Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion

The p53 core domain binds to response elements (REs) that contain two continuous half-sites as a cooperative tetramer, but how p53 recognizes discontinuous REs is not well understood. Here we describe the crystal structure of the p53 core domain bound to a naturally occurring RE located at the promoter of the Bcl-2-associated X protein (BAX) gene, which contains a one base-pair insertion between the two half-sites. Surprisingly, p53 forms a tetramer on the BAX-RE that is nearly identical to what has been reported on other REs with a 0-bp spacer. Each p53 dimer of the tetramer binds in register to a half-site and maintains the same protein–DNA interactions as previously observed, and the two dimers retain all the protein–protein contacts without undergoing rotation or translation. To accommodate the additional base pair, the DNA is deformed and partially disordered around the spacer region, resulting in an apparent unwinding and compression, such that the interactions between the dimers are maintained. Furthermore, DNA deformation within the p53-bound BAX-RE is confirmed in solution by site-directed spin labeling measurements. Our results provide a structural insight into the mechanism by which p53 binds to discontinuous sites with one base-pair spacer.

[1]  P. Qin,et al.  Site-directed spin labeling studies on nucleic acid structure and dynamics. , 2008, Progress in nucleic acid research and molecular biology.

[2]  J. Levine,et al.  Surfing the p53 network , 2000, Nature.

[3]  M. Kimmel,et al.  Conflict of interest statement. None declared. , 2010 .

[4]  P. Fajer,et al.  Practical Pulsed Dipolar ESR (DEER) , 2007 .

[5]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[6]  B. Honig,et al.  Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs , 2010, Nature Structural &Molecular Biology.

[7]  Ian S Haworth,et al.  Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe , 2007, Nature Protocols.

[8]  M. Kitayner,et al.  Structural basis of DNA recognition by p53 tetramers. , 2006, Molecular cell.

[9]  R. Lavery,et al.  Defining the structure of irregular nucleic acids: conventions and principles. , 1989, Journal of biomolecular structure & dynamics.

[10]  Yongheng Chen,et al.  Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer. , 2010, Structure.

[11]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[12]  H. Zimmermann,et al.  DeerAnalysis2006—a comprehensive software package for analyzing pulsed ELDOR data , 2006 .

[13]  H. Stunnenberg,et al.  Characterization of genome-wide p53-binding sites upon stress response , 2008, Nucleic acids research.

[14]  P. Jeffrey,et al.  Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. , 1994, Science.

[15]  K. Vousden,et al.  Coping with stress: multiple ways to activate p53 , 2007, Oncogene.

[16]  Z. Weng,et al.  A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome , 2006, Cell.

[17]  C. Prives,et al.  Transcriptional regulation by p53. , 2010, Cold Spring Harbor perspectives in biology.

[18]  J. Shay,et al.  A transcriptionally active DNA-binding site for human p53 protein complexes , 1992, Molecular and cellular biology.

[19]  Ronen Marmorstein,et al.  Structure of the p53 Core Domain Dimer Bound to DNA*♦ , 2006, Journal of Biological Chemistry.

[20]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[21]  A. Inga,et al.  Structure of p73 DNA-binding domain tetramer modulates p73 transactivation , 2012, Proceedings of the National Academy of Sciences.

[22]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[23]  A. Fersht,et al.  Structural biology of the tumor suppressor p53. , 2008, Annual review of biochemistry.

[24]  Z. Kelman,et al.  Structures of p63 DNA binding domain in complexes with half-site and with spacer-containing full response elements , 2011, Proceedings of the National Academy of Sciences.

[25]  S. Emamzadah,et al.  Crystal Structure of a Multidomain Human p53 Tetramer Bound to the Natural CDKN1A (p21) p53-Response Element , 2011, Molecular Cancer Research.

[26]  Eduardo Sontag,et al.  Transcriptional control of human p53-regulated genes , 2008, Nature Reviews Molecular Cell Biology.

[27]  J. Stroud,et al.  Structure of NFAT1 bound as a dimer to the HIV-1 LTR kappa B element. , 2003, Nature structural biology.

[28]  Jeffrey A. Lefstin,et al.  Allosteric effects of DNA on transcriptional regulators , 1998, Nature.

[29]  David Baltimore,et al.  One Nucleotide in a κB Site Can Determine Cofactor Specificity for NF-κB Dimers , 2004, Cell.

[30]  K. Kinzler,et al.  Definition of a consensus binding site for p53 , 1992, Nature Genetics.

[31]  A. Fersht,et al.  Comparative binding of p53 to its promoter and DNA recognition elements. , 2005, Journal of molecular biology.

[32]  Ruth Nussinov,et al.  Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View , 2009, PLoS Comput. Biol..

[33]  K. Yamamoto,et al.  Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA , 2003, Nature.

[34]  S. Harrison,et al.  Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA , 1998, Nature.

[35]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination , 2022 .

[36]  C. Tung,et al.  Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling. , 2012, Journal of the American Chemical Society.

[37]  Thomas J Petty,et al.  An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity , 2011, The EMBO journal.

[38]  L. Berliner,et al.  ESR Spectroscopy in Membrane Biophysics , 2007 .

[39]  K. Yamamoto,et al.  DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity , 2009, Science.

[40]  A. Levine,et al.  Surfing the p53 network , 2000, Nature.

[41]  G. Jeschke,et al.  Dead-time free measurement of dipole-dipole interactions between electron spins. , 2000, Journal of magnetic resonance.

[42]  C. Prives,et al.  Transcriptional regulation by p53: one protein, many possibilities , 2006, Cell Death and Differentiation.

[43]  K. Malecka,et al.  Crystal Structure of a p53 Core Tetramer Bound to DNA , 2008, Oncogene.

[44]  K. Hideg,et al.  Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe , 2006, Nucleic acids research.

[45]  H. Khorana,et al.  Structural studies on transmembrane proteins. 2. Spin labeling of bacteriorhodopsin mutants at unique cysteines. , 1989, Biochemistry.

[46]  C. Prives,et al.  Blinded by the Light: The Growing Complexity of p53 , 2009, Cell.