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Ni(ll) coordination to mixed sites modulates DNA binding of HpNikR via a long-range effect

Helicobacder pylori NikR (HpNikR) is a nickel-dependent transcription factor that regulates multiple genes in the H. pylori pathogen. There are conflicting data regarding the locations of the Ni(ll) sites and the role of Ni(ll) coordination in DNA recognition. Herein, we report crystal structures of... Full description

Journal Title: Proceedings of the National Academy of Sciences of the United States of America 10 April 2012, Vol.109(15), pp.5633-5638
Main Author: West, Abby L.
Other Authors: Evans, Sarah E. , González, Javier M. , Carter, Lester G. , Tsuruta, Hiro , Pozharski, Edwin , Michel, Sarah L. J.
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: ISSN: 00278424
Link: https://www.jstor.org/stable/41588217
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recordid: jstor_archive_2341588217
title: Ni(ll) coordination to mixed sites modulates DNA binding of HpNikR via a long-range effect
format: Article
creator:
  • West, Abby L.
  • Evans, Sarah E.
  • González, Javier M.
  • Carter, Lester G.
  • Tsuruta, Hiro
  • Pozharski, Edwin
  • Michel, Sarah L. J.
subjects:
  • Physical sciences -- Chemistry -- Chemical compounds
  • Biological sciences -- Biology -- Microbiology
  • Physical sciences -- Physics -- Condensed matter physics
  • Physical sciences -- Chemistry -- Chemical compounds
  • Mathematics -- Pure mathematics -- Geometry
  • Physical sciences -- Physics -- Condensed matter physics
  • Mathematics -- Pure mathematics -- Geometry
  • Biological sciences -- Biology -- Genetics
  • Biological sciences -- Biology -- Genetics
  • Physical sciences -- Chemistry -- Chemical compounds
ispartof: Proceedings of the National Academy of Sciences of the United States of America, 10 April 2012, Vol.109(15), pp.5633-5638
description: Helicobacder pylori NikR (HpNikR) is a nickel-dependent transcription factor that regulates multiple genes in the H. pylori pathogen. There are conflicting data regarding the locations of the Ni(ll) sites and the role of Ni(ll) coordination in DNA recognition. Herein, we report crystal structures of (i) the metal-binding domain (MBD) of HpNikR (3.08 Å) and (ii) a mutant H74A (2.04 Å), designed to disrupt native Ni(ll) coordination. In the MBD structure, four nickel ions are coordinated to two different types of nickel sites (4-coordinate, square planar, and 5/6-coordinate, square pyramidal/octahedral). In the H74A structure, all four nickel ions are coordinated to 4-coordinate square-planar sites. DNA-binding studies reveal tighter binding for target DNA sequences for holo-HpNikR compared with the affinities of Ni(ll) reconstituted apo-HpNikR and H74A for these same DNA targets, supporting a role for Ni(ll) coordination to 5/6 sites in DNA recognition. Small-angle X-ray scattering studies of holo-HpNikR and H74A reveal a high degree of conformational flexibility centered at the DNA-binding domains of H74A, which is consistent with disorder observed in the crystal structure of the protein. A model of DNA recognition by HpNikR is proposed in which Ni(ll) coordination to specific sites in the MBD have a long-range effect on the flexibility of the DNA-binding domains and, consequently, the DNA recognition properties.
language: eng
source:
identifier: ISSN: 00278424
fulltext: fulltext
issn:
  • 0027-8424
  • 00278424
url: Link


