Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA

Roberto Melero, Sridharan Rajagopalan, Melisa Lázaro, Andreas C. Joerger, Tobias Brandt, Dmitry B. Veprintsev, Gorka Lasso, David Gil, Sjors H.W. Scheres, José María Carazo, Alan R. Fersht, Mikel Valle

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

The multidomain homotetrameric tumor suppressor p53 has two modes of binding dsDNA that are thought to be responsible for scanning and recognizing specific response elements (REs). The C termini bind nonspecifically to dsDNA. The four DNA-binding domains (DBDs) bind REs that have two symmetric 10 base-pair sequences. p53 bound to a 20-bp RE has the DBDs enveloping the DNA, which is in the center of the molecule surrounded by linker sequences to the tetramerization domain (Tet). We investigated by electron microscopy structures of p53 bound to DNA sequences consisting of a 20-bp RE with either 12 or 20 bp nonspecific extensions on either end. We found a variety of structures that give clues to recognition and scanning mechanisms. The 44- and 60-bp sequences gave rise to three and four classes of structures, respectively. One was similar to the known 20-bp structure, but the DBDs in the other classes were loosely arranged and incompatible with specific DNA recognition. Some of the complexes had density consistent with the C termini extending from Tet to the DNA, adjacent to the DBDs. Single-molecule fluorescence resonance energy transfer experiments detected the approach of the C termini towards the DBDs on addition of DNA. The structural data are consistent with p53 sliding along DNA via its C termini and the DNA-binding domains hopping on and off during searches for REs. The loose structures and posttranslational modifications account for the affinity of nonspecific DNA for p53 and point to a mechanism of enhancement of specificity by its binding to effector proteins.

Original languageEnglish (US)
Pages (from-to)458-462
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume108
Issue number2
DOIs
StatePublished - Jan 11 2011
Externally publishedYes

Fingerprint

Electron Microscopy
DNA
Response Elements
Fluorescence Resonance Energy Transfer
Post Translational Protein Processing
Base Pairing

Keywords

  • Protein
  • Recognition
  • Specificity

ASJC Scopus subject areas

  • General

Cite this

Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA. / Melero, Roberto; Rajagopalan, Sridharan; Lázaro, Melisa; Joerger, Andreas C.; Brandt, Tobias; Veprintsev, Dmitry B.; Lasso, Gorka; Gil, David; Scheres, Sjors H.W.; Carazo, José María; Fersht, Alan R.; Valle, Mikel.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 108, No. 2, 11.01.2011, p. 458-462.

Research output: Contribution to journalArticle

Melero, R, Rajagopalan, S, Lázaro, M, Joerger, AC, Brandt, T, Veprintsev, DB, Lasso, G, Gil, D, Scheres, SHW, Carazo, JM, Fersht, AR & Valle, M 2011, 'Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA', Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 2, pp. 458-462. https://doi.org/10.1073/pnas.1012231108
Melero, Roberto ; Rajagopalan, Sridharan ; Lázaro, Melisa ; Joerger, Andreas C. ; Brandt, Tobias ; Veprintsev, Dmitry B. ; Lasso, Gorka ; Gil, David ; Scheres, Sjors H.W. ; Carazo, José María ; Fersht, Alan R. ; Valle, Mikel. / Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA. In: Proceedings of the National Academy of Sciences of the United States of America. 2011 ; Vol. 108, No. 2. pp. 458-462.
@article{1d51115b66fc4ff4ac98c0c38b5bac50,
title = "Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA",
abstract = "The multidomain homotetrameric tumor suppressor p53 has two modes of binding dsDNA that are thought to be responsible for scanning and recognizing specific response elements (REs). The C termini bind nonspecifically to dsDNA. The four DNA-binding domains (DBDs) bind REs that have two symmetric 10 base-pair sequences. p53 bound to a 20-bp RE has the DBDs enveloping the DNA, which is in the center of the molecule surrounded by linker sequences to the tetramerization domain (Tet). We investigated by electron microscopy structures of p53 bound to DNA sequences consisting of a 20-bp RE with either 12 or 20 bp nonspecific extensions on either end. We found a variety of structures that give clues to recognition and scanning mechanisms. The 44- and 60-bp sequences gave rise to three and four classes of structures, respectively. One was similar to the known 20-bp structure, but the DBDs in the other classes were loosely arranged and incompatible with specific DNA recognition. Some of the complexes had density consistent with the C termini extending from Tet to the DNA, adjacent to the DBDs. Single-molecule fluorescence resonance energy transfer experiments detected the approach of the C termini towards the DBDs on addition of DNA. The structural data are consistent with p53 sliding along DNA via its C termini and the DNA-binding domains hopping on and off during searches for REs. The loose structures and posttranslational modifications account for the affinity of nonspecific DNA for p53 and point to a mechanism of enhancement of specificity by its binding to effector proteins.",
keywords = "Protein, Recognition, Specificity",
author = "Roberto Melero and Sridharan Rajagopalan and Melisa L{\'a}zaro and Joerger, {Andreas C.} and Tobias Brandt and Veprintsev, {Dmitry B.} and Gorka Lasso and David Gil and Scheres, {Sjors H.W.} and Carazo, {Jos{\'e} Mar{\'i}a} and Fersht, {Alan R.} and Mikel Valle",
year = "2011",
month = "1",
day = "11",
doi = "10.1073/pnas.1012231108",
language = "English (US)",
volume = "108",
pages = "458--462",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "2",

