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DNA-binding protein PDB id
Protein chains
195 a.a. *
_ZN ×2
Waters ×391
* Residue conservation analysis
PDB id:
Name: DNA-binding protein
Title: Crystal structure of the human p53 core domain mutant m133l/v203a/n239y/n268d at 1.9 a resolution.
Structure: Cellular tumor antigen p53. Chain: a, b. Fragment: DNA binding (core) domain, residues 94-312. Synonym: tumor suppressor p53, phosphoprotein p53, antigen ny-co-13. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
1.9Å     R-factor:   0.192     R-free:   0.230
Authors: A.C.Joerger,M.D.Allen,A.R.Fersht
Key ref:
A.C.Joerger et al. (2004). Crystal structure of a superstable mutant of human p53 core domain. Insights into the mechanism of rescuing oncogenic mutations. J Biol Chem, 279, 1291-1296. PubMed id: 14534297 DOI: 10.1074/jbc.M309732200
19-Sep-03     Release date:   16-Oct-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P04637  (P53_HUMAN) -  Cellular tumor antigen p53
393 a.a.
195 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     apoptotic process   2 terms 
  Biochemical function     transcription regulatory region DNA binding     3 terms  


DOI no: 10.1074/jbc.M309732200 J Biol Chem 279:1291-1296 (2004)
PubMed id: 14534297  
Crystal structure of a superstable mutant of human p53 core domain. Insights into the mechanism of rescuing oncogenic mutations.
A.C.Joerger, M.D.Allen, A.R.Fersht.
Most of the cancer-associated mutations in the tumor suppressor p53 map to its DNA-binding core domain. Many of them inactivate p53 by decreasing its thermodynamic stability. We have previously designed the superstable quadruple mutant M133L/V203A/N239Y/N268D containing the second-site suppressor mutations N239Y and N268D, which specifically restore activity and stability in several oncogenic mutants. Here we present the x-ray structure of this quadruple mutant at 1.9 A resolution, which was solved in a new crystal form in the absence of DNA. This structure reveals that the four point mutations cause only small local structural changes, whereas the overall structure of the central beta-sandwich and the DNA-binding surface is conserved. The suppressor mutation N268D results in an altered hydrogen bond pattern connecting strands S1 and S10, thus bridging the two sheets of the beta-sandwich scaffold in an energetically more favorable way. The second suppressor mutation N239Y, which is located in close proximity to the DNA-binding surface in loop L3, seems to reduce the plasticity of the structure in large parts of loop L3 as indicated by decreased crystallographic temperature factors. The same is observed for residues in the vicinity of the N268D substitution. This increase in rigidity provides the structural basis for the increase in thermostability and an understanding how N268D and N239Y rescue some of the common cancer mutants.
  Selected figure(s)  
Figure 3.
FIG. 3. The structure of p53 core domain quadruple mutant M133L/V203A/N239Y/N268D (chain A, yellow) superimposed on the wild type structure (chain A, transparent light gray). A, mutation site M133L; B, mutation site V203A; C, mutation site N268D; D, mutation site N239Y. The zinc ion is shown as a gray sphere. The large semi-transparent red spheres indicate the location of the two cancer hot-spot sites Gly-245 and Arg-249.
Figure 4.
FIG. 4. Polypeptide-backbone mobility in the structures of p53 core domain quadruple mutant M133L/V203A/N239Y/N268D and wild type. A, distribution of average isotropic B-factors for main-chain atoms in chains A (thick solid line) and B (thin solid line) of the quadruple mutant, and chain A (DNA-free) of wild type (dotted line). Secondary structural elements are given for reference; blocks represent -strands and open circles indicate helical segments. B, relative backbone mobility as calculated by (B-)/ [B] in chains A (thick solid line) and B (thin solid line) of the superstable quadruple mutant, and chain A (DNA-free) of wild type (dotted line). B- is the deviation of the average isotropic main-chain B-factor for a particular residue from the mean for the whole chain (backbone atoms only), [B] the standard deviation.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 1291-1296) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21472523 J.Scotcher, D.J.Clarke, S.K.Weidt, C.L.Mackay, T.R.Hupp, P.J.Sadler, and P.R.Langridge-Smith (2011).
