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Crystal structure of a p53 core tetramer bound to DNA.

Malecka KA, Ho WC, Marmorstein R - Oncogene (2008)

Bottom Line: The structure reveals that two p53DBD dimers bind to B form DNA with no relative twist and that a p53 tetramer can bind to DNA without introducing significant DNA bending.The numerous dimer-dimer interactions involve several strictly conserved residues, thus suggesting a molecular basis for p53DBD-DNA binding cooperativity.Surface residue conservation of the p53DBD tetramer bound to DNA highlights possible regions of other p53 domain or p53 cofactor interactions.

View Article: PubMed Central - PubMed

Affiliation: The Wistar Institute, Philadelphia, PA 19104, USA.

ABSTRACT
The tumor suppressor p53 regulates downstream genes in response to many cellular stresses and is frequently mutated in human cancers. Here, we report the use of a crosslinking strategy to trap a tetrameric p53 DNA-binding domain (p53DBD) bound to DNA and the X-ray crystal structure of the protein/DNA complex. The structure reveals that two p53DBD dimers bind to B form DNA with no relative twist and that a p53 tetramer can bind to DNA without introducing significant DNA bending. The numerous dimer-dimer interactions involve several strictly conserved residues, thus suggesting a molecular basis for p53DBD-DNA binding cooperativity. Surface residue conservation of the p53DBD tetramer bound to DNA highlights possible regions of other p53 domain or p53 cofactor interactions.

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Structure 1 of the tetrameric p53DBD/DNA-complex and crystal packing. (a) Overall view of the tetramer in cartoon representation (DeLano, 2002). Subunits A (blue) and B (cyan) represent one dimer and subunits C (purple) and D (pink) represent the other. Zn2+ ions are shown as yellow spheres. The DNA consensus sequence is rendered in red and other bases are rendered in gray. (b) View of DNA base pairing between crystallographic DNA duplexes in structures 1 and 2 with involved bases numbered as in Figure 2a. One duplex is colored in green and the crystallographic duplex is colored in blue. Hydrogen bonds are colored in orange. (c) View of tetramer crystal packing in both structures 1 and 2. Structure 1 is colored red and structure 2 is colored gray. A tetramer is shown for both structures with a dimer from the adjacent crystallographic tetramer shown to the right. A clear gap is seen between structure 1 and its crystallographic dimer neighbor while no such gap is seen for structure 2. (d) View of the tetramer perpendicular to the DNA helical axis. (e) Close up view of the L1 loops from human (2OCJ, orange) and mouse (1HU8, red) p53DBD; human p53DBD (1TSR, yellow), human p53DBD dimer (2AC0, magenta), mouse p53DBD dimer (2GEQ, cyan) bound to DNA; Cep-1 p53 ortholog (1T4W, blue), mouse p53DBD tetramer bound to DNA structure 1 (green) and mouse p53DBD tetramer bound to DNA structure 2 (light green).
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Figure 1: Structure 1 of the tetrameric p53DBD/DNA-complex and crystal packing. (a) Overall view of the tetramer in cartoon representation (DeLano, 2002). Subunits A (blue) and B (cyan) represent one dimer and subunits C (purple) and D (pink) represent the other. Zn2+ ions are shown as yellow spheres. The DNA consensus sequence is rendered in red and other bases are rendered in gray. (b) View of DNA base pairing between crystallographic DNA duplexes in structures 1 and 2 with involved bases numbered as in Figure 2a. One duplex is colored in green and the crystallographic duplex is colored in blue. Hydrogen bonds are colored in orange. (c) View of tetramer crystal packing in both structures 1 and 2. Structure 1 is colored red and structure 2 is colored gray. A tetramer is shown for both structures with a dimer from the adjacent crystallographic tetramer shown to the right. A clear gap is seen between structure 1 and its crystallographic dimer neighbor while no such gap is seen for structure 2. (d) View of the tetramer perpendicular to the DNA helical axis. (e) Close up view of the L1 loops from human (2OCJ, orange) and mouse (1HU8, red) p53DBD; human p53DBD (1TSR, yellow), human p53DBD dimer (2AC0, magenta), mouse p53DBD dimer (2GEQ, cyan) bound to DNA; Cep-1 p53 ortholog (1T4W, blue), mouse p53DBD tetramer bound to DNA structure 1 (green) and mouse p53DBD tetramer bound to DNA structure 2 (light green).

