PDBsum entry 2bio

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protein metals links
DNA-binding protein PDB id
Jmol PyMol
Protein chain
186 a.a. *
Waters ×89
* Residue conservation analysis
PDB id:
Name: DNA-binding protein
Title: Human p53 core domain mutant m133l-v203a-n239y-r249s-n268d
Structure: Cellular tumor antigen p53. Chain: a. Fragment: DNA-binding (core) domain, residues 94-312. Synonym: tumour 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:   0.210     R-free:   0.234
Authors: A.C.Joerger,A.R.Fersht
Key ref:
A.C.Joerger et al. (2005). Structures of p53 cancer mutants and mechanism of rescue by second-site suppressor mutations. J Biol Chem, 280, 16030-16037. PubMed id: 15703170 DOI: 10.1074/jbc.M500179200
25-Jan-05     Release date:   26-Jan-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P04637  (P53_HUMAN) -  Cellular tumor antigen p53
393 a.a.
186 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 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.M500179200 J Biol Chem 280:16030-16037 (2005)
PubMed id: 15703170  
Structures of p53 cancer mutants and mechanism of rescue by second-site suppressor mutations.
A.C.Joerger, H.C.Ang, D.B.Veprintsev, C.M.Blair, A.R.Fersht.
We have solved the crystal structures of three oncogenic mutants of the core domain of the human tumor suppressor p53. The mutations were introduced into a stabilized variant. The cancer hot spot mutation R273H simply removes an arginine involved in DNA binding without causing structural distortions in neighboring residues. In contrast, the "structural" oncogenic mutations H168R and R249S induce substantial structural perturbation around the mutation site in the L2 and L3 loops, respectively. H168R is a specific intragenic suppressor mutation for R249S. When both cancer mutations are combined in the same molecule, Arg(168) mimics the role of Arg(249) in wild type, and the wild type conformation is largely restored in both loops. Our structural and biophysical data provide compelling evidence for the mechanism of rescue of mutant p53 by intragenic suppressor mutations and reveal features by which proteins can adapt to deleterious mutations.
  Selected figure(s)  
Figure 1.
FIG. 1. Structure of human p53 core domain. A, ribbon diagram of the structure of the DNA binding (core) domain in complex with consensus DNA (PDB code 1TSR [PDB] , molecule B). A -sandwich provides the basic scaffold for a loop-sheet-helix motif and two large loops tethered by a zinc ion, which interact with the major and minor groove of the DNA, respectively. The zinc ion is shown as a gray sphere, and the two DNA strands are in magenta and blue. For selected residues the side chains are shown. Among these are the six hot spot sites Arg^175, Gly^245, Arg^248, Arg^249, Arg^273, and Arg^282, which are most frequently mutated in human cancers (colored in orange). The four mutation sites in the superstable quadruple mutant M133L/V203A/N239Y/N268D (T-p53C) are highlighted as green spheres. B, close-up view of loops L2 and L3 in the DNA binding surface including the zinc coordination sphere in the structure of wild type in complex with consensus DNA (PDB code 1TSR [PDB] , molecule B). The orientation is different from the one shown for the whole molecule in A. The zinc ion is depicted as a gray sphere. Specific interactions mediated via the guanidinium group of Arg^249 are highlighted with dotted lines. These include hydrogen bonds with backbone oxygens of residues Gly^245 and Met^246 on the same loop and a salt bridge with Glu^171 on the L2 loop. DNA contacts are made via Arg^248. Selected DNA residues in the proximity of Arg^248 are shown in magenta and cyan.
Figure 3.
FIG. 3. Structure of T-p53C mutants H168R and R249S. A, superposition of C atoms in the structures of T-p53C-H168R (magenta) and T-p53C-R249S (yellow) on the structure of T-p53C (PDB code 1UOL [PDB] , molecule A; black). C atoms before and after chain breaks are marked with spheres in the color of the respective chain. B, structure of T-p53-R249S (yellow) superimposed on the structure of p53 wild type (PDB code 1TSR [PDB] , molecule A; light gray). The zinc ion in both structures is shown as a gray or yellow sphere. * denotes wild type residues. Cys^238 in the structure of T-p53C-R249S was refined in two alternative conformations, both contacting the zinc ion. Only the conformation that was refined with higher occupancy (0.7) is shown. C, stereo view of the final (2F[o] – F[c]) electron density map at 1.9 Å resolution for mutant T-p53C-R249S showing the peptide segment Cys^242-Met^243, the zinc ion, and two residues that make contact with Met^243. The orientation is the same as in B. The contour level is at 1.2 .
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 16030-16037) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  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.  
20100603 B.Xue, R.L.Dunbrack, R.W.Williams, A.K.Dunker, and V.N.Uversky (2010).
PONDR-FIT: a meta-predictor of intrinsically disordered amino acids.
  Biochim Biophys Acta, 1804, 996.  
20407015 J.J.Jordan, A.Inga, K.Conway, S.Edmiston, L.A.Carey, L.Wu, and M.A.Resnick (2010).
Altered-function p53 missense mutations identified in breast cancers can have subtle effects on transactivation.
  Mol Cancer Res, 8, 701-716.  