Identification of Two Reactive Cysteine Residues in the Tumor Suppressor Protein p53 Using Top-Down FTICR Mass Spectrometry.
  J Am Soc Mass Spectrom, 22, 888-897.  
20952436 M.R.Fernandez-Fernandez, and B.Sot (2011).
The relevance of protein-protein interactions for p53 function: the CPE contribution.
  Protein Eng Des Sel, 24, 41-51.  
  20516128 A.C.Joerger, and A.R.Fersht (2010).
The tumor suppressor p53: from structures to drug discovery.
  Cold Spring Harb Perspect Biol, 2, a000919.  
20113312 A.Merabet, H.Houlleberghs, K.Maclagan, E.Akanho, T.T.Bui, B.Pagano, A.F.Drake, F.Fraternali, and P.V.Nikolova (2010).
Mutants of the tumour suppressor p53 L1 loop as second-site suppressors for restoring DNA binding to oncogenic p53 mutations: structural and biochemical insights.
  Biochem J, 427, 225-236.  
20878668 J.L.Kaar, N.Basse, A.C.Joerger, E.Stephens, T.J.Rutherford, and A.R.Fersht (2010).
Stabilization of mutant p53 via alkylation of cysteines and effects on DNA binding.
  Protein Sci, 19, 2267-2278.  
20142040 N.Basse, J.L.Kaar, G.Settanni, A.C.Joerger, T.J.Rutherford, and A.R.Fersht (2010).
Toward the rational design of p53-stabilizing drugs: probing the surface of the oncogenic Y220C mutant.
  Chem Biol, 17, 46-56.
PDB codes: 2x0u 2x0v 2x0w
19625409 E.Luna, A.Rodríguez-Huete, V.Rincón, R.Mateo, and M.G.Mateu (2009).
Systematic study of the genetic response of a variable virus to the introduction of deleterious mutations in a functional capsid region.
  J Virol, 83, 10140-10151.  
19667193 E.Natan, D.Hirschberg, N.Morgner, C.V.Robinson, and A.R.Fersht (2009).
Ultraslow oligomerization equilibria of p53 and its implications.
  Proc Natl Acad Sci U S A, 106, 14327-14332.  
19933326 F.Huang, S.Rajagopalan, G.Settanni, R.J.Marsh, D.A.Armoogum, N.Nicolaou, A.J.Bain, E.Lerner, E.Haas, L.Ying, and A.R.Fersht (2009).
Multiple conformations of full-length p53 detected with single-molecule fluorescence resonance energy transfer.
  Proc Natl Acad Sci U S A, 106, 20758-20763.  
19297317 J.van Dieck, M.R.Fernandez-Fernandez, D.B.Veprintsev, and A.R.Fersht (2009).
Modulation of the oligomerization state of p53 by differential binding of proteins of the S100 family to p53 monomers and tetramers.
  J Biol Chem, 284, 13804-13811.  
19515728 K.H.Khoo, A.C.Joerger, S.M.Freund, and A.R.Fersht (2009).
Stabilising the DNA-binding domain of p53 by rational design of its hydrophobic core.
  Protein Eng Des Sel, 22, 421-430.
PDB code: 2wgx
19700401 K.H.Khoo, S.Mayer, and A.R.Fersht (2009).
Effects of stability on the biological function of p53.
  J Biol Chem, 284, 30974-30980.  
18802452 M.Olivier, A.Petitjean, V.Marcel, A.Pétré, M.Mounawar, A.Plymoth, Fromentel, and P.Hainaut (2009).
Recent advances in p53 research: an interdisciplinary perspective.
  Cancer Gene Ther, 16, 1.  
19084536 M.Petrovich, and D.B.Veprintsev (2009).
Effects of CpG methylation on recognition of DNA by the tumour suppressor p53.
  J Mol Biol, 386, 72-80.  
19717093 P.Hainaut, and K.G.Wiman (2009).
30 years and a long way into p53 research.
