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Tumor protein p53 (Li-Fraumeni syndrome)

PDB rendering based on 1TUP.
Available structures
1a1u, 1aie, 1c26, 1gzh, 1hs5, 1kzy, 1olg, 1olh, 1pes, 1pet, 1sae, 1saf, 1sag, 1sah, 1sai, 1saj, 1sak, 1sal, 1tsr, 1tup, 1uol, 1ycs, 2ac0, 2ady, 2ahi, 2ata, 2b3g, 2bim, 2bin, 2bio, 2bip, 2biq, 2fej, 2gs0, 2h1l, 2j1w, 2j1x, 2j1y, 2j1z, 2j20, 2j21, 2ocj, 3sak
Identifiers
Symbols TP53; LFS1; TRP53; p53
External IDs OMIM191170 MGI98834 HomoloGene460 GeneCards: TP53 Gene
RNA expression pattern
PBB GE TP53 201746 at tn.png
PBB GE TP53 211300 s at tn.png
More reference expression data
Orthologs
Species Human Mouse
Entrez 7157 22059
Ensembl ENSG00000141510 ENSMUSG00000059552
UniProt P04637 O70366
RefSeq (mRNA) NM_000546 NM_011640
RefSeq (protein) NP_000537 NP_035770
Location (UCSC) Chr 17:
7.51 - 7.53 Mb
Chr 11:
69.4 - 69.41 Mb
PubMed search [1] [2]

p53 (also known as protein 53 or tumor protein 53), is a tumor suppressor protein that in humans is encoded by the TP53 gene.[1][2][3] p53 is important in multicellular organisms, where it regulates the cell cycle and thus functions as a tumor suppressor that is involved in preventing cancer. As such, p53 has been described as "the guardian of the genome," "the guardian angel gene," and the "master watchman," referring to its role in conserving stability by preventing genome mutation.[4]

The name p53 is in reference to its apparent molecular mass: it runs as a 53 kilodalton (kDa) protein on SDS-PAGE. But based on calculations from its amino acid residues, p53's mass is actually only 43.7kDa. This difference is due to the high number of proline residues in the protein which slow its migration on SDS-PAGE, thus making it appear heavier than it actually is.[5] This effect is observed with p53 from a variety of species, including humans, rodents, frogs, and fish.

Contents

Nomenclature

p53 is also known as:

  • UniProt name: Cellular tumor antigen p53
  • Antigen NY-CO-13
  • Phosphoprotein p53
  • Transformation-related protein 53 (TRP53)
  • Tumor suppressor p53

Gene

In humans, p53 is encoded by the TP53 gene located on the short arm of chromosome 17 (17p13.1).[1][2][3] TP53 orthologs [6] have been identified in most mammals for which complete genome data are available.

For these mammals, the gene is located on different chromosomes:

(Italics are used to denote the TP53 gene name and distinguish it from the protein it encodes.)

Structure

Human p53 is 393 amino acids long and has seven domains:

  1. N-terminal transcription-activation domain (TAD), also known as activation domain 1 (AD1) which activates transcription factors: residues 1-42.
  2. activation domain 2 (AD2) important for apoptotic activity: residues 43-63.
  3. Proline rich domain important for the apoptotic activity of p53: residues 64-92.
  4. central DNA-binding core domain (DBD). Contains one zinc atom and several arginine amino acids: residues 100-300.
  5. nuclear localization signaling domain, residues 316-325.
  6. homo-oligomerisation domain (OD): residues 307-355. Tetramerization is essential for the activity of p53 in vivo.
  7. C-terminal involved in downregulation of DNA binding of the central domain: residues 356-393.[7]

A tandem of nine-amino-acid transactivation domains (9aaTAD) was identified in the AD1 and AD2 regions of transcription factor p53.[8] KO mutations and position for p53 interaction with TFIID are listed below:[9]

Piskacek p53b.jpg

9aaTADs mediate p53 interaction with general coactivators - TAF9, CBP/p300 (all four domains KIX, TAZ1, TAZ2 and IBiD), GCN5 and PC4, regulatory protein MDM2 and replication protein A (RPA).[10][11]

Piskacek p53a.jpg

Mutations that deactivate p53 in cancer usually occur in the DBD. Most of these mutations destroy the ability of the protein to bind to its target DNA sequences, and thus prevents transcriptional activation of these genes. As such, mutations in the DBD are recessive loss-of-function mutations. Molecules of p53 with mutations in the OD dimerise with wild-type p53, and prevent them from activating transcription. Therefore OD mutations have a dominant negative effect on the function of p53.

