P53-DNA Recognition: Difference between revisions
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<Structure load='P53tetra.pdb.zip' size='250' frame='true' align='left' caption='Figure 4: Crystal structure of p53 tetramerization domain, [http://www.rcsb.org/pdb/explore.do?structureId=1c26 PDB ID 1C26].' scene='Sandbox_Reserved_170/Tetra/2' /> | <Structure load='P53tetra.pdb.zip' size='250' frame='true' align='left' caption='Figure 4: Crystal structure of p53 tetramerization domain, [http://www.rcsb.org/pdb/explore.do?structureId=1c26 PDB ID 1C26].' scene='Sandbox_Reserved_170/Tetra/2' /> | ||
<Structure load='3kz8bio.pdb.zip' size='500' frame='true' align='right' caption='Figure | <Structure load='3kz8bio.pdb.zip' size='500' frame='true' align='right' caption='Figure 5: Crystal structure of p53 DBD tetramer-DNA complex, PDB ID 3KZ8.' scene='Sandbox_Reserved_170/Complex/6' /> | ||
The p53 protein consists of the N-terminal transactivation, the DNA binding or core, the tetramerization, and the C-terminal regulatory domain (Figure 3). This Proteopedia page discusses protein-DNA recognition by p53, thus focuses on the DBD of p53. The only other domain for which structural information is available is the <scene name='Sandbox_Reserved_170/Tetra/1'>tetramerization domain</scene>, which forms as a dimer of dimers with one alpha helix and one beta strand contributed by each p53 monomer. | The p53 protein consists of the N-terminal transactivation, the DNA binding or core, the tetramerization, and the C-terminal regulatory domain (Figure 3). This Proteopedia page discusses protein-DNA recognition by p53, thus focuses on the DBD of p53. The only other domain for which structural information is available is the <scene name='Sandbox_Reserved_170/Tetra/1'>tetramerization domain</scene>, which forms as a dimer of dimers with one alpha helix and one beta strand contributed by each p53 monomer. | ||
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===Major Groove Base Readout=== | ===Major Groove Base Readout=== | ||
[[Image:p53-motif.jpg|thumb|right|300px|Figure 6: p53 binding site motif with G/C base pairs most conserved. ]] | |||
Protein side chains and base pairs form direct contacts in the major groove among which the <scene name='Sandbox_Reserved_170/Arg280_contact/5'>contact between Arg280 and the guanine of the core element</scene> contributes most to binding specificity. This highly specific readout is due to the <scene name='Sandbox_Reserved_170/Arg280_contact/4'>bidentate hydrogen bond formed between Arg280 and guanine</scene>. As a result the identity of the G/C base pairs in the CWWG core elements is the most conserved position in p53 response elements (Figure 5). | Protein side chains and base pairs form direct contacts in the major groove among which the <scene name='Sandbox_Reserved_170/Arg280_contact/5'>contact between Arg280 and the guanine of the core element</scene> contributes most to binding specificity. This highly specific readout is due to the <scene name='Sandbox_Reserved_170/Arg280_contact/4'>bidentate hydrogen bond formed between Arg280 and guanine</scene>. As a result the identity of the G/C base pairs in the CWWG core elements is the most conserved position in p53 response elements (Figure 5). | ||
<scene name='Sandbox_Reserved_170/Lys_120/3'>Lys120</scene> | <scene name='Sandbox_Reserved_170/Lys_120/3'>Lys120</scene> | ||