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Two high-mobility group box domains act together to underwind and kink DNA.

Sánchez-Giraldo R, Acosta-Reyes FJ, Malarkey CS, Saperas N, Churchill ME, Campos JL
Acta Crystallogr D Biol Crystallogr 71 1423-32 (2015)
Cited: 26 times
EuropePMC logo PMID: 26143914

Abstract

High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1-DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.

Reviews - 4qr9 mentioned but not cited (1)

  1. Studying protein-DNA interactions using atomic force microscopy. Beckwitt EC, Kong M, Van Houten B. Semin Cell Dev Biol 73 220-230 (2018)

Articles - 4qr9 mentioned but not cited (5)

  1. Citrullination Licenses Calpain to Decondense Nuclei in Neutrophil Extracellular Trap Formation. Gößwein S, Lindemann A, Mahajan A, Maueröder C, Martini E, Patankar J, Schett G, Becker C, Wirtz S, Naumann-Bartsch N, Bianchi ME, Greer PA, Lochnit G, Herrmann M, Neurath MF, Leppkes M. Front Immunol 10 2481 (2019)
  2. Two high-mobility group box domains act together to underwind and kink DNA. Sánchez-Giraldo R, Acosta-Reyes FJ, Malarkey CS, Saperas N, Churchill ME, Campos JL. Acta Crystallogr D Biol Crystallogr 71 1423-1432 (2015)
  3. Insights into telomeric G-quadruplex DNA recognition by HMGB1 protein. Amato J, Cerofolini L, Brancaccio D, Giuntini S, Iaccarino N, Zizza P, Iachettini S, Biroccio A, Novellino E, Rosato A, Fragai M, Luchinat C, Randazzo A, Pagano B. Nucleic Acids Res 47 9950-9966 (2019)
  4. A small molecule binding HMGB1 inhibits caspase-11-mediated lethality in sepsis. Wang X, Li Z, Bai Y, Zhang R, Meng R, Chen F, Wang H, Billiar TR, Xiao X, Lu B, Tang Y. Cell Death Dis 12 402 (2021)
  5. An 8-Hydroxy-Quinoline Derivative Protects Against Lipopolysaccharide-Induced Lethality in Endotoxemia by Inhibiting HMGB1-Mediated Caspase-11 Signaling. Wang X, Shi J, Li Z, Li L, Zhang R, Bai Y, Li J, Liang F, Tang Y. Front Pharmacol 12 673818 (2021)


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  1. Immunological Significance of HMGB1 Post-Translational Modification and Redox Biology. Kwak MS, Kim HS, Lee B, Kim YH, Son M, Shin JS. Front Immunol 11 1189 (2020)
  2. The progression of HMGB1-induced autophagy in cancer biology. Xu T, Jiang L, Wang Z. Onco Targets Ther 12 365-377 (2019)
  3. The self-association of HMGB1 and its possible role in the binding to DNA and cell membrane receptors. Anggayasti WL, Mancera RL, Bottomley S, Helmerhorst E. FEBS Lett 591 282-294 (2017)
  4. Yeast HMO1: Linker Histone Reinvented. Panday A, Grove A. Microbiol Mol Biol Rev 81 e00037-16 (2017)
  5. The role of high mobility group protein B3 (HMGB3) in tumor proliferation and drug resistance. Wen B, Wei YT, Zhao K. Mol Cell Biochem 476 1729-1739 (2021)
  6. The role of high mobility group box 1 protein in acute cerebrovascular diseases. Mu SW, Dang Y, Wang SS, Gu JJ. Biomed Rep 9 191-197 (2018)
  7. Herpesvirus tegument and immediate early proteins are pioneers in the battle between viral infection and nuclear domain 10-related host defense. Zhang K, van Drunen Littel-van den Hurk S. Virus Res 238 40-48 (2017)