}

TY - JOUR

T1 - Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA

AU - Melero, Roberto

AU - Rajagopalan, Sridharan

AU - Lázaro, Melisa

AU - Joerger, Andreas C.

AU - Brandt, Tobias

AU - Veprintsev, Dmitry B.

AU - Lasso, Gorka

AU - Gil, David

AU - Scheres, Sjors H.W.

AU - Carazo, José María

AU - Fersht, Alan R.

AU - Valle, Mikel

PY - 2011/1/11

Y1 - 2011/1/11

N2 - The multidomain homotetrameric tumor suppressor p53 has two modes of binding dsDNA that are thought to be responsible for scanning and recognizing specific response elements (REs). The C termini bind nonspecifically to dsDNA. The four DNA-binding domains (DBDs) bind REs that have two symmetric 10 base-pair sequences. p53 bound to a 20-bp RE has the DBDs enveloping the DNA, which is in the center of the molecule surrounded by linker sequences to the tetramerization domain (Tet). We investigated by electron microscopy structures of p53 bound to DNA sequences consisting of a 20-bp RE with either 12 or 20 bp nonspecific extensions on either end. We found a variety of structures that give clues to recognition and scanning mechanisms. The 44- and 60-bp sequences gave rise to three and four classes of structures, respectively. One was similar to the known 20-bp structure, but the DBDs in the other classes were loosely arranged and incompatible with specific DNA recognition. Some of the complexes had density consistent with the C termini extending from Tet to the DNA, adjacent to the DBDs. Single-molecule fluorescence resonance energy transfer experiments detected the approach of the C termini towards the DBDs on addition of DNA. The structural data are consistent with p53 sliding along DNA via its C termini and the DNA-binding domains hopping on and off during searches for REs. The loose structures and posttranslational modifications account for the affinity of nonspecific DNA for p53 and point to a mechanism of enhancement of specificity by its binding to effector proteins.

AB - The multidomain homotetrameric tumor suppressor p53 has two modes of binding dsDNA that are thought to be responsible for scanning and recognizing specific response elements (REs). The C termini bind nonspecifically to dsDNA. The four DNA-binding domains (DBDs) bind REs that have two symmetric 10 base-pair sequences. p53 bound to a 20-bp RE has the DBDs enveloping the DNA, which is in the center of the molecule surrounded by linker sequences to the tetramerization domain (Tet). We investigated by electron microscopy structures of p53 bound to DNA sequences consisting of a 20-bp RE with either 12 or 20 bp nonspecific extensions on either end. We found a variety of structures that give clues to recognition and scanning mechanisms. The 44- and 60-bp sequences gave rise to three and four classes of structures, respectively. One was similar to the known 20-bp structure, but the DBDs in the other classes were loosely arranged and incompatible with specific DNA recognition. Some of the complexes had density consistent with the C termini extending from Tet to the DNA, adjacent to the DBDs. Single-molecule fluorescence resonance energy transfer experiments detected the approach of the C termini towards the DBDs on addition of DNA. The structural data are consistent with p53 sliding along DNA via its C termini and the DNA-binding domains hopping on and off during searches for REs. The loose structures and posttranslational modifications account for the affinity of nonspecific DNA for p53 and point to a mechanism of enhancement of specificity by its binding to effector proteins.

KW - Protein

KW - Recognition

KW - Specificity

UR - http://www.scopus.com/inward/record.url?scp=79551670110&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79551670110&partnerID=8YFLogxK

U2 - 10.1073/pnas.1012231108

DO - 10.1073/pnas.1012231108

M3 - Article

C2 - 21178074

AN - SCOPUS:79551670110

VL - 108

SP - 458

EP - 462

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 2

ER -