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titleNi(ll) coordination to mixed sites modulates DNA binding of HpNikR via a long-range effect
creatorWest, Abby L. ; Evans, Sarah E. ; González, Javier M. ; Carter, Lester G. ; Tsuruta, Hiro ; Pozharski, Edwin ; Michel, Sarah L. J.
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subjectPhysical sciences -- Chemistry -- Chemical compounds ; Biological sciences -- Biology -- Microbiology ; Physical sciences -- Physics -- Condensed matter physics ; Physical sciences -- Chemistry -- Chemical compounds ; Mathematics -- Pure mathematics -- Geometry ; Physical sciences -- Physics -- Condensed matter physics ; Mathematics -- Pure mathematics -- Geometry ; Biological sciences -- Biology -- Genetics ; Biological sciences -- Biology -- Genetics ; Physical sciences -- Chemistry -- Chemical compounds
descriptionHelicobacder pylori NikR (HpNikR) is a nickel-dependent transcription factor that regulates multiple genes in the H. pylori pathogen. There are conflicting data regarding the locations of the Ni(ll) sites and the role of Ni(ll) coordination in DNA recognition. Herein, we report crystal structures of (i) the metal-binding domain (MBD) of HpNikR (3.08 Å) and (ii) a mutant H74A (2.04 Å), designed to disrupt native Ni(ll) coordination. In the MBD structure, four nickel ions are coordinated to two different types of nickel sites (4-coordinate, square planar, and 5/6-coordinate, square pyramidal/octahedral). In the H74A structure, all four nickel ions are coordinated to 4-coordinate square-planar sites. DNA-binding studies reveal tighter binding for target DNA sequences for holo-HpNikR compared with the affinities of Ni(ll) reconstituted apo-HpNikR and H74A for these same DNA targets, supporting a role for Ni(ll) coordination to 5/6 sites in DNA recognition. Small-angle X-ray scattering studies of holo-HpNikR and H74A reveal a high degree of conformational flexibility centered at the DNA-binding domains of H74A, which is consistent with disorder observed in the crystal structure of the protein. A model of DNA recognition by HpNikR is proposed in which Ni(ll) coordination to specific sites in the MBD have a long-range effect on the flexibility of the DNA-binding domains and, consequently, the DNA recognition properties.
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titleNi(ll) coordination to mixed sites modulates DNA binding of HpNikR via a long-range effect
descriptionHelicobacder pylori NikR (HpNikR) is a nickel-dependent transcription factor that regulates multiple genes in the H. pylori pathogen. There are conflicting data regarding the locations of the Ni(ll) sites and the role of Ni(ll) coordination in DNA recognition. Herein, we report crystal structures of (i) the metal-binding domain (MBD) of HpNikR (3.08 Å) and (ii) a mutant H74A (2.04 Å), designed to disrupt native Ni(ll) coordination. In the MBD structure, four nickel ions are coordinated to two different types of nickel sites (4-coordinate, square planar, and 5/6-coordinate, square pyramidal/octahedral). In the H74A structure, all four nickel ions are coordinated to 4-coordinate square-planar sites. DNA-binding studies reveal tighter binding for target DNA sequences for holo-HpNikR compared with the affinities of Ni(ll) reconstituted apo-HpNikR and H74A for these same DNA targets, supporting a role for Ni(ll) coordination to 5/6 sites in DNA recognition. Small-angle X-ray scattering studies of holo-HpNikR and H74A reveal a high degree of conformational flexibility centered at the DNA-binding domains of H74A, which is consistent with disorder observed in the crystal structure of the protein. A model of DNA recognition by HpNikR is proposed in which Ni(ll) coordination to specific sites in the MBD have a long-range effect on the flexibility of the DNA-binding domains and, consequently, the DNA recognition properties.
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abstractHelicobacder pylori NikR (HpNikR) is a nickel-dependent transcription factor that regulates multiple genes in the H. pylori pathogen. There are conflicting data regarding the locations of the Ni(ll) sites and the role of Ni(ll) coordination in DNA recognition. Herein, we report crystal structures of (i) the metal-binding domain (MBD) of HpNikR (3.08 Å) and (ii) a mutant H74A (2.04 Å), designed to disrupt native Ni(ll) coordination. In the MBD structure, four nickel ions are coordinated to two different types of nickel sites (4-coordinate, square planar, and 5/6-coordinate, square pyramidal/octahedral). In the H74A structure, all four nickel ions are coordinated to 4-coordinate square-planar sites. DNA-binding studies reveal tighter binding for target DNA sequences for holo-HpNikR compared with the affinities of Ni(ll) reconstituted apo-HpNikR and H74A for these same DNA targets, supporting a role for Ni(ll) coordination to 5/6 sites in DNA recognition. Small-angle X-ray scattering studies of holo-HpNikR and H74A reveal a high degree of conformational flexibility centered at the DNA-binding domains of H74A, which is consistent with disorder observed in the crystal structure of the protein. A model of DNA recognition by HpNikR is proposed in which Ni(ll) coordination to specific sites in the MBD have a long-range effect on the flexibility of the DNA-binding domains and, consequently, the DNA recognition properties.
pubNational Academy of Sciences
eissn10916490
date2012-04-10