Structure of NaeI–DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement

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Abstract

NaeI, a novel DNA endonuclease, shows topoisomerase and recombinase activities when a Lys residue is substituted for Leu 43. The NaeI–DNA structure demonstrates that each of the two domains of NaeI recognizes one molecule of DNA duplex. DNA recognition induces dramatic rearrangements: narrowing the binding site of the Topo domain 16 Å to grip DNA, widening that of the Endo domain 8 Å to encircle and bend DNA 45° for cleavage, and completely rebuilding the homodimer interface. The NaeI–DNA structure presents the first example of novel recognition of two copies of one DNA sequence by two different amino acid sequences and two different structural motifs in one polypeptide.

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Figure 1: Dimeric structure of NaeI–DNA complex.
Figure 2: DNA binding.
Figure 3: Stereo view of conformational change of NaeI upon DNA binding.

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Protein Data Bank

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Acknowledgements

We thank R. Sweet for help with data collection at beamline X12C in the National Synchrotron Light Source. This research is partially supported by the NIH.

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Correspondence to Michael D. Topal or Hengming Ke.

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Huai, Q., Colandene, J., Topal, M. et al. Structure of NaeI–DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement. Nat Struct Mol Biol 8, 665–669 (2001) doi:10.1038/90366

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