The C-terminal domain of p53 catalyzes DNA-renaturation and strand exchange toward annealing between intact ssDNAs and toward eliminating damaged ssDNA from duplex formation through preferential recognition of damaged DNA by a duocarmycin

The C-terminal domain of p53 may bind single-stranded (ss) DNA ends and catalyze renaturation of ss complementary DNA molecules, suggesting a possible direct role for p53 in DNA repair (Proc. Natl. Acad. Sci. USA, 92, 9455-9459, 1995). We found that DU-86, a duocarmycin derivative which alkylates DNA, bound ssDNA and enhanced the DNA binding activity of the p53 C-terminus. DU-86 weakened p53-mediated catalysis of complementary ssDNA renaturation. p53 C-terminus catalyzed DNA strand transfer toward annealing between intact ssDNAs and toward eliminating DU-86-damaged ssDNA from duplex formation. These results suggest that p53, via the C-terminal domain, may play a direct role in DNA repair by preferential recognization and elimination of damaged DNA.     

High affinity insertion/deletion lesion binding by p53. Evidence for a role of the p53 central domain

In addition to binding DNA in a sequence-specific manner, p53 can interact with nucleic acids in a sequence-independent manner. p53 can bind short single-stranded DNA and double-stranded DNA containing nucleotide loops; these diverse associations may be critical for p53 signal transduction. In this study, we analyzed p53 binding to DNA fragments containing insertion/deletion mismatches (IDLs). p53 required an intact central domain and dimerization domain for high affinity complex formation with IDLs. In fact, the C terminus of p53 (amino acids 293-393) was functionally replaceable with a foreign dimerization domain in IDL binding assays. From saturation binding studies we determined that the KD of p53 binding to IDLs was 45 pM as compared with a KD of 31 pM for p53 binding to DNA fragments containing a consensus binding site. Consistent with these dissociation constants, p53-IDL complexes were dissociated with relatively low concentrations of competitor consensus site-containing DNA. Although p53 has a higher affinity for DNA with a consensus site as compared with IDLs, the relative number and availability of each form of DNA in a cell immediately after DNA damage may promote p53 interaction with DNA lesions. Understanding how the sequence-specific and nonspecific DNA binding activities of p53 are integrated will contribute to our knowledge of how signaling cascades are initiated after DNA damage.     

Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations

Mutations in the p53 tumor suppressor are the most frequently observed genetic alterations in human cancer. The majority of the mutations occur in the core domain which contains the sequence-specific DNA binding activity of the p53 protein (residues 102-292), and they result in loss of DNA binding. The crystal structure of a complex containing the core domain of human p53 and a DNA binding site has been determined at 2.2 angstroms resolution and refined to a crystallographic R factor of 20.5 percent. The core domain structure consists of a beta sandwich that serves as a scaffold for two large loops and a loop-sheet-helix motif. The two loops, which are held together in part by a tetrahedrally coordinated zinc atom, and the loop-sheet-helix motif form the DNA binding surface of p53. Residues from the loop-sheet-helix motif interact in the major groove of the DNA, while an arginine from one of the two large loops interacts in the minor groove. The loops and the loop-sheet-helix motif consist of the conserved regions of the core domain and contain the majority of the p53 mutations identified in tumors. The structure supports the hypothesis that DNA binding is critical for the biological activity of p53, and provides a framework for understanding how mutations inactivate it.     

The C-terminal domain of p53 recognizes DNA damaged by ionizing radiation

p53 accumulates after DNA damage and arrests cellular growth. These findings suggest a possible role for p53 in the cellular response to DNA damage. We have previously shown that the C terminus of p53 binds DNA nonspecifically and assembles stable tetramers. In this study, we have utilized purified segments of human and murine p53s to determine which p53 domains may participate in a DNA damage response pathway. We find that the C-terminal 75 amino acids of human or murine p53 are necessary and sufficient for the DNA annealing and strand-transfer activities of p53. In addition, both full-length wild-type p53 and the C-terminal 75 amino acids display an increased binding affinity for DNA damaged by restriction digestion, DNase I treatment, or ionizing radiation. In contrast, the central site-specific DNA-binding domain together with the tetramerization domain does not have these activities. We propose that interactions of the C terminus of p53 with damaged DNA may play a role in the activation of p53 in response to DNA damage.     

Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction

HIV-1 integrase specifically recognizes and cleaves viral end DNA during the initial step of retroviral integration. The protein and DNA determinants of the specificity of viral end DNA binding have not been clearly identified. We have used mutational analysis of the viral end LTR sequence, in vitro selection of optimal viral end sequences, and specific photocrosslinking to identify regions of integrase that interact with specific bases in the LTR termini. The results highlight the involvement of the disordered loop of the integrase core domain, specifically residues Q148 and Y143, in binding to the terminal portion of the viral DNA ends. Additionally, we have identified positions upstream in the LTR termini which interact with the C-terminal domain of integrase, providing evidence for the role of that domain in stabilization of viral DNA binding. Finally, we have located a region centered 12 bases from the viral DNA terminus which appears essential for viral end DNA binding in the presence of magnesium, but not in the presence of manganese, suggesting a differential effect of divalent cations on sequence-specific binding. These results help to define important regions of contact between integrase and viral DNA, and assist in the formulation of a molecular model of this vital interaction.     