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  2. Functional and structural analysis of AT-specific minor groove binders that disrupt DNA-protein interactions and cause disintegration of the Trypanosoma brucei kinetoplast. Millan CR, Acosta-Reyes FJ, Lagartera L, Ebiloma GU, Lemgruber L, Nué Martínez JJ, Saperas N, Dardonville C, de Koning HP, Campos JL. Nucleic Acids Res 45 8378-8391 (2017)
  3. Histone H1 Differentially Inhibits DNA Bending by Reduced and Oxidized HMGB1 Protein. Štros M, Polanská E, Kučírek M, Pospíšilová Š. PLoS One 10 e0138774 (2015)
  4. The HMGB1 C-Terminal Tail Regulates DNA Bending. Blair RH, Horn AE, Pazhani Y, Grado L, Goodrich JA, Kugel JF. J Mol Biol 428 4060-4072 (2016)
  5. Real-time analysis of RAG complex activity in V(D)J recombination. Zagelbaum J, Shimazaki N, Esguerra ZA, Watanabe G, Lieber MR, Rothenberg E. Proc Natl Acad Sci U S A 113 11853-11858 (2016)
  6. The extracellular innate-immune effector HMGB1 limits pathogenic bacterial biofilm proliferation. Devaraj A, Novotny LA, Robledo-Avila FH, Buzzo JR, Mashburn-Warren L, Jurcisek JA, Tjokro NO, Partida-Sanchez S, Bakaletz LO, Goodman SD. J Clin Invest 131 140527 (2021)
  7. Intercalation of small molecules into DNA in chromatin is primarily controlled by superhelical constraint. Bosire R, Nánási P, Imre L, Dienes B, Szöőr Á, Mázló A, Kovács A, Seidel R, Vámosi G, Szabó G. PLoS One 14 e0224936 (2019)
  8. The roles of HMGB1-produced DNA gaps in DNA protection and aging biomarker reversal. Yasom S, Watcharanurak P, Bhummaphan N, Thongsroy J, Puttipanyalears C, Settayanon S, Chalertpet K, Khumsri W, Kongkaew A, Patchsung M, Siriwattanakankul C, Pongpanich M, Pin-On P, Jindatip D, Wanotayan R, Odton M, Supasai S, Oo TT, Arunsak B, Pratchayasakul W, Chattipakorn N, Chattipakorn S, Mutirangura A. FASEB Bioadv 4 408-434 (2022)
  9. Discovery of 5,5'-Methylenedi-2,3-Cresotic Acid as a Potent Inhibitor of the Chemotactic Activity of the HMGB1·CXCL12 Heterocomplex Using Virtual Screening and NMR Validation. De Leo F, Quilici G, De Marchis F, Mantonico MV, Bianchi ME, Musco G. Front Chem 8 598710 (2020)
  10. Doxorubicin impacts chromatin binding of HMGB1, Histone H1 and retinoic acid receptor. Bosire R, Fadel L, Mocsár G, Nánási P, Sen P, Sharma AK, Naseem MU, Kovács A, Kugel J, Kroemer G, Vámosi G, Szabó G. Sci Rep 12 8087 (2022)
  11. Dynamic and static control of the off-target interactions of antisense oligonucleotides using toehold chemistry. Terada C, Oh K, Tsubaki R, Chan B, Aibara N, Ohyama K, Shibata MA, Wada T, Harada-Shiba M, Yamayoshi A, Yamamoto T. Nat Commun 14 7972 (2023)
  12. Thermo-Sensitive Spikelet Defects 1 acclimatizes rice spikelet initiation and development to high temperature. Cai Z, Wang G, Li J, Kong L, Tang W, Chen X, Qu X, Lin C, Peng Y, Liu Y, Deng Z, Ye Y, Wu W, Duan Y. Plant Physiol 191 1684-1701 (2023)
  13. Zinc-finger BED domains drive the formation of the active Hermes transpososome by asymmetric DNA binding. Lannes L, Furman CM, Hickman AB, Dyda F. Nat Commun 14 4470 (2023)


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