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Literature DB >> 11473254

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

Q Huai¹, J D Colandene, M D Topal, H Ke.

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 A to grip DNA, widening that of the Endo domain 8 A to encircle and bend DNA 45 degrees 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.

Entities: Chemical

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Year: 2001 PMID： 11473254 DOI： 10.1038/90366

Source DB: PubMed Journal: Nat Struct Biol ISSN： 1072-8368

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Cited

17 in total

1. Diversity of type II restriction endonucleases that require two DNA recognition sites.

Authors: Merlind Mucke; Detlev H Kruger; Monika Reuter
Journal: Nucleic Acids Res Date: 2003-11-01 Impact factor: 16.971

2. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.

Authors: Richard J Roberts; Marlene Belfort; Timothy Bestor; Ashok S Bhagwat; Thomas A Bickle; Jurate Bitinaite; Robert M Blumenthal; Sergey Kh Degtyarev; David T F Dryden; Kevin Dybvig; Keith Firman; Elizaveta S Gromova; Richard I Gumport; Stephen E Halford; Stanley Hattman; Joseph Heitman; David P Hornby; Arvydas Janulaitis; Albert Jeltsch; Jytte Josephsen; Antal Kiss; Todd R Klaenhammer; Ichizo Kobayashi; Huimin Kong; Detlev H Krüger; Sanford Lacks; Martin G Marinus; Michiko Miyahara; Richard D Morgan; Noreen E Murray; Valakunja Nagaraja; Andrzej Piekarowicz; Alfred Pingoud; Elisabeth Raleigh; Desirazu N Rao; Norbert Reich; Vladimir E Repin; Eric U Selker; Pang-Chui Shaw; Daniel C Stein; Barry L Stoddard; Waclaw Szybalski; Thomas A Trautner; James L Van Etten; Jorge M B Vitor; Geoffrey G Wilson; Shuang-yong Xu
Journal: Nucleic Acids Res Date: 2003-04-01 Impact factor: 16.971

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

1. Diversity of type II restriction endonucleases that require two DNA recognition sites.

2. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.

3. EcoRII: a restriction enzyme evolving recombination functions?

4. Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.

5. One recognition sequence, seven restriction enzymes, five reaction mechanisms.

6. Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure.

7. Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.

8. Uncoupling metallonuclease metal ion binding sites via nudge mutagenesis.

9. Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.

10. Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje.