p53, also known as tumor protein p53, TP53, cellular tumor antigen p53 (UniProt name), or transformation-related protein 53 (TRP53) is a regulatory transcription factor protein that is often mutated in human cancers. The p53 proteins (originally thought to be, and often spoken of as, a single protein) are crucial in vertebrates, where they prevent cancer formation. As such, p53 has been described as "the guardian of the genome" because of its role in conserving stability by preventing genome mutation. Hence TP53italics are used to denote the TP53 gene name and distinguish it from the protein it encodes is classified as a tumor suppressor gene.
The TP53 gene is inactivated in a majority (>50%) of human cancer cases. This can be caused by any various factors, including mutations in the gene, epigenetic events, or interactions with other proteins. This association indicates that the TP53 gene plays a crucial role in preventing cancer formation. TP53 gene encodes proteins that bind to DNA and regulate gene expression to prevent mutations of the genome. In addition to the full-length protein, the human TP53 gene encodes at least 12 protein isoforms.
Comparative genomic studies found pathogenic mutations absent in some Neanderthal populations, while modern humans exhibit an expansion of over 1,000 mutated variations. Evidence suggests that the vast majority of these protein-coding variants arose very recently in human history, specifically concentrated within a window of 5,000 to 10,000 years ago.
Gene In humans, the TP53 gene is located on the short arm of chromosome 17 (17p13.1). The gene spans 20 kb, with a non-coding exon 1 and a very long first intron of 10 kb, overlapping the Hp53int1 gene. The coding sequence contains five regions showing a high degree of conservation in vertebrates, predominantly in exons 2, 5, 6, 7 and 8, but the sequences found in invertebrates show only distant resemblance to mammalian TP53. TP53 orthologs have been identified in most mammals for which complete genome data are available. Elephants, with 20 genes for TP53, rarely get cancer.
Structure
The full-length p53 protein (p53α) comprises seven distinct protein domains: An acidic N-terminus transactivation domain (TAD), including activation domains 1 and 2 (AD1: residues 1–42; AD2: residues 43–63), which regulate transcription of several pro-apoptotic genes. A proline-rich domain (residues 64–92), involved in apoptotic function and nuclear export via MAPK signaling. A central DNA-binding domain (DBD; residues 102–292), containing a zinc atom and multiple arginine residues, essential for sequence-specific DNA interaction and co-repressor binding such as LMO3. A nuclear localization sequence (NLS; residues 316–325), required for nuclear import. A homo-oligomerization domain (OD; residues 307–355), which mediates tetramerization—essential for p53 activity in vivo. A C-terminal regulatory domain (residues 356–393), which modulates the DNA-binding activity of the central domain.
Most cancer-associated mutations in TP53 occur in the DBD, impairing DNA binding and transcriptional activation. These are typically recessive loss-of-function mutations. By contrast, mutations in the OD can exert dominant negative effects by forming inactive complexes with wild-type p53.
Wild-type p53 is a labile protein containing both folded and intrinsically disordered regions that act synergistically.
Although designated as a 53 kDa protein by SDS-PAGE, the actual molecular weight of p53α is 43.7 kDa. The discrepancy is due to its high proline content, which slows electrophoretic migration.
Tetramerization p53 initially forms dimers cotranslationally during protein synthesis on ribosomes. Each dimer consists of two p53 monomers joined through their oligomerization domains.
The dimerization interface spans residues 325–356 and includes a beta-strand (residues 325–333), a alpha-helix (residues 335–356), and a sharp turn at the conserved hinge residue Gly334. This configuration links the beta-strand and alpha-helix to form a V-shaped monomer topology. The beta-strand contributes to the formation of an antiparallel intermolecular beta-sheet between two p53 monomers, stabilized by hydrophobic interactions involving Phe328, Leu330, and Ile332. The alpha-helix forms an antiparallel coiled-coil between the two monomers, with a packing angle of 156°. Helix–helix interactions are stabilized by hydrophobic contacts (e.g., Phe338, Phe341, Leu344) and electrostatic interactions, such as the Arg337–Asp352 salt bridge.
Following dimer formation, p53 dimers associate posttranslationally to form tetramers (dimers of dimers). The tetramerization domain (residues 325–356) plays a central role in stabilizing the tetrameric structure. In the tetramer, the two primary dimers associate at an angle described as "roughly orthogonal," with a helix bundle packing angle (θ) of approximately 80°.
Tetramers represent the active form of p53 for DNA binding and transcriptional regulation.
Isoforms
Like 95% of human genes, TP53 encodes multiple proteins, collectively known as the p53 isoforms. These vary in size from 3.5 to 43.7 kDa. Since their initial discovery in 2005, 12 human p53 isoforms have been identified: p53α, p53β, p53γ, ∆40p53α, ∆40p53β, ∆40p53γ, ∆133p53α, ∆133p53β, ∆133p53γ, ∆160p53α, ∆160p53β, and ∆160p53γ. Isoform expression is tissue-dependent, and p53α is never expressed alone.
The isoforms differ by the inclusion or exclusion of specific domains. Some, such as Δ133p53β/γ and Δ160p53α/β/γ, lack the transactivation or proline-rich domains and are deficient in apoptosis induction, illustrating the functional diversity of TP53.
Isoforms are generated through multiple mechanisms: Alternative splicing of intron 9 creates the β and γ isoforms with altered C-termini. An internal promoter in intron 4 produces the ∆133 and ∆160 isoforms, which lack part of the TAD and DBD. Alternative translation initiation at codons 40 or 160 results in ∆40p53 and ∆160p53 isoforms, respectively.
Function
DNA damage and repair
p53 regulates cell cycle progression, apoptosis, and genomic stability through multiple mechanisms:
Activates DNA repair proteins in response to DNA damage, suggesting a potential role in aging. Arrests the cell cycle at the G1/S checkpoint upon DNA damage, allowing time for repair before progression. Initiates apoptosis if the damage is beyond repair. Essential for the senescence response triggered by short telomeres.
p53 functions as a transcription factor by binding DNA as a tetramer, a structure that is essential for its stability and effective DNA binding activity. Once bound to DNA, p53 induces the transcription of numerous genes involved in DNA repair pathways. This includes components of base excision repair (BER) such as OGG1 and MUTYH, nucleotide excision repair (NER) factors like DDB2 and XPC, mismatch repair (MMR) genes such as MSH2 and MLH1, and elements of homologous recombination (HR) and non-homologous end-joining (NHEJ) repair. These transcriptional responses are crucial for the DNA damage response (DDR), allowing cells to efficiently repair damaged DNA and maintain genomic integrity. While p53's role is most clearly defined in transcriptional activation of repair genes, it also participates in non-transcriptional regulation of DNA repair processes, particularly in HR and NHEJ, by modulating protein interactions and chromatin accessibility.
p53 binds specific elements in the promoter of target genes, including CDKN1A, which encodes p21. Upon activation by p53, p21 inhibits cyclin-dependent kinases, leading to cell cycle arrest and contributing to tumor suppression. However, p21 can also be induced independently of p53 during processes such as differentiation, development, and in response to serum stimulation.
p21 (WAF1) binds to cyclin-CDK complexes (notably CDK2, CDK1, CDK4, and CDK6), inhibiting their activity and blocking the G1/S transition. This inhibition enforces a cell cycle pause that allows DNA repair to occur. In cells with functional p53, p21 is upregulated in response to DNA damage, ensuring this checkpoint control. In contrast, p53 mutations impair p21 induction and compromise this control.
In human embryonic stem cells (hESCs), although p21 mRNA is upregulated following DNA damage, the protein is not detectable. This reflects a nonfunctional p53-p21 axis at the G1/S checkpoint. This discrepancy is largely due to post-transcriptional repression, particularly by the miR-302 family of microRNAs, which inhibit p21 translation. Although p53 binds the CDKN1A promoter in hESCs, it does not regulate miR-302, which is constitutively expressed and suppresses p21 expression.
The p53 pathway is interconnected with the RB1 pathway via p14^ARF, which links the regulation of these key tumor suppressors.
p53 expression can be induced by UV radiation, which also causes DNA damage. In this context, p53 activation can initiate processes that lead to melanin production and tanning.
Stem cells Levels of p53 play an important role in the maintenance of stem cells throughout development and the rest of human life.
In human embryonic stem cells (hESCs)s, p53 is maintained at low inactive levels. This is because activation of p53 leads to rapid differentiation of hESCs. Studies have shown that knocking out p53 delays differentiation and that adding p53 causes spontaneous differentiation, showing how p53 promotes differentiation of hESCs and plays a key role in cell cycle as a differentiation regulator. When p53 becomes stabilized and activated in hESCs, it increases p21 to establish a longer G1. This typically leads to abolition of S-phase entry, which stops the cell cycle in G1, leading to differentiation. Work in mouse embryonic stem cells has recently shown however that the expression of P53 does not necessarily lead to differentiation. p53 also activates miR-34a and miR-145, which then repress the hESCs pluripotency factors, further instigating differentiation.
In adult stem cells, p53 regulation is important for maintenance of stemness in adult stem cell niches. Mechanical signals such as hypoxia affect levels of p53 in these niche cells through the hypoxia inducible factors, HIF-1α and HIF-2α. While HIF-1α stabilizes p53, HIF-2α suppresses it. Suppression of p53 plays important roles in cancer stem cell phenotype, induced pluripotent stem cells and other stem cell roles and behaviors, such as blastema formation. Cells with decreased levels of p53 have been shown to reprogram into stem cells with a much greater efficiency than normal cells. Papers suggest that the lack of cell cycle arrest and apoptosis gives more cells the chance to be reprogrammed. Decreased levels of p53 were also shown to be a crucial aspect of blastema formation in the legs of salamanders. p53 regulation is very important in acting as a barrier between stem cells and a differentiated stem cell state, as well as a barrier between stem cells being functional and being cancerous.
Other
Apart from the cellular and molecular effects above, p53 has a tissue-level anticancer effect that works by inhibiting angiogenesis. As tumors grow they need to recruit new blood vessels to supply them, and p53 inhibits that by (i) interfering with regulators of tumor hypoxia that also affect angiogenesis, such as HIF1 and HIF2, (ii) inhibiting the production of angiogenic promoting factors, and (iii) directly increasing the production of angiogenesis inhibitors, such as arresten.
p53 by regulating Leukemia Inhibitory Factor has been shown to facilitate implantation in the mouse and possibly human reproduction.
The immune response to infection also involves p53 and NF-κB. Checkpoint control of the cell cycle and of apoptosis by p53 is inhibited by some infections such as Mycoplasma bacteria, raising the specter of oncogenic infection.
Regulation
Basal regulation