  20182602 M.Olivier, M.Hollstein, and P.Hainaut (2010).
TP53 mutations in human cancers: origins, consequences, and clinical use.
  Cold Spring Harb Perspect Biol, 2, a001008.  
20581117 R.Baronio, S.A.Danziger, L.V.Hall, K.Salmon, G.W.Hatfield, R.H.Lathrop, and P.Kaiser (2010).
All-codon scanning identifies p53 cancer rescue mutations.
  Nucleic Acids Res, 38, 7079-7088.  
20589832 R.E.Perez, C.D.Knights, G.Sahu, J.Catania, V.K.Kolukula, D.Stoler, A.Graessmann, V.Ogryzko, M.Pishvaian, C.Albanese, and M.L.Avantaggiati (2010).
Restoration of DNA-binding and growth-suppressive activity of mutant forms of p53 via a PCAF-mediated acetylation pathway.
  J Cell Physiol, 225, 394-405.  
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.  
19411067 J.M.Lambert, P.Gorzov, D.B.Veprintsev, M.Söderqvist, D.Segerbäck, J.Bergman, A.R.Fersht, P.Hainaut, K.G.Wiman, and V.J.Bykov (2009).
PRIMA-1 reactivates mutant p53 by covalent binding to the core domain.
  Cancer Cell, 15, 376-388.  
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
19139068 M.Brázdová, T.Quante, L.Tögel, K.Walter, C.Loscher, V.Tichý, L.Cincárová, W.Deppert, and G.V.Tolstonog (2009).
Modulation of gene expression in U251 glioblastoma cells by binding of mutant p53 R273H to intronic and intergenic sequences.
  Nucleic Acids Res, 37, 1486-1500.  
19756158 S.A.Danziger, R.Baronio, L.Ho, L.Hall, K.Salmon, G.W.Hatfield, P.Kaiser, and R.H.Lathrop (2009).
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.
  PLoS Comput Biol, 5, e1000498.  
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.  
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
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
18621913 M.M.García-Alai, H.Tidow, E.Natan, F.M.Townsley, D.B.Veprintsev, and A.R.Fersht (2008).
The novel p53 isoform "delta p53" is a misfolded protein and does not bind the p21 promoter site.
  Protein Sci, 17, 1671-1678.  
18654622 T.M.Cheng, Y.E.Lu, M.Vendruscolo, P.Lio', and T.L.Blundell (2008).
Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.
  PLoS Comput Biol, 4, e1000135.  
17401432 A.C.Joerger, and A.R.Fersht (2007).
Structure-function-rescue: the diverse nature of common p53 cancer mutants.
  Oncogene, 26, 2226-2242.  
17986463 B.Ma, and A.J.Levine (2007).
Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements.
  Nucleic Acids Res, 35, 7733-7747.  
17401433 G.Selivanova, and K.G.Wiman (2007).
Reactivation of mutant p53: molecular mechanisms and therapeutic potential.
  Oncogene, 26, 2243-2254.  
17391014 H.Xie, S.Vucetic, L.M.Iakoucheva, C.J.Oldfield, A.K.Dunker, V.N.Uversky, and Z.Obradovic (2007).
Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions.
  J Proteome Res, 6, 1882-1898.  
17914225 J.D.Wright, and C.Lim (2007).
Mechanism of DNA-binding loss upon single-point mutation in p53.
  J Biosci, 32, 827-839.  
17417775 K.Otsuka, S.Kato, Y.Kakudo, S.Mashiko, H.Shibata, and C.Ishioka (2007).
The screening of the second-site suppressor mutations of the common p53 mutants.
  Int J Cancer, 121, 559-566.  
17401429 L.Weisz, M.Oren, and V.Rotter (2007).
Transcription regulation by mutant p53.
  Oncogene, 26, 2202-2211.  
17091337 M.Pandey, and P.C.Rath (2007).
Organization of the interferon-inducible 2',5'-oligoadenylate-dependent ribonuclease L (RNase L) gene of mouse.
  Mol Biol Rep, 34, 97.  
17824689 Q.Lu, Y.H.Tan, and R.Luo (2007).
Molecular dynamics simulations of p53 DNA-binding domain.
  J Phys Chem B, 111, 11538-11545.  
17974918 T.Okawa, C.Z.Michaylira, J.Kalabis, D.B.Stairs, H.Nakagawa, C.D.Andl, C.N.Johnstone, A.J.Klein-Szanto, W.S.El-Deiry, E.Cukierman, M.Herlyn, and A.K.Rustgi (2007).
The functional interplay between EGFR overexpression, hTERT activation, and p53 mutation in esophageal epithelial cells with activation of stromal fibroblasts induces tumor development, invasion, and differentiation.
  Genes Dev, 21, 2788-2803.  
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.  
16498444 G.Trigiante, and X.Lu (2006).
ASPP [corrected] and cancer.
  Nat Rev Cancer, 6, 217-226.  
16683757 H.Roder, K.Maki, and H.Cheng (2006).
Early events in protein folding explored by rapid mixing methods.
  Chem Rev, 106, 1836-1861.  
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
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 code is shown on the right.