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Crystal structure and nuclear magnetic resonance analyses of the SAND domain from glucocorticoid modulatory element binding protein-1 reveals deoxyribonucleic acid and zinc binding regions.

Surdo PL, Bottomley MJ, Sattler M, Scheffzek K
Mol Endocrinol 17 1283-95 (2003)
Cited: 33 times
EuropePMC logo PMID: 12702733

Abstract

The glucocorticoid-modulatory element-binding proteins, GMEB1 and GMEB2, are ubiquitous, multifunctional DNA-binding proteins with important roles in the modulation of transcription upon steroid hormone activation. The GMEB proteins have intrinsic transactivation ability, but also control the glucocorticoid response via direct binding to the glucocorticoid receptor. They are also mandatory host proteins for Parvovirus replication. Here we present the 1.55 A resolution crystal structure of a central portion of GMEB1, encompassing its SAND domain, which shares 80% sequence identity with the GMEB2 SAND domain. We demonstrate that this domain, also present in numerous proteins implicated in chromatin-associated transcriptional regulation, is necessary and sufficient to bind the glucocorticoid-modulatory element (GME) DNA target. We use nuclear magnetic resonance (NMR) and binding studies to map the DNA recognition surface to an alpha-helical region exposing the conserved KDWK motif. Using site-directed mutagenesis, key residues for DNA binding are identified. In contrast to the previously determined NMR structure of the Sp100b SAND domain, we find that the GMEB1 SAND domain also comprises a zinc-binding motif. Although the zinc ion is not necessary for DNA binding, it is found to determine the C-terminal conformation of the GMEB1 SAND domain. We also show that homologous zinc-binding motifs exist in a subset of SAND domain proteins and probe the roles of this novel motif.

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Reviews citing this publication (8)

  1. Aire. Mathis D, Benoist C. Annu Rev Immunol 27 287-312 (2009)
  2. Transcriptional regulation by AIRE: molecular mechanisms of central tolerance. Peterson P, Org T, Rebane A. Nat Rev Immunol 8 948-957 (2008)
  3. AIRE and APECED: molecular insights into an autoimmune disease. Villaseñor J, Benoist C, Mathis D. Immunol Rev 204 156-164 (2005)
  4. Autoimmune regulator and self-tolerance - molecular and clinical aspects. Abramson J, Husebye ES. Immunol Rev 271 127-140 (2016)
  5. NMR analysis of protein interactions. Bonvin AM, Boelens R, Kaptein R. Curr Opin Chem Biol 9 501-508 (2005)
  6. Recent insights into the role and molecular mechanisms of the autoimmune regulator (AIRE) gene in autoimmunity. Fierabracci A. Autoimmun Rev 10 137-143 (2011)
  7. AIRE: From promiscuous molecular partnerships to promiscuous gene expression. Abramson J, Goldfarb Y. Eur J Immunol 46 22-33 (2016)
  8. Recent trends in total reflection X-ray fluorescence spectrometry for biological applications. Szoboszlai N, Polgári Z, Mihucz VG, Záray G. Anal Chim Acta 633 1-18 (2009)