  Lancet Oncol, 10, 913-919.  
20030809 T.Brandt, M.Petrovich, A.C.Joerger, and D.B.Veprintsev (2009).
Conservation of DNA-binding specificity and oligomerisation properties within the p53 family.
  BMC Genomics, 10, 628.  
19066201 T.S.Wong, S.Rajagopalan, F.M.Townsley, S.M.Freund, M.Petrovich, D.Loakes, and A.R.Fersht (2009).
Physical and functional interactions between human mitochondrial single-stranded DNA-binding protein and tumour suppressor p53.
  Nucleic Acids Res, 37, 568-581.  
19748724 Y.H.Tan, Y.M.Chen, X.Ye, Q.Lu, V.Tretyachenko-Ladokhina, W.Yang, D.F.Senear, and R.Luo (2009).
Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations.
  Biophys Chem, 145, 37-44.  
18410249 A.C.Joerger, and A.R.Fersht (2008).
Structural biology of the tumor suppressor p53.
  Annu Rev Biochem, 77, 557-582.  
18315848 A.Madhumalar, D.J.Smith, and C.Verma (2008).
Stability of the core domain of p53: insights from computer simulations.
  BMC Bioinformatics, 9, S17.  
18453682 C.Tu, Y.H.Tan, G.Shaw, Z.Zhou, Y.Bai, R.Luo, and X.Ji (2008).
Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 angstroms resolution.
  Acta Crystallogr D Biol Crystallogr, 64, 471-477.
PDB code: 2pcx
18234719 D.B.Veprintsev, and A.R.Fersht (2008).
Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA.
  Nucleic Acids Res, 36, 1589-1598.  
18650397 F.M.Boeckler, A.C.Joerger, G.Jaggi, T.J.Rutherford, D.B.Veprintsev, and A.R.Fersht (2008).
Targeted rescue of a destabilized mutant of p53 by an in silico screened drug.
  Proc Natl Acad Sci U S A, 105, 10360-10365.
PDB code: 2vuk
18195360 J.Liu, and R.Nussinov (2008).
Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design.
  Proc Natl Acad Sci U S A, 105, 901-906.  
18391200 M.Wells, H.Tidow, T.J.Rutherford, P.Markwick, M.R.Jensen, E.Mylonas, D.I.Svergun, M.Blackledge, and A.R.Fersht (2008).
Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain.
  Proc Natl Acad Sci U S A, 105, 5762-5767.  
18812399 S.Rajagopalan, A.M.Jaulent, M.Wells, D.B.Veprintsev, and A.R.Fersht (2008).
14-3-3 activation of DNA binding of p53 by enhancing its association into tetramers.
  Nucleic Acids Res, 36, 5983-5991.  
17401432 A.C.Joerger, and A.R.Fersht (2007).
Structure-function-rescue: the diverse nature of common p53 cancer mutants.
  Oncogene, 26, 2226-2242.  
17401433 G.Selivanova, and K.G.Wiman (2007).
Reactivation of mutant p53: molecular mechanisms and therapeutic potential.
  Oncogene, 26, 2243-2254.  
17620598 H.Tidow, R.Melero, E.Mylonas, S.M.Freund, J.G.Grossmann, J.M.Carazo, D.I.Svergun, M.Valle, and A.R.Fersht (2007).
Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex.
  Proc Natl Acad Sci U S A, 104, 12324-12329.  
17441504 K.N.Parent, and C.M.Teschke (2007).
GroEL/S substrate specificity based on substrate unfolding propensity.
  Cell Stress Chaperones, 12, 20-32.  
17151123 R.Mateo, and M.G.Mateu (2007).
Deterministic, compensatory mutational events in the capsid of foot-and-mouth disease virus in response to the introduction of mutations found in viruses from persistent infections.
  J Virol, 81, 1879-1887.  
17327663 Y.Wang, A.Rosengarth, and H.Luecke (2007).
Structure of the human p53 core domain in the absence of DNA.
  Acta Crystallogr D Biol Crystallogr, 63, 276-281.