Mentions: Two tetrameric p53DBD/DNA complex structures, referred to as structure 1 and structure 2, were determined to resolutions of 2.00 and 2.20 Å respectively (Table 1). While both protein/DNA complexes crystallized in spacegroup C2, the cell parameters and asymmetric units of these complexes differ, with structure 1 containing a p53DBD dimer bound to a DNA half site and structure 2 containing a p53DBD subunit bound to a DNA quarter site. As a result of these differences, the crystal packing contacts show significant differences between the two structures. The most significant difference lies along the direction of the DNA helical axis. The DNA in structure 1 forms end-end Hoogsteen base-pairs involving the overhanging 5′ thymine base of one DNA duplex with the Watson-Crick base-paired adenine of another duplex (Figure 1b). In contrast, the DNA duplex in structure 2 does not show electron density for the overhanging 5′ thymine base or the adjacent adenine-thymine base pair, which are presumably looped out of the DNA helix. As a result of this, two adjacent DNA duplexes of structure 2 stack end-to-end forming a pseudo continuous helix with the terminal DNA base-pairs from adjacent DNA duplexes about 3.6 Å apart (Figure 1b). The shorter ordered DNA duplex within structure 2 relative to structure 1 results in more extensive protein contacts between adjacent p53DBD tetramer/DNA complexes within the crystal lattice of structure 2 relative to structure 1 (Figure 1c). Despite these crystal packing differences between structure 1 and 2, the overall structures of the p53DBD tetramer/DNA complexes are essentially superimposable in the two crystal lattices (Figure 1c), arguing for the biological relevance of the crystallographic tetramer. Unless otherwise stated, discussion will focus on the higher resolution structure 1.


Crystal structure of a p53 core tetramer bound to DNA.

Malecka KA, Ho WC, Marmorstein R - Oncogene (2008)