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  1. Ipr1 gene mediates innate immunity to tuberculosis. Pan H, Yan BS, Rojas M, Shebzukhov YV, Zhou H, Kobzik L, Higgins DE, Daly MJ, Bloom BR, Kramnik I. Nature 434 767-772 (2005)
  2. Mechanisms of an autoimmunity syndrome in mice caused by a dominant mutation in Aire. Su MA, Giang K, Zumer K, Jiang H, Oven I, Rinn JL, Devoss JJ, Johannes KP, Lu W, Gardner J, Chang A, Bubulya P, Chang HY, Peterlin BM, Anderson MS. J Clin Invest 118 1712-1726 (2008)
  3. Letter No associations of human pulmonary tuberculosis with Sp110 variants. Thye T, Browne EN, Chinbuah MA, Gyapong J, Osei I, Owusu-Dabo E, Niemann S, Rüsch-Gerdes S, Horstmann RD, Meyer CG. J Med Genet 43 e32 (2006)
  4. A novel ADP- and zinc-binding fold from function-directed in vitro evolution. Lo Surdo P, Walsh MA, Sollazzo M. Nat Struct Mol Biol 11 382-383 (2004)
  5. Functional analysis of SAND mutations in AIRE supports dominant inheritance of the G228W mutation. Ilmarinen T, Eskelin P, Halonen M, Rüppell T, Kilpikari R, Torres GD, Kangas H, Ulmanen I. Hum Mutat 26 322-331 (2005)
  6. Mapping DNA-binding domains of the autoimmune regulator protein. Purohit S, Kumar PG, Laloraya M, She JX. Biochem Biophys Res Commun 327 939-944 (2005)
  7. DEAF-1 regulates immunity gene expression in Drosophila. Reed DE, Huang XM, Wohlschlegel JA, Levine MS, Senger K. Proc Natl Acad Sci U S A 105 8351-8356 (2008)
  8. SP100B, a repressor of gene expression preferentially binds to DNA with unmethylated CpGs. Isaac A, Wilcox KW, Taylor JL. J Cell Biochem 98 1106-1122 (2006)
  9. The Myb-domain protein ULTRAPETALA1 INTERACTING FACTOR 1 controls floral meristem activities in Arabidopsis. Moreau F, Thévenon E, Blanvillain R, Lopez-Vidriero I, Franco-Zorrilla JM, Dumas R, Parcy F, Morel P, Trehin C, Carles CC. Development 143 1108-1119 (2016)
  10. The VARL gene family and the evolutionary origins of the master cell-type regulatory gene, regA, in Volvox carteri. Duncan L, Nishii I, Harryman A, Buckley S, Howard A, Friedman NR, Miller SM. J Mol Evol 65 1-11 (2007)
  11. DEAF1 is a Pellino1-interacting protein required for interferon production by Sendai virus and double-stranded RNA. Ordureau A, Enesa K, Nanda S, Le Francois B, Peggie M, Prescott A, Albert PR, Cohen P. J Biol Chem 288 24569-24580 (2013)
  12. SPE-44 implements sperm cell fate. Kulkarni M, Shakes DC, Guevel K, Smith HE. PLoS Genet 8 e1002678 (2012)
  13. Identification of a nuclear export signal and protein interaction domains in deformed epidermal autoregulatory factor-1 (DEAF-1). Jensik PJ, Huggenvik JI, Collard MW. J Biol Chem 279 32692-32699 (2004)
  14. Orthologs and paralogs of regA, a master cell-type regulatory gene in Volvox carteri. Duncan L, Nishii I, Howard A, Kirk D, Miller SM. Curr Genet 50 61-72 (2006)
  15. Association of SP110 gene polymorphisms with susceptibility to tuberculosis in a Chinese population. Liang L, Zhao YL, Yue J, Liu JF, Han M, Wang H, Xiao H. Infect Genet Evol 11 934-939 (2011)
  16. ULTRAPETALA1 and LEAFY pathways function independently in specifying identity and determinacy at the Arabidopsis floral meristem. Engelhorn J, Moreau F, Fletcher JC, Carles CC. Ann Bot 114 1497-1505 (2014)
  17. SP140L, an Evolutionarily Recent Member of the SP100 Family, Is an Autoantigen in Primary Biliary Cirrhosis. Saare M, Hämarik U, Venta R, Panarina M, Zucchelli C, Pihlap M, Remm A, Kisand K, Toots U, Möll K, Salupere R, Musco G, Uibo R, Peterson P. J Immunol Res 2015 526518 (2015)
  18. DEAF1 binds unmethylated and variably spaced CpG dinucleotide motifs. Jensik PJ, Vargas JD, Reardon SN, Rajamanickam S, Huggenvik JI, Collard MW. PLoS One 9 e115908 (2014)
  19. PML Body Component Sp100A Restricts Wild-Type Herpes Simplex Virus 1 Infection. Ma Y, Li J, Dong H, Yang Z, Zhou L, Xu P. J Virol 96 e0027922 (2022)
  20. Wild-type AIRE cooperates with p63 in HLA class II expression of medullary thymic stromal cells. Tonooka A, Kubo T, Ichimiya S, Tamura Y, Ilmarinen T, Ulmanen I, