Structure and operation of the DNA-translocating type I DNA restriction enzymes.
Type I DNA restriction/modification (RM) enzymes are molecular machines found in the majority of bacterial species. Their early discovery paved the way for the development of genetic engineering. They control (restrict) the influx of foreign DNA via horizontal gene transfer into the bacterium while maintaining sequence-specific methylation (modification) of host DNA. The endonuclease reaction of these enzymes on unmethylated DNA is preceded by bidirectional translocation of thousands of base pairs of DNA toward the enzyme. We present the structures of two type I RM enzymes, EcoKI and EcoR124I, derived using electron microscopy (EM), small-angle scattering (neutron and X-ray), and detailed molecular modeling. DNA binding triggers a large contraction of the open form of the enzyme to a compact form. The path followed by DNA through the complexes is revealed by using a DNA mimic anti-restriction protein. The structures reveal an evolutionary link between type I RM enzymes and type II RM enzymes.
Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.
Christopher K
CK
Kennaway
Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
James E N
JEN
Taylor
Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.
Chun Feng
CF
Song
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, PL-02-109 Warsaw, Poland
Wojciech
W
Potrzebowski
Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.
William
W
Nicholson
EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
John H
JH
White
Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
Anna
A
Swiderska
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, PL-02-109 Warsaw, Poland
Agnieszka
A
Obarska-Kosinska
Partnership for Structural Biology, Institut Laue-Langevin, Grenoble, Cedex 9, France
Philip
P
Callow
EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
Laurie P
LP
Cooper
EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
Gareth A
GA
Roberts
Partnership for Structural Biology, Institut Laue-Langevin, Grenoble, Cedex 9, France|EPSAM and ISTM, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
Jean-Baptiste
JB
Artero
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, PL-02-109 Warsaw, Poland|Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, PL-61-614 Poznan, Poland
Janusz M
JM
Bujnicki
Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.
John
J
Trinick
Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
G Geoff
GG
Kneale
EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
David T F
DT
Dryden
D004262:DNA Restriction Enzymes / Q000737:chemistry* / Q000648:ultrastructure*; D015253:Deoxyribonucleases, Type I Site-Specific / Q000737:chemistry / Q000648:ultrastructure; D008854:Microscopy, Electron; D008958:Models, Molecular; D016624:Negative Staining; D017434:Protein Structure, Tertiary
D004262:DNA Restriction Enzymes; C089629:endodeoxyribonuclease EcoKI; C048242:endodeoxyribonuclease EcoR124I; D015253:Deoxyribonucleases, Type I Site-Specific