Wild-type p53 is a labile protein, comprising folded and unstructured regions which function in a synergistic manner.[12]

Function

In its anti-cancer role, p53 works through several mechanisms:

  • It can activate DNA repair proteins when DNA has sustained damage.
  • It can induce growth arrest by holding the cell cycle at the G1/S regulation point on DNA damage recognition (if it holds the cell here for long enough, the DNA repair proteins will have time to fix the damage and the cell will be allowed to continue the cell cycle.)
  • It can initiate apoptosis, the programmed cell death, if the DNA damage proves to be irreparable.
p53 pathway: In a normal cell p53 is inactivated by its negative regulator, mdm2. Upon DNA damage or other stress, various pathways will lead to the dissociation of the p53 and mdm2 complex. Once activated, p53 will either induce a cell cycle arrest to allow repair and survival of the cell or apoptosis to discard the damage cell. How p53 makes this choice is currently unknown.

Activated p53 binds DNA and activates expression of several genes including WAF1/CIP1 encoding for p21. p21(WAF1) binds to the G1-S/CDK (CDK2) and S/CDK complexes (molecules important for the G1/S transition in the cell cycle) inhibiting their activity. p53 has many anticancer mechanisms, and plays a role in apoptosis, genetic stability, and inhibition of angiogenesis.

When p21(WAF1) is complexed with cdk2 the cell cannot pass through to the next stage of cell division. Mutant p53 can no longer bind DNA in an effective way, and as a consequence the p21 protein is not made available to act as the 'stop signal' for cell division. Thus cells divide uncontrollably, and form tumors.[13 ]

Recent research has also linked the p53 and RB1 pathways, via p14ARF, raising the possibility that the pathways may regulate each other.[14]

When p53 expression is stimulated by sunlight, it begins the chain of events leading to tanning.[15][16]

Regulation

p53 becomes activated in response to myriad stress types, which include but is not limited to DNA damage (induced by either UV, IR, or chemical agents such as hydrogen peroxide), oxidative stress,[17] osmotic shock, ribonucleotide depletion and deregulated oncogene expression. This activation is marked by two major events. Firstly, the half-life of the p53 protein is increased drastically, leading to a quick accumulation of p53 in stressed cells. Secondly, a conformational change forces p53 to take on an active role as a transcription regulator in these cells. The critical event leading to the activation of p53 is the phosphorylation of its N-terminal domain. The N-terminal transcriptional activation domain contains a large number of phosphorylation sites and can be considered as the primary target for protein kinases transducing stress signals.

The protein kinases that are known to target this transcriptional activation domain of p53 can be roughly divided into two groups. A first group of protein kinases belongs to the MAPK family (JNK1-3, ERK1-2, p38 MAPK), which is known to respond to several types of stress, such as membrane damage, oxidative stress, osmotic shock, heat shock, etc. A second group of protein kinases (ATR, ATM, CHK1 and CHK2, DNA-PK, CAK) is implicated in the genome integrity checkpoint, a molecular cascade that detects and responds to several forms of DNA damage caused by genotoxic stress. Oncogenes also stimulate p53 activation, mediated by the protein p14ARF.

In unstressed cells, p53 levels are kept low through a continuous degradation of p53. A protein called Mdm2 (also called HDM2 in humans) binds to p53, preventing its action and transports it from the nucleus to the cytosol. Also Mdm2 acts as ubiquitin ligase and covalently attaches ubiquitin to p53 and thus marks p53 for degradation by the proteasome. However, ubiquitylation of p53 is reversible. A ubiqiutin specific protease, USP7 (or HAUSP), can cleave ubiquitin off p53, thereby protecting it from proteasome-dependent degradation. This is one means by which p53 is stabilized in response to oncogenic insults.

Phosphorylation of the N-terminal end of p53 by the above-mentioned protein kinases disrupts Mdm2-binding. Other proteins, such as Pin1, are then recruited to p53 and induce a conformational change in p53 which prevents Mdm2-binding even more. Phosphorylation also allows for binding of trancriptional coactivators, like p300 or PCAF, which then acetylate the carboxy-terminal end of p53, exposing the DNA binding domain of p53, allowing it to activate or repress specific genes. Deacetylase enzymes, such as Sirt1 and Sirt7, can deacetylate p53, leading to an inhibition of apoptosis.[18] Some oncogenes can also stimulate the transcription of proteins which bind to MDM2 and inhibit its activity.

