-subdomain fold where the DNA-binding region is situated between the subdomains on a surface cleft having positive electrostatic potential. The smaller subdomains of the methyltransferases differ in length and sequences and therefore only the target recognition domain loop was modelled to show the location of an ICF-causing mutation. Based on the model, the DNMT3B recognizes the GC sequence and flips the cytosine from the double-stranded DNA to the catalytic pocket. The amino acids in the cofactor and target cytosine binding sites and also the electrostatic properties of the binding pockets are conserved. In addition, a registry of all known ICF-causing mutations, DNMT3Bbase, was constructed. The structural principles of the pathogenic mutations based on the modelled structure and the analysis of {chi} angle rotation changes of mutated side chains are discussed.


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