Structures and functions of the tumor suppressor p53

The tumour suppressor p53 plays a crucial role in the cellular response to DNA damage. The p53 protein is able both to detect sites of DNA damage and to interact with DNA in a sequence-specific manner and function in the regulation of target gene expression. These two properties map to discrete functional domains of the protein, the C-terminus and the central core domain respectively. They are essential for integration of a normal cellular response to DNA damage, with initiation of either G1 cell cycle arrest or apoptosis. This review considers the domain structure of p53 in relation to the protein's various functions, together with the importance of tertiary structure and conformational flexibility. The precise regulation of p53 function remains to be established, although the protein is known to be phosphorylated/de-phosphorylated by a number of specific protein kinases/phosphatases. A recent discovery indicates that p53 may be activated by autoproteolysis and that proteolytic cleavage is induced by direct interaction with sites of DNA damage. This process is reminiscent of the bacterial Lex A system and would provide one mechanism for activation of p53 in response to cellular DNA damage.     

Proteolytic cleavage of p53: a model for the activation of p53 in response to DNA damage

p53 is a multifunctional protein that reacts to DNA damage within the cell and regulates the cell growth arrest and/ or apoptotic pathways. However, the mechanism of p53 activation in response to DNA damage is unknown. Recently we have shown that interaction of p53 with sites of DNA damage induces selective proteolytic cleavage of p53, resulting in fragments of 40 and 35 kDa molecular weight. We have also shown that interaction of p53 with single-stranded (ss)DNAs results in a different pattern of selective proteolysis. This interaction gives a novel of 50-kDa protein generated by C-terminal cleavage of the full length protein and released from the p53-ssDNA complexes. Here we discuss a model where p53 responds to the DNA damage by generating different sets of the proteolytic fragments according to the type of the damage.     

Chromosome location of genes encoding human blood groups

In this study the transactivation potential and DNA binding activities of p53 protein were examined following exposure of A2780 cells, a human ovarian carcinoma cell line, to the DNA damaging agent, cis-diamminedichloroplatinum II (cisplatin). The endogenous murine double minute-2 gene (mdm-2) was used to monitor the ability of p53 to transactivate genes. Northern analysis showed an induction of mdm-2 mRNA upon cisplatin treatment. It was further demonstrated, using an RNase protection assay, that the p53-responsive, mdm-2 promoter (P2) was activated in cisplatin-treated A2780 cells. However, when p53 protein DNA binding activity was analyzed, there was no detectable increase in p53 sequence-specific DNA binding activity during the period of time following DNA damage when mdm-2 mRNA was induced. Instead the increase in p53 protein observed in nuclear, cytoplasmic, and whole cell extracts correlated with a latent conformation of p53 that lacked sequence-specific DNA binding activity. At low doses of cisplatin, these latent pools of p53 increased in parallel with mdm-2 gene activation and were detectable as early as 4 h following cisplatin treatment. In vitro attempts to convert the latent p53 into an active, sequence-specific DNA binding conformation were unsuccessful. Even though cisplatin-induced p53 lacked sequence-specific DNA binding activity, it does possess an increased affinity for cisplatin-damaged duplex DNA molecules. This represents the first identification where cisplatin treatment induces a p53 protein, lacking sequence-specific DNA binding but with an increased affinity for platinated DNA molecules.     

The J domain of simian virus 40 large T antigen is required to functionally inactivate RB family proteins

Transformation by simian virus 40 large T antigen (TAg) is dependent on the inactivation of cellular tumor suppressors. Transformation minimally requires the following three domains: (i) a C-terminal domain that mediates binding to p53; (ii) the LXCXE domain (residues 103 to 107), necessary for binding to the retinoblastoma tumor suppressor protein, pRB, and the related p107 and p130; and (iii) an N-terminal domain that is homologous to the J domain of DnaJ molecular chaperone proteins. We have previously demonstrated that the N-terminal J domain of TAg affects the RB-related proteins by perturbing the phosphorylation status of p107 and p130 and promoting the degradation of p130 and that this domain is required for transformation of cells that express either p107 or p130. In this work, we demonstrate that the J domain of TAg is required to inactivate the ability of each member of the pRB family to induce a G1 arrest in Saos-2 cells. Furthermore, the J domain is required to override the repression of E2F activity mediated by p130 and pRB and to disrupt p130-E2F DNA binding complexes. These results imply that while the LXCXE domain serves as a binding site for the RB-related proteins, the J domain plays an important role in inactivating their function.     

Voltammetric behaviour of mitoxantrone at a DNA-biosensor

The surface of an electrochemical glassy carbon electrode was modified with a layer of double-stranded DNA (dsDNA) or with double-stranded DNA conditioned in single-stranded DNA (ssDNA) and was used to investigate mitoxantrone-DNA interactions. Differential pulse and square wave voltammetry were applied to develop an electroanalytical procedure for the determination of mitoxantrone and evaluate its interaction with dsDNA or ssDNA immobilized on the electrode surface. The results demonstrate that MTX interaction with DNA is not specific to either guanine or adenine bases. The kinetics of the mitoxantrone-DNA interaction is slow and damage to DNA was followed with time.