P53 DNA-binding domain

The thermal average, < T>, of the number of hydrogen bond partnerships involving water molecules hydrating the p53 DNA-binding domain was obtained from... 

Fig. 5.3 Dehydrons for p53 DNA-binding domain. The backbone is indicated by blue virtual bonds joining a-carbons and dehydrons are shown as green segments joining the a-carbons of residues paired by backbone hydrogen bonds. Reprinted with permission from [19] copyright 2007 American Chemical Society...

A Study Case Dielectric Quenching in the p53 DNA-Binding Domain... 

Demma M, Maxwell E, Ramos R et al (2010) SCH529074, a small-molecule activator of mutant p53, which binds p53 DNA binding domain (DBD), restores growth-suppressive function to mutant p53 and interrupts HDM2-mediated ubiquitination of wild type p53. J Biol Chem 285 10198-10212... 

The polypeptide chain of p53 is divided in three domains, each with its own function (Figure 9.16). Like many other transcription factors, p53 has an N-terminal activation domain followed by a DNA-binding domain, while the C-terminal 100 residues form an oligomerization domain involved in the formation of the p53 tetramers. Mutants lacking the C-terminal domain do not form tetramers, but the monomeric mutant molecules retain their sequence-specific DNA-binding properties in vitro. 

Figure 9.18 Schematic digram of the structure of the DNA-binding domain of p53. (a) The DNA binding domain of p53 folds into an antiparallel p barrel with long loop regions—...

Figure 9.19 Nucleotide sequence of the 21-base pair DNA fragment cocrystalUzed with the DNA-binding domain of p53. The p53 binds in a sequence-specific manner to the shaded region.

POU regions bind to DNA by two tandemly oriented helix-turn-helix motifs Much remains to be learnt about the function of homeodomains in vivo Understanding tumorigenic mutations The monomeric p53 polypeptide chain is divided in three domains The oligomerization domain forms tetramers The DNA-binding domain of p53 is an antiparallel P barrel... 

Fig. 14.8. DNA binding domain of the tnmor suppressor protein p53 in complex with DNA. Crystal structure of the core domain of p53 (amino acids 102-292) in complex with a double-stranded DNA that contains a specific binding site for p53 (Cho et al., 1994). The amino acid positions are highhghted at which frequent oncogenic mutations are observed (see Fig. 14.9). MOLSKRIPT representation according to Krauhs, (1991).

Fig. 14.9. Mutation spectrum of the p53 protein in tumors. The linear strnctnre is shown of p53 and the frequency of mutations found in tumors. The black bars indicate the approximate position and the relative frequency of the p53 mutations. The frequency of mutations in the region of the DNA binding domain is of note. The sites of the most frequent mutations coincide with positions of the p53 protein that are directly involved in interactions with the DNA sequence (see Fig. 14.8). According to Cho et al., (1994), with permission.

The other class includes mutations that are assumed to change the overall structure of the DNA binding domain of p53 so that a specific interaction is no longer possible with the DNA. 

This assay can also be used to determine intra- and inter-array variabilities (see Note 10). p53 is a tumor suppressor protein and, as part of its function as a transcription factor, it has a specific DNA-binding domain (21,22). The DNA-binding assay therefore comprises binding a Cy3-labeled duplex DNA containing a p53 recognition site to the active immobilized p53 proteins, and provides a measurement of activity of the proteins immobilized in each spot. 

Fig. 5.7 Backbone/dehydron representation of the dimer interface for the DNA-binding domain of p53 (PDB.2GEQ). The side chains of the Argl78 of each monomer involved in a resonance pair are shown. Reprinted with permission from [19] copyright 2007 American Chemical...

Most mutations of p53 genes are somatic missense mutations involving amino acid substitutions in the DNA binding domain. The mutant forms of p53 are misfolded proteins with abnormal conformations and the inability to bind to DNA, or they are less stable. Individuals with the rare disorder Li-Fraumeni syndrome, (an autosomal dominant trait) have one mutated p5 > gene and one normal p53 gene. These individuals have increased susceptibility to many cancers, such as leukemia, breast carcinomas, soft-tissue sarcomas, brain tumors, and osteosarcomas. 

The major domains of p53 characterized as transcriptional activation (TA), proline-rich domain (PRD), DNA-binding domain (DBD), nuclear localization signal (NLS), and carboxy-terminal domain (CTD). 

The p53 protein is a tetrameric protein that binds to DNA elements with the consensus sequence 5 -RRRC(A/T)(T/A)GYYY-3 (R = purine, Y = pyrimidine). The structure of the complex of the central DNA-binding domain of p53 with an oligonucleotide that carries one half-site of the p53 recognition sequence is shown in Fig. 14.10. 

The large number of known sequences of the p53 gene from tumor patients was particularly valuable for interpretation of the crystal structure, since a spectrum could be assembled for p53 mutation in association with tumor formation. The mutation spectrum shown in Fig. 14.11 shows hotspots , positions at which p53 mutations are seen particularly frequently in tumor patients. These hotspots cluster in the core domain of p53 responsible for sequence-specific DNA binding. Remarkably, few oncogenic mutations are found outside of the DNA-binding domain. 

Comparison of the mutation spectrum with the structure of the p53-DNA complex indicates that the positions of frequent mutations coincide with the conserved structural elements of the DNA-binding domains. It is particularly noticeable that the most frequently mutated position in tumors, namely Arg248, is also the position at which the p53 protein forms a specific contact to recognition sequences. 

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