PDB code: 2ocj
17015838 A.C.Joerger, H.C.Ang, and A.R.Fersht (2006).
Structural basis for understanding oncogenic p53 mutations and designing rescue drugs.
  Proc Natl Acad Sci U S A, 103, 15056-15061.
PDB codes: 2j1w 2j1x 2j1y 2j1z 2j20 2j21
16461914 D.B.Veprintsev, S.M.Freund, A.Andreeva, S.E.Rutledge, H.Tidow, J.M.Cañadillas, C.M.Blair, and A.R.Fersht (2006).
Core domain interactions in full-length p53 in solution.
  Proc Natl Acad Sci U S A, 103, 2115-2119.  
16395672 E.Mathe, M.Olivier, S.Kato, C.Ishioka, I.Vaisman, and P.Hainaut (2006).
Predicting the transactivation activity of p53 missense mutants using a four-body potential score derived from Delaunay tessellations.
  Hum Mutat, 27, 163-172.  
16432196 G.W.Yu, S.Rudiger, D.Veprintsev, S.Freund, M.R.Fernandez-Fernandez, and A.R.Fersht (2006).
The central region of HDM2 provides a second binding site for p53.
  Proc Natl Acad Sci U S A, 103, 1227-1232.  
20141510 J.Deng, R.Dayam, and N.Neamati (2006).
Patented small molecule inhibitors of p53-MDM2 interaction.
  Expert Opin Ther Pat, 16, 165-188.  
16461916 J.M.Cañadillas, H.Tidow, S.M.Freund, T.J.Rutherford, H.C.Ang, and A.R.Fersht (2006).
Solution structure of p53 core domain: structural basis for its instability.
  Proc Natl Acad Sci U S A, 103, 2109-2114.
PDB code: 2fej
16983711 L.Römer, C.Klein, A.Dehner, H.Kessler, and J.Buchner (2006).
p53--a natural cancer killer: structural insights and therapeutic concepts.
  Angew Chem Int Ed Engl, 45, 6440-6460.  
17139084 W.C.Ho, C.Luo, K.Zhao, X.Chai, M.X.Fitzgerald, and R.Marmorstein (2006).
High-resolution structure of the p53 core domain: implications for binding small-molecule stabilizing compounds.
  Acta Crystallogr D Biol Crystallogr, 62, 1484-1493.
PDB codes: 2ioi 2iom 2ioo
17156454 Y.Taniguchi, S.Takeda, M.Furutani-Seiki, Y.Kamei, T.Todo, T.Sasado, T.Deguchi, H.Kondoh, J.Mudde, M.Yamazoe, M.Hidaka, H.Mitani, A.Toyoda, Y.Sakaki, R.H.Plasterk, and E.Cuppen (2006).
Generation of medaka gene knockout models by target-selected mutagenesis.
  Genome Biol, 7, R116.  
16218947 A.K.Dunker, M.S.Cortese, P.Romero, L.M.Iakoucheva, and V.N.Uversky (2005).
Flexible nets. The roles of intrinsic disorder in protein interaction networks.
  FEBS J, 272, 5129-5148.  
15738397 B.Ma, Y.Pan, K.Gunasekaran, R.B.Venkataraghavan, A.J.Levine, and R.Nussinov (2005).
Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface.
  Proc Natl Acad Sci U S A, 102, 3988-3993.  
15929994 N.Sánchez-Puig, D.B.Veprintsev, and A.R.Fersht (2005).
Human full-length Securin is a natively unfolded protein.
  Protein Sci, 14, 1410-1418.  
15629713 N.Sánchez-Puig, D.B.Veprintsev, and A.R.Fersht (2005).
Binding of natively unfolded HIF-1alpha ODD domain to p53.
  Mol Cell, 17, 11-21.  
15037740 T.E.Baroni, T.Wang, H.Qian, L.R.Dearth, L.N.Truong, J.Zeng, A.E.Denes, S.W.Chen, and R.K.Brachmann (2004).
A global suppressor motif for p53 cancer mutants.
  Proc Natl Acad Sci U S A, 101, 4930-4935.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.