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The structure of SgrAI bound to DNA; recognition of an 8 base pair target

The three-dimensional X-ray crystal structure of the ‘rare cutting’ type II restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a dimer bound to one duplex of DNA. Two Ca(2+) bind in the enzyme active site, with one ion at the interface between the protein and DNA, and the...

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Autores principales: Dunten, Pete W., Little, Elizabeth J., Gregory, Mark T., Manohar, Veena M., Dalton, Michael, Hough, David, Bitinaite, Jurate, Horton, Nancy C.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2532715/
https://www.ncbi.nlm.nih.gov/pubmed/18701646
http://dx.doi.org/10.1093/nar/gkn510
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author Dunten, Pete W.
Little, Elizabeth J.
Gregory, Mark T.
Manohar, Veena M.
Dalton, Michael
Hough, David
Bitinaite, Jurate
Horton, Nancy C.
author_facet Dunten, Pete W.
Little, Elizabeth J.
Gregory, Mark T.
Manohar, Veena M.
Dalton, Michael
Hough, David
Bitinaite, Jurate
Horton, Nancy C.
author_sort Dunten, Pete W.
collection PubMed
description The three-dimensional X-ray crystal structure of the ‘rare cutting’ type II restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a dimer bound to one duplex of DNA. Two Ca(2+) bind in the enzyme active site, with one ion at the interface between the protein and DNA, and the second bound distal from the DNA. These sites are differentially occupied by Mn(2+), with strong binding at the protein–DNA interface, but only partial occupancy of the distal site. The DNA remains uncleaved in the structures from crystals grown in the presence of either divalent cation. The structure of the dimer of SgrAI is similar to those of Cfr10I, Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed. DNA contacts to the central CCGG base pairs of the SgrAI canonical target sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC). Specificity at the degenerate YR base pairs of the SgrAI sequence may occur via indirect readout using DNA distortion. Recognition of the outer GC base pairs occurs through a single contact to the G from an arginine side chain located in a region unique to SgrAI.
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spelling pubmed-25327152009-01-22 The structure of SgrAI bound to DNA; recognition of an 8 base pair target Dunten, Pete W. Little, Elizabeth J. Gregory, Mark T. Manohar, Veena M. Dalton, Michael Hough, David Bitinaite, Jurate Horton, Nancy C. Nucleic Acids Res Structural Biology The three-dimensional X-ray crystal structure of the ‘rare cutting’ type II restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a dimer bound to one duplex of DNA. Two Ca(2+) bind in the enzyme active site, with one ion at the interface between the protein and DNA, and the second bound distal from the DNA. These sites are differentially occupied by Mn(2+), with strong binding at the protein–DNA interface, but only partial occupancy of the distal site. The DNA remains uncleaved in the structures from crystals grown in the presence of either divalent cation. The structure of the dimer of SgrAI is similar to those of Cfr10I, Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed. DNA contacts to the central CCGG base pairs of the SgrAI canonical target sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC). Specificity at the degenerate YR base pairs of the SgrAI sequence may occur via indirect readout using DNA distortion. Recognition of the outer GC base pairs occurs through a single contact to the G from an arginine side chain located in a region unique to SgrAI. Oxford University Press 2008-09 2008-08-13 /pmc/articles/PMC2532715/ /pubmed/18701646 http://dx.doi.org/10.1093/nar/gkn510 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Structural Biology
Dunten, Pete W.
Little, Elizabeth J.
Gregory, Mark T.
Manohar, Veena M.
Dalton, Michael
Hough, David
Bitinaite, Jurate
Horton, Nancy C.
The structure of SgrAI bound to DNA; recognition of an 8 base pair target
title The structure of SgrAI bound to DNA; recognition of an 8 base pair target
title_full The structure of SgrAI bound to DNA; recognition of an 8 base pair target
title_fullStr The structure of SgrAI bound to DNA; recognition of an 8 base pair target
title_full_unstemmed The structure of SgrAI bound to DNA; recognition of an 8 base pair target
title_short The structure of SgrAI bound to DNA; recognition of an 8 base pair target
title_sort structure of sgrai bound to dna; recognition of an 8 base pair target
topic Structural Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2532715/
https://www.ncbi.nlm.nih.gov/pubmed/18701646
http://dx.doi.org/10.1093/nar/gkn510
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