1ga5 Citations

DNA deformability as a recognition feature in the reverb response element.

Biochemistry 40 12833-43 (2001)
Cited: 26 times
EuropePMC logo PMID: 11669620

Abstract

Most nuclear receptors recognize the same consensus hexameric sequence, AGGTCA. An important question has been how the various members of this transcription factor family distinguish identity features in these closely related DNA sites. We determined structures from several crystal forms of the RevErb-DNA complex and analyzed the patterns of protein-DNA interactions and DNA distortions. We found a significant and consistent DNA distortion at a TA step directly preceding the first consensus 5'-AGGTCA-3' recognition sequence. Importantly, while this base-pair sequence is associated with RevErb's high-affinity sites, there are no sequence-specific contacts formed with the protein. Our study shows that RevErb relies instead on the intrinsic geometry and flexibility of this TA site to make the required fit between the proteins' independent major groove and minor groove binding interactions, which occur on both sides of the TA step. Our findings extend the description of response element discrimination to include a role for sequence-dependent DNA deformations and suggest how other monomeric members of this superfamily, such as NGFI-B, SF-1, and ROR, could also recognize unique geometric features in their DNA targets.

Articles - 1ga5 mentioned but not cited (4)

  1. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. F1000Res 2 286 (2013)
  2. Structural overview and perspectives of the nuclear receptors, a major family as the direct targets for small-molecule drugs. Li F, Song C, Zhang Y, Wu D. Acta Biochim Biophys Sin (Shanghai) 54 12-24 (2022)
  3. research-article Identifying Human Specific Adverse Outcome Pathways of Per- and Polyfluoroalkyl Substances Using Liver-Chimeric Humanized Mice. Robarts DR, Paine-Cabrera D, Kotulkar M, Venneman KK, Gunewardena S, Corton JC, Lau C, Foquet L, Bial G, Apte U. bioRxiv 2023.02.01.526711 (2023)
  4. Structural basis of the farnesoid X receptor/retinoid X receptor heterodimer on inverted repeat DNA. Jiang L, Liu X, Liang X, Dai S, Wei H, Guo M, Chen Z, Xiao D, Chen Y. Comput Struct Biotechnol J 21 3149-3157 (2023)


Reviews citing this publication (9)

  1. Origins of specificity in protein-DNA recognition. Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. Annu Rev Biochem 79 233-269 (2010)
  2. Understanding nuclear receptor form and function using structural biology. Rastinejad F, Huang P, Chandra V, Khorasanizadeh S. J Mol Endocrinol 51 T1-T21 (2013)
  3. Retinoic acid actions through mammalian nuclear receptors. Huang P, Chandra V, Rastinejad F. Chem Rev 114 233-254 (2014)
  4. General molecular biology and architecture of nuclear receptors. Pawlak M, Lefebvre P, Staels B. Curr Top Med Chem 12 486-504 (2012)
  5. The role of SF1 in adrenal and reproductive function: insight from naturally occurring mutations in humans. Ozisik G, Achermann JC, Jameson JL. Mol Genet Metab 76 85-91 (2002)
  6. Modulation of nuclear receptor function by cellular redox poise. Carter EL, Ragsdale SW. J Inorg Biochem 133 92-103 (2014)
  7. Motif grammar: The basis of the language of gene expression. Nagy G, Nagy L. Comput Struct Biotechnol J 18 2026-2032 (2020)
  8. Pathogenic mechanism and modeling of neuroferritinopathy. Cozzi A, Santambrogio P, Ripamonti M, Rovida E, Levi S. Cell Mol Life Sci 78 3355-3367 (2021)
  9. The protein architecture and allosteric landscape of HNF4α. Rastinejad F. Front Endocrinol (Lausanne) 14 1219092 (2023)

Articles citing this publication (13)

  1. Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA. Chandra V, Huang P, Hamuro Y, Raghuram S, Wang Y, Burris TP, Rastinejad F. Nature 456 350-356 (2008)
  2. Structure of the heterodimeric ecdysone receptor DNA-binding complex. Devarakonda S, Harp JM, Kim Y, Ozyhar A, Rastinejad F. EMBO J 22 5827-5840 (2003)
  3. Identification of pregnane X receptor binding sites in the regulatory regions of genes involved in bile acid homeostasis. Frank C, Makkonen H, Dunlop TW, Matilainen M, Väisänen S, Carlberg C. J Mol Biol 346 505-519 (2005)
  4. Nucleosome positioning determinants. Fernandez AG, Anderson JN. J Mol Biol 371 649-668 (2007)
  5. Predicting specificity-determining residues in two large eukaryotic transcription factor families. Donald JE, Shakhnovich EI. Nucleic Acids Res 33 4455-4465 (2005)
  6. Statistical and conformational analysis of the electron density of protein side chains. Shapovalov MV, Dunbrack RL. Proteins 66 279-303 (2007)
  7. Minimal Purkinje Cell-Specific PCP2/L7 Promoter Virally Available for Rodents and Non-human Primates. Nitta K, Matsuzaki Y, Konno A, Hirai H. Mol Ther Methods Clin Dev 6 159-170 (2017)
  8. Daily rhythms in expression of genes of hepatic lipid metabolism in Atlantic salmon (Salmo salar L.). Betancor MB, McStay E, Minghetti M, Migaud H, Tocher DR, Davie A. PLoS One 9 e106739 (2014)
  9. Benchmarks for flexible and rigid transcription factor-DNA docking. Kim R, Corona RI, Hong B, Guo JT. BMC Struct Biol 11 45 (2011)
  10. RevErbα preferentially deforms DNA by induced fit. Chung YH, van der Vaart A. Chembiochem 15 643-646 (2014)
  11. DNA deformability changes of single base pair mutants within CDE binding sites in S. Cerevisiae centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries. Hennemuth B, Marx KA. BMC Mol Biol 7 12 (2006)
  12. Hidden modes of DNA binding by human nuclear receptors. Bhimsaria D, Rodríguez-Martínez JA, Mendez-Johnson JL, Ghoshdastidar D, Varadarajan A, Bansal M, Daniels DL, Ramanathan P, Ansari AZ. Nat Commun 14 4179 (2023)
  13. Asymmetric dimerization in a transcription factor superfamily is promoted by allosteric interactions with DNA. Patel AKM, Vilela P, Shaik TB, McEwen AG, Hazemann I, Brillet K, Ennifar E, Hamiche A, Markov GV, Laudet V, Moras D, Klaholz BP, Billas IML. Nucleic Acids Res 51 8864-8879 (2023)


Related citations provided by authors (1)

  1. Structural Elements of an Orphan Nuclear Receptor-DNA Complex. Zhao Q, Khorasanizadeh S, Miyoshi Y, Lazar M, Rastinejad F Mol. Cell 1 849-861 (1998)