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Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions.

Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R, Shakked Z - Nucleic Acids Res. (2013)

Bottom Line: The structures show that inactivation of p53 results from the incapacity of the mutated residues to form stabilizing interactions with the DNA backbone, and that reactivation is achieved through alternative interactions formed by the suppressor mutations.Contrary to our previously studied wild-type (wt) p53-DNA complexes showing non-canonical Hoogsteen A/T base pairs of the DNA helix that lead to local minor-groove narrowing and enhanced electrostatic interactions with p53, the current structures display Watson-Crick base pairs associated with direct or water-mediated hydrogen bonds with p53 at the minor groove.These findings highlight the pivotal role played by R273 residues in supporting the unique geometry of the DNA target and its sequence-specific complex with p53.

View Article: PubMed Central - PubMed

Affiliation: Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel and Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA.

ABSTRACT
A p53 hot-spot mutation found frequently in human cancer is the replacement of R273 by histidine or cysteine residues resulting in p53 loss of function as a tumor suppressor. These mutants can be reactivated by the incorporation of second-site suppressor mutations. Here, we present high-resolution crystal structures of the p53 core domains of the cancer-related proteins, the rescued proteins and their complexes with DNA. The structures show that inactivation of p53 results from the incapacity of the mutated residues to form stabilizing interactions with the DNA backbone, and that reactivation is achieved through alternative interactions formed by the suppressor mutations. Detailed structural and computational analysis demonstrates that the rescued p53 complexes are not fully restored in terms of DNA structure and its interface with p53. Contrary to our previously studied wild-type (wt) p53-DNA complexes showing non-canonical Hoogsteen A/T base pairs of the DNA helix that lead to local minor-groove narrowing and enhanced electrostatic interactions with p53, the current structures display Watson-Crick base pairs associated with direct or water-mediated hydrogen bonds with p53 at the minor groove. These findings highlight the pivotal role played by R273 residues in supporting the unique geometry of the DNA target and its sequence-specific complex with p53.

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Related in: MedlinePlus

DNA helix parameters and electrostatic potential in type II complexes. (A) Helix diameter as a function of the base sequence showing the compression of the DNA helix at the center of each half-site. A larger effect is displayed by the DNA helix of the wt complex (shown in gray) as a result of the Hoogsteen geometry of the A/T base pairs at each half-site. (B) Minor-groove width and the corresponding electrostatic potential as a function of the base sequence. The four minor-groove minima are aligned with the electrostatic potential minima. The positions of the four R248 residues are indicated by arrows.
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gkt630-F7: DNA helix parameters and electrostatic potential in type II complexes. (A) Helix diameter as a function of the base sequence showing the compression of the DNA helix at the center of each half-site. A larger effect is displayed by the DNA helix of the wt complex (shown in gray) as a result of the Hoogsteen geometry of the A/T base pairs at each half-site. (B) Minor-groove width and the corresponding electrostatic potential as a function of the base sequence. The four minor-groove minima are aligned with the electrostatic potential minima. The positions of the four R248 residues are indicated by arrows.

Mentions: The variations in the DNA helix diameter and minor-groove width of the wt complex and those of the current crystal structures are shown in Figure 7. We have previously shown that the distinct narrowing of the minor groove as a result of the Hoogsteen geometry leads to enhanced negative electrostatic potential at the four regions close to the interaction sites of the positively charged R248 residues. Such electrostatic interactions at the minor groove contribute to the stabilization of the wt p53-DNA complex, highlighting the role of DNA shape in its recognition by p53. In the current structures, however, as a result of the Watson–Crick geometry of the A/T base pairs, the corresponding minor-groove regions are shallower, and their associated electrostatic potential is less negative, resulting in a relatively smaller contribution to complex stabilization through electrostatic interactions (Figure 7B).Figure 7.


Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions.

Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R, Shakked Z - Nucleic Acids Res. (2013)

DNA helix parameters and electrostatic potential in type II complexes. (A) Helix diameter as a function of the base sequence showing the compression of the DNA helix at the center of each half-site. A larger effect is displayed by the DNA helix of the wt complex (shown in gray) as a result of the Hoogsteen geometry of the A/T base pairs at each half-site. (B) Minor-groove width and the corresponding electrostatic potential as a function of the base sequence. The four minor-groove minima are aligned with the electrostatic potential minima. The positions of the four R248 residues are indicated by arrows.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3794590&req=5

gkt630-F7: DNA helix parameters and electrostatic potential in type II complexes. (A) Helix diameter as a function of the base sequence showing the compression of the DNA helix at the center of each half-site. A larger effect is displayed by the DNA helix of the wt complex (shown in gray) as a result of the Hoogsteen geometry of the A/T base pairs at each half-site. (B) Minor-groove width and the corresponding electrostatic potential as a function of the base sequence. The four minor-groove minima are aligned with the electrostatic potential minima. The positions of the four R248 residues are indicated by arrows.
Mentions: The variations in the DNA helix diameter and minor-groove width of the wt complex and those of the current crystal structures are shown in Figure 7. We have previously shown that the distinct narrowing of the minor groove as a result of the Hoogsteen geometry leads to enhanced negative electrostatic potential at the four regions close to the interaction sites of the positively charged R248 residues. Such electrostatic interactions at the minor groove contribute to the stabilization of the wt p53-DNA complex, highlighting the role of DNA shape in its recognition by p53. In the current structures, however, as a result of the Watson–Crick geometry of the A/T base pairs, the corresponding minor-groove regions are shallower, and their associated electrostatic potential is less negative, resulting in a relatively smaller contribution to complex stabilization through electrostatic interactions (Figure 7B).Figure 7.

Bottom Line: The structures show that inactivation of p53 results from the incapacity of the mutated residues to form stabilizing interactions with the DNA backbone, and that reactivation is achieved through alternative interactions formed by the suppressor mutations.Contrary to our previously studied wild-type (wt) p53-DNA complexes showing non-canonical Hoogsteen A/T base pairs of the DNA helix that lead to local minor-groove narrowing and enhanced electrostatic interactions with p53, the current structures display Watson-Crick base pairs associated with direct or water-mediated hydrogen bonds with p53 at the minor groove.These findings highlight the pivotal role played by R273 residues in supporting the unique geometry of the DNA target and its sequence-specific complex with p53.

View Article: PubMed Central - PubMed

Affiliation: Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel and Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA.

ABSTRACT
A p53 hot-spot mutation found frequently in human cancer is the replacement of R273 by histidine or cysteine residues resulting in p53 loss of function as a tumor suppressor. These mutants can be reactivated by the incorporation of second-site suppressor mutations. Here, we present high-resolution crystal structures of the p53 core domains of the cancer-related proteins, the rescued proteins and their complexes with DNA. The structures show that inactivation of p53 results from the incapacity of the mutated residues to form stabilizing interactions with the DNA backbone, and that reactivation is achieved through alternative interactions formed by the suppressor mutations. Detailed structural and computational analysis demonstrates that the rescued p53 complexes are not fully restored in terms of DNA structure and its interface with p53. Contrary to our previously studied wild-type (wt) p53-DNA complexes showing non-canonical Hoogsteen A/T base pairs of the DNA helix that lead to local minor-groove narrowing and enhanced electrostatic interactions with p53, the current structures display Watson-Crick base pairs associated with direct or water-mediated hydrogen bonds with p53 at the minor groove. These findings highlight the pivotal role played by R273 residues in supporting the unique geometry of the DNA target and its sequence-specific complex with p53.

Show MeSH
Related in: MedlinePlus