Role in disease

Overview of signal transduction pathways involved in apoptosis.

If the TP53 gene is damaged, tumor suppression is severely reduced. People who inherit only one functional copy of the TP53 gene will most likely develop tumors in early adulthood, a disease known as Li-Fraumeni syndrome. The TP53 gene can also be damaged in cells by mutagens (chemicals, radiation, or viruses), increasing the likelihood that the cell will begin decontrolled division. More than 50 percent of human tumors contain a mutation or deletion of the TP53 gene. Increasing the amount of p53, which may initially seem a good way to treat tumors or prevent them from spreading, is in actuality not a usable method of treatment, since it can cause premature aging.[19] However, restoring endogenous p53 function holds a lot of promise.[20] Loss of p53 creates genomic instability that most often results in the aneuploidy phenotype.[21]

Certain pathogens can also affect the p53 protein that the TP53 gene expresses. One such example, the Human papillomavirus (HPV), encodes a protein, E6, which binds the p53 protein and inactivates it. This, in synergy with the inactivation of another cell cycle regulator, p105RB, allows for repeated cell division manifested in the clinical disease of warts. Infection by oncogenic HPV types, especially HPV16, can also lead to progression from a benign wart to low or high-grade cervical dysplasia which are reversible forms of precancerous lesions. Persistent infection over the years causes irreversible changes leading to Carcinoma in situ and eventually invasive cervical cancer. This results from the effects of HPV genes, particularly those encoding E6 and E7, which are the two viral oncoproteins that are preferentially retained and expressed in cervical cancers by integration of the viral DNA into the host genome.[22]

In healthy humans, the p53 protein is continually produced and degraded in the cell. The degradation of the p53 protein is, as mentioned, associated with MDM2 binding. In a negative feedback loop MDM2 is itself induced by the p53 protein. However mutant p53 proteins often don't induce MDM2, and are thus able to accumulate at very high concentrations. Worse, mutant p53 protein itself can inhibit normal p53 protein levels.

Discovery

p53 was identified in 1979 by Lionel Crawford, David P. Lane, Arnold Levine, and Lloyd Old, working at Imperial Cancer Research Fund (UK) Princeton University/UMDNJ (Cancer Institute of New Jersey), and Sloan-Kettering Memorial Hospital, respectively. It had been hypothesized to exist before as the target of the SV40 virus, a strain that induced development of tumors. The TP53 gene from the mouse was first cloned by Peter Chumakov of the Russian Academy of Sciences in 1982,[23] and independently in 1983 by Moshe Oren (Weizmann Institute).[24] The human TP53 gene was cloned in 1984.[1]

It was initially presumed to be an oncogene due to the use of mutated cDNA following purification of tumour cell mRNA. Its character as a tumor suppressor gene was finally revealed in 1989 by Bert Vogelstein working at Johns Hopkins School of Medicine.[25]

Warren Maltzman, of the Waksman Institute of Rutgers University first demonstrated that TP53 was responsive to DNA damage in the form of ultraviolet radiation.[26] In a series of publications in 1991-92, Michael Kastan, Johns Hopkins University, reported that TP53 was a critical part of a signal transduction pathway that helped cells respond to DNA damage.[27]

In 1992, Wafik El-Deiry when he was working with Bert Vogelstein at Johns Hopkins University identified the consensus sequence to which human p53 could bind to by immunoprecipitating human genomic DNA that could be bound by baculovirus-produced human p53 protein. This sequence was published in the first issue of the journal Nature Genetics in 1992 in work that is highly cited. The consensus sequence is 5'-RRRCWWGYYY-N(0-13)-RRRCWWGYYY-3' and is located in the regulatory regions of genes that are activated by the p53 transcription factor. The presence of p53 response elements in or around genes (promoters, upstream sequences, introns) is a powerful predictor of regulation and activation of a particular gene by p53.

In 1993, p53 was voted molecule of the year by Science magazine.[28]

That same year, 1993, Wafik El-Deiry when he was working with Bert Vogelstein at Johns Hopkins University discovered p21(WAF1) as a gene regulated directly by p53. This work was reported in the most highly cited paper ever published in the journal Cell, and provided a molecular mechanism by which mammalian cells undergo growth arrest when damaged. The p21(WAF1) protein binds directly to cyclin-CDK complexes that drive forward the cell cycle and inhibits their kinase activity thereby causing cell cycle arrest to allow repair to take place. p21 can also mediate growth arrest associated with differentiation and a more permanent growth arrest associated with cellular senescence. The p21 gene contains several p53 response elements that mediate direct binding of the p53 protein resulting in transcriptional activation of the gene encoding the p21(WAF1) protein.

