Summary
PDB 2J20 deposited: 2006-08-15 modified: 2009-02-24
Title HUMAN P53 CORE DOMAIN MUTANT M133L-V203A-N239Y-N268D-R273C
Authors Ang, H.C., Fersht, A.R., Joerger, A.C.
Method X-RAY DIFFRACTION
Structure factors resolution 1.8 rfactor 0.188 rfree 0.206
DPI 0.28 theoretical min: 0.13
Related PDB Entries 1UOL 2BIM 2BIN 2BIO 2BIP 2BIQ 2J1W 2J1X 2J1Y 2J1Z 2J21 2VUK 2WGX 2X0U 2X0V 2X0W 3ZME 4AGL 4AGM 4AGN 4AGO 4AGP 4AGQ
Citations

The DNA-binding domain of the tumor suppressor p53 is inactivated by mutation in approximately 50% of human cancers. We have solved high-resolution crystal structures of several oncogenic mutants to investigate the structural basis of inactivation and provide information for designing drugs that may rescue inactivated mutants. We found a variety of structural consequences upon mutation: (i) the removal of an essential contact with DNA, (ii) creation of large, water-accessible crevices or hydrophobic internal cavities with no other structural changes but with a large loss of thermodynamic stability, (iii) distortion of the DNA-binding surface, and (iv) alterations to surfaces not directly involved in DNA binding but involved in domain-domain interactions on binding as a tetramer. These findings explain differences in functional properties and associated phenotypes (e.g., temperature sensitivity). Some mutants have the potential of being rescued by a generic stabilizing drug. In addition, a mutation-induced crevice is a potential target site for a mutant-selective stabilizing drug.

Proc.Natl.Acad.Sci.USA 2006 Oct; 103(41):15056- doi:10.1073/PNAS.0607286103

"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."

J.Biol.Chem. 2005 Apr; 280(16):16030- doi:10.1074/JBC.M500179200

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.

J.Biol.Chem. 2004 Jan; 279(2):1291- doi:10.1074/JBC.M309732200

Cross References
Database source Identifier Description
PubMed 17015838 PNASA6
PubMed 15703170 JBCHA3
PubMed 14534297 JBCHA3
Biomolecule Structure Assembly Serial Assembly Type Conformational State Chains Ligands Atoms
2J20/1 2J20 1 monomer 0 1 2 1591
2J20/2 2J20 2 monomer 0 1 2 1625