PDBsum entry 2bim

DNA binding protein

PDB id: 2bim

Contents

Protein chains

195 a.a.

Ligands

SO4 ×2

Metals

_ZN ×2

Waters ×386

References listed in PDB file

Key reference

Title

Structures of p53 cancer mutants and mechanism of rescue by second-Site suppressor mutations.

Authors

A.C.Joerger, H.C.Ang, D.B.Veprintsev, C.M.Blair, A.R.Fersht.

Ref.

J Biol Chem, 2005, 280, 16030-16037. [DOI no: 10.1074/jbc.M500179200]

PubMed id

15703170

Abstract

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.

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.

Secondary reference #1

Title

Crystal structure of a superstable mutant of human p53 core domain. Insights into the mechanism of rescuing oncogenic mutations.

Authors

A.C.Joerger, M.D.Allen, A.R.Fersht.

Ref.

J Biol Chem, 2004, 279, 1291-1296. [DOI no: 10.1074/jbc.M309732200]

PubMed id

14534297

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 reproduced from the cited reference with permission from the ASBMB

Secondary reference #2

Title

Crystal structure of a p53 tumor suppressor-Dna complex: understanding tumorigenic mutations.

Authors

Y.Cho, S.Gorina, P.D.Jeffrey, N.P.Pavletich.

Ref.

Science, 1994, 265, 346-355. [DOI no: 10.1126/science.8023157]

PubMed id

8023157