Interactions

P53 has been shown to interact with HIPK1,[29] Replication protein A1,[30][31] ERCC6,[32][33] TSG101,[34] Protein kinase R,[35] CFLAR,[36] XPB,[32] CREB binding protein,[37][38][39] CREB1,[39] Mitogen-activated protein kinase 9,[40][41] Prohibitin,[42] RPL11,[43] Ataxia telangiectasia mutated,[44][45][46][47][48] DNA-PKcs,[48][49][50] ATF3,[51][52] HIPK2,[53][54] HIF1A,[55][56][57][58] MED1,[59][60] Zif268,[61] GPS2,[62] EFEMP2,[63] Promyelocytic leukemia protein,[64][65][66] PLK3,[67][68] TP53INP1,[69][70] Aurora A kinase,[71] BRE,[72] PTTG1,[73] CHEK1,[74][75][49] CCNG1,[76] Cyclin H,[77] TOP1,[78][79] PIAS1,[63][80] CDC14B,[81] BRCA2,[72][82] BRCA1,[83][84][72][85][86] RCHY1,[87][88] CDC14A,[81] E4F1,[89][90] PARP1,[91][92] ZNF148,[93] HMGB1,[94][95] Multisynthetase complex auxiliary component p38,[96] PRKRA,[97] Ataxia telangiectasia and Rad3 related,[45][48] TP53BP1,[98][75][99][100][101][102][103] Cdk1,[104][105] TP53BP2,[103][106] TOP2B,[107] TOP2A,[107] Bloom syndrome protein,[75][108][109][110] BAK1,[111] PARC,[112] RAD51,[72][113][114] BARD1,[72] PSME3,[115] Aprataxin,[91] S100B,[116] UBE2I,[117][63][118][119] PIN1,[120][121] Small ubiquitin-related modifier 1,[117][122] Huntingtin,[123] PTEN,[124] KPNB1,[125] Cyclin-dependent kinase 7,[126][77] ING5,[127] ELL,[128] PTK2,[129] NUMB,[130] ING1,[131][132] P16,[43][89][133] USP7,[134] ING4,[127][135] YWHAZ,[136] UBE2A,[137] Ubiquitin C,[96][138][122][139][140][141][115][142] Werner syndrome ATP-dependent helicase,[110][143] GNL3,[144] BRCC3,[72] CCAAT/enhancer binding protein zeta,[145] WWOX,[146] Y box binding protein 1,[147][148] IκBα,[149] TATA binding protein,[150][151] HSPA9,[152] MDM4,[153][154] Mdm2,[155][156][43][64][124][37][157][158][159][133][160][161][162][131][163][164][165][166][167][168][115][169][130] GSK3B,[170] SMN1,[171] Heat shock protein 90kDa alpha (cytosolic), member A1,[172][125][173] TFAP2A,[174] ANKRD2,[147] PLAGL1,[175] Nucleolin,[176] NDN,[177] SMARCB1,[178] EP300,[179][180][38][157] SMARCA4,[178] MNAT1[126] and TFDP1.[181]

References

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  11. ^ The prediction for 9aaTADs (for both acidic and hydrophilic transactivation domains) is available online from ExPASy http://us.expasy.org/tools/ and EMBnet Spain http://www.es.embnet.org/Services/EMBnetAT/htdoc/9aatad/
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  29. ^ Kondo, Seiji; Lu Ying, Debbas Michael, Lin Athena W, Sarosi Ildiko, Itie Annick, Wakeham Andrew, Tuan JoAnn, Saris Chris, Elliott Gary, Ma Weili, Benchimol Samuel, Lowe Scott W, Mak Tak Wah, Thukral Sushil K (Apr. 2003). "Characterization of cells and gene-targeted mice deficient for the p53-binding kinase homeodomain-interacting protein kinase 1 (HIPK1)". Proc. Natl. Acad. Sci. U.S.A. 100 (9): 5431–6. doi:10.1073/pnas.0530308100. PMID 12702766.  
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  33. ^ Yu, A; Fan H Y, Liao D, Bailey A D, Weiner A M (May. 2000). "Activation of p53 or loss of the Cockayne syndrome group B repair protein causes metaphase fragility of human U1, U2, and 5S genes". Mol. Cell 5 (5): 801–10. PMID 10882116.  
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