Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis

• Published in: Proteins, structure, function, and bioinformatics Vol. 63; no. 4; pp. 1059 - 1068
• Main Authors: Skowronek, Krzysztof J., Kosinski, Jan, Bujnicki, Janusz M.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01-06-2006
• Subjects: Amino Acid Sequence; Binding Sites; Conserved Sequence; Deoxyribonucleases, Type II Site-Specific - chemistry; Deoxyribonucleases, Type II Site-Specific - genetics; Deoxyribonucleases, Type II Site-Specific - metabolism; Dimerization; DNA - chemistry; DNA - genetics; DNA - metabolism; GeneSilico; Hydrogen Bonding; model evaluation; Models, Molecular; Molecular Sequence Data; Mutagenesis, Site-Directed; Nucleic Acid Conformation; ORFan; Protein Binding; Protein Folding; Protein Structure, Quaternary; Protein Structure, Tertiary; remote homology; Reproducibility of Results; Sequence Alignment; Structural Homology, Protein; threading
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.20920

Type II restriction enzymes are commercially important deoxyribonucleases and very attractive targets for protein engineering of new specificities. At the same time they are a very challenging test bed for protein structure prediction methods. Typically, enzymes that recognize different sequences show little or no amino acid sequence similarity to each other and to other proteins. Based on crystallographic analyses that revealed the same PD‐(D/E)XK fold for more than a dozen case studies, they were nevertheless considered to be related until the combination of bioinformatics and mutational analyses has demonstrated that some of these proteins belong to other, unrelated folds PLD, HNH, and GIY‐YIG. As a part of a large‐scale project aiming at identification of a three‐dimensional fold for all type II REases with known sequences (currently ∼ 1000 proteins), we carried out preliminary structure prediction and selected candidates for experimental validation. Here, we present the analysis of HpaI REase, an ORFan with no detectable homologs, for which we detected a structural template by protein fold recognition, constructed a model using the FRankenstein monster approach and identified a number of residues important for the DNA binding and catalysis. These predictions were confirmed by site‐directed mutagenesis and in vitro analysis of the mutant proteins. The experimentally validated model of HpaI will serve as a low‐resolution structural platform for evolutionary considerations in the subgroup of blunt‐cutting REases with different specificities. The research protocol developed in the course of this work represents a streamlined version of the previously used techniques and can be used in a high‐throughput fashion to build and validate models for other enzymes, especially ORFans that exhibit no sequence similarity to any other protein in the database. Proteins 2006. © 2006 Wiley‐Liss, Inc.