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Protein Science (2007), 16:683-694. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions

Jonathan M. Elkins, Evangelos Papagrigoriou, Georgina Berridge, Xiaowen Yang, Claire Phillips, Carina Gileadi, Pavel Savitsky, and Declan A. Doyle

Structural Genomics Consortium, Oxford University, Botnar Research Centre, Oxford, OX3 7LD, United Kingdom

(RECEIVED November 8, 2006; FINAL REVISION January 16, 2007; ACCEPTED January 23, 2007)

PDZ domains are protein–protein interaction modules that generally bind to the C termini of their target proteins. The C-terminal four amino acids of a prospective binding partner of a PDZ domain are typically the determinants of binding specificity. In an effort to determine the structures of a number of PDZ domains we have included appropriate four residue extensions on the C termini of PDZ domain truncation mutants, designed for self-binding. Multiple truncations of each PDZ domain were generated. The four residue extensions, which represent known specificity sequences of the target PDZ domains and cover both class I and II motifs, form intermolecular contacts in the expected manner for the interactions of PDZ domains with protein C termini for both classes. We present the structures of eight unique PDZ domains crystallized using this approach and focus on four which provide information on selectivity (PICK1 and the third PDZ domain of DLG2), binding site flexibility (the third PDZ domain of MPDZ), and peptide–domain interactions (MPDZ 12th PDZ domain). Analysis of our results shows a clear improvement in the chances of obtaining PDZ domain crystals by using this approach compared to similar truncations of the PDZ domains without the C-terminal four residue extensions.

Keywords: PDZ; PDZ domain; crystallization; PICK1; DLG2; DLG3; MPDZ; NHERF-2


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