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Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex
Agnieszka Obarska1, Alex Blundell, Marcin Feder
1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.
Nucleic Acids Research
|April 15, 2006
Summary
A new structural model of the Type I restriction-modification enzyme M.EcoR124I DNA methyltransferase (MTase) reveals key DNA-binding residues. This model aids in understanding protein-DNA interactions in these molecular motors.
Area of Science:
- Molecular Biology
- Structural Biology
- Biochemistry
Background:
- Type I restriction-modification (R-M) enzymes are multisubunit molecular motors with uncharacterized DNA-binding subunits (HsdS).
- Recent crystal structures of HsdS subunits from MjaXIP and MgeORF438 provide a template for structural analysis.
Purpose of the Study:
- To present a structural model of the Type IC M.EcoR124I DNA methyltransferase (MTase).
- To identify functionally important residues involved in DNA-binding.
- To analyze the location of mutations and surface-modifiable lysines within the HsdS subunit.
Main Methods:
- Docking of individual subunit models generated by fold-recognition and comparative modeling.
- Optimization of inter-subunit contacts using energy minimization.
- Mapping of known and newly generated mutations within the hsdS gene.
Main Results:
- A structural model of the M.EcoR124I MTase complex, including HsdS, HsdM subunits, AdoMet, and DNA, was generated.
- Several functionally important residues involved in DNA-binding were identified.
- The locations of misincorporation mutagenesis-induced mutations and previously identified DNA-binding mutants were mapped.
Conclusions:
- The structural model provides a framework for studying protein-protein and protein-DNA interactions in Type I R-M systems.
- Understanding these interactions is crucial for characterizing the function of these molecular motors.