Structure 1 of the tetrameric p53DBD/DNA-complex and crystal packing. (a) Overall view of the tetramer in cartoon representation (DeLano, 2002). Subunits A (blue) and B (cyan) represent one dimer and subunits C (purple) and D (pink) represent the other. Zn2+ ions are shown as yellow spheres. The DNA consensus sequence is rendered in red and other bases are rendered in gray. (b) View of DNA base pairing between crystallographic DNA duplexes in structures 1 and 2 with involved bases numbered as in Figure 2a. One duplex is colored in green and the crystallographic duplex is colored in blue. Hydrogen bonds are colored in orange. (c) View of tetramer crystal packing in both structures 1 and 2. Structure 1 is colored red and structure 2 is colored gray. A tetramer is shown for both structures with a dimer from the adjacent crystallographic tetramer shown to the right. A clear gap is seen between structure 1 and its crystallographic dimer neighbor while no such gap is seen for structure 2. (d) View of the tetramer perpendicular to the DNA helical axis. (e) Close up view of the L1 loops from human (2OCJ, orange) and mouse (1HU8, red) p53DBD; human p53DBD (1TSR, yellow), human p53DBD dimer (2AC0, magenta), mouse p53DBD dimer (2GEQ, cyan) bound to DNA; Cep-1 p53 ortholog (1T4W, blue), mouse p53DBD tetramer bound to DNA structure 1 (green) and mouse p53DBD tetramer bound to DNA structure 2 (light green).
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Figure 1: Structure 1 of the tetrameric p53DBD/DNA-complex and crystal packing. (a) Overall view of the tetramer in cartoon representation (DeLano, 2002). Subunits A (blue) and B (cyan) represent one dimer and subunits C (purple) and D (pink) represent the other. Zn2+ ions are shown as yellow spheres. The DNA consensus sequence is rendered in red and other bases are rendered in gray. (b) View of DNA base pairing between crystallographic DNA duplexes in structures 1 and 2 with involved bases numbered as in Figure 2a. One duplex is colored in green and the crystallographic duplex is colored in blue. Hydrogen bonds are colored in orange. (c) View of tetramer crystal packing in both structures 1 and 2. Structure 1 is colored red and structure 2 is colored gray. A tetramer is shown for both structures with a dimer from the adjacent crystallographic tetramer shown to the right. A clear gap is seen between structure 1 and its crystallographic dimer neighbor while no such gap is seen for structure 2. (d) View of the tetramer perpendicular to the DNA helical axis. (e) Close up view of the L1 loops from human (2OCJ, orange) and mouse (1HU8, red) p53DBD; human p53DBD (1TSR, yellow), human p53DBD dimer (2AC0, magenta), mouse p53DBD dimer (2GEQ, cyan) bound to DNA; Cep-1 p53 ortholog (1T4W, blue), mouse p53DBD tetramer bound to DNA structure 1 (green) and mouse p53DBD tetramer bound to DNA structure 2 (light green).
Mentions: Two tetrameric p53DBD/DNA complex structures, referred to as structure 1 and structure 2, were determined to resolutions of 2.00 and 2.20 Å respectively (Table 1). While both protein/DNA complexes crystallized in spacegroup C2, the cell parameters and asymmetric units of these complexes differ, with structure 1 containing a p53DBD dimer bound to a DNA half site and structure 2 containing a p53DBD subunit bound to a DNA quarter site. As a result of these differences, the crystal packing contacts show significant differences between the two structures. The most significant difference lies along the direction of the DNA helical axis. The DNA in structure 1 forms end-end Hoogsteen base-pairs involving the overhanging 5′ thymine base of one DNA duplex with the Watson-Crick base-paired adenine of another duplex (Figure 1b). In contrast, the DNA duplex in structure 2 does not show electron density for the overhanging 5′ thymine base or the adjacent adenine-thymine base pair, which are presumably looped out of the DNA helix. As a result of this, two adjacent DNA duplexes of structure 2 stack end-to-end forming a pseudo continuous helix with the terminal DNA base-pairs from adjacent DNA duplexes about 3.6 Å apart (Figure 1b). The shorter ordered DNA duplex within structure 2 relative to structure 1 results in more extensive protein contacts between adjacent p53DBD tetramer/DNA complexes within the crystal lattice of structure 2 relative to structure 1 (Figure 1c). Despite these crystal packing differences between structure 1 and 2, the overall structures of the p53DBD tetramer/DNA complexes are essentially superimposable in the two crystal lattices (Figure 1c), arguing for the biological relevance of the crystallographic tetramer. Unless otherwise stated, discussion will focus on the higher resolution structure 1.

Bottom Line: The structure reveals that two p53DBD dimers bind to B form DNA with no relative twist and that a p53 tetramer can bind to DNA without introducing significant DNA bending.The numerous dimer-dimer interactions involve several strictly conserved residues, thus suggesting a molecular basis for p53DBD-DNA binding cooperativity.Surface residue conservation of the p53DBD tetramer bound to DNA highlights possible regions of other p53 domain or p53 cofactor interactions.

View Article: PubMed Central - PubMed

Affiliation: The Wistar Institute, Philadelphia, PA 19104, USA.

ABSTRACT
The tumor suppressor p53 regulates downstream genes in response to many cellular stresses and is frequently mutated in human cancers. Here, we report the use of a crosslinking strategy to trap a tetrameric p53 DNA-binding domain (p53DBD) bound to DNA and the X-ray crystal structure of the protein/DNA complex. The structure reveals that two p53DBD dimers bind to B form DNA with no relative twist and that a p53 tetramer can bind to DNA without introducing significant DNA bending. The numerous dimer-dimer interactions involve several strictly conserved residues, thus suggesting a molecular basis for p53DBD-DNA binding cooperativity. Surface residue conservation of the p53DBD tetramer bound to DNA highlights possible regions of other p53 domain or p53 cofactor interactions.

Show MeSH
Related in: MedlinePlus