title: Key Players in I-DmoI Endonuclease Catalysis Revealed from Structure and Dynamics.
abstract: Homing endonucleases, such as I-DmoI, specifically recognize and cleave long DNA target sequences (∼20 bp) and are potentially powerful tools for genome manipulation. However, inefficient and off-target DNA cleavage seriously limits specific editing in complex genomes. One approach to overcome these limitations is to unambiguously identify the key structural players involved in catalysis. Here, we report the E117A I-DmoI mutant crystal structure at 2.2 Å resolution that, together with the wt and Q42A/K120M constructs, is combined with computational approaches to shed light on protein cleavage activity. The cleavage mechanism was related both to key structural effects, such as the position of water molecules and ions participating in the cleavage reaction, and to dynamical effects related to protein behavior. In particular, we found that the protein perturbation pattern significantly changes between cleaved and noncleaved DNA strands when the ions and water molecules are correctly positioned for the nucleophilic attack that initiates the cleavage reaction, in line with experimental enzymatic activity. The proposed approach paves the way for an effective, general, and reliable procedure to analyze the enzymatic activity of endonucleases from a very limited data set, i.e., structure and dynamics.
authors.affiliation: Structural Biology and Biocomputing Programme, Macromolecular Crystallography Group, Spanish National Cancer Research Centre (CNIO) , c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Molina
authors.affiliation: CINECA, SuperComputing Applications and Innovations , via dei Tizii 6, 00185 Rome, Italy.
authors.forename: Neva
authors.initials: N
authors.lastname: Besker
authors.affiliation: Structural Biology and Biocomputing Programme, Macromolecular Crystallography Group, Spanish National Cancer Research Centre (CNIO) , c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain.
authors.forename: Maria Jose
authors.initials: MJ
authors.lastname: Marcaida
authors.affiliation: Structural Biology and Biocomputing Programme, Macromolecular Crystallography Group, Spanish National Cancer Research Centre (CNIO) , c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain.|Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Blegdamsvej 3B, 2200 Copenhagen, Denmark.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Montoya
authors.affiliation: Structural Biology and Biocomputing Programme, Macromolecular Crystallography Group, Spanish National Cancer Research Centre (CNIO) , c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Prieto
authors.affiliation: Department of Chemistry, University of Rome "La Sapienza" , p.le A. Moro, 5, 00185 Rome, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: D'Abramo
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004247:DNA / Q000378:metabolism; D015253:Deoxyribonucleases, Type I Site-Specific / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D019620:Desulfurococcaceae / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D017354:Point Mutation; D011487:Protein Conformation; D016415:Sequence Alignment
chemical_list: D004247:DNA; C081755:endodeoxyribonuclease I-Dmo I; D015253:Deoxyribonucleases, Type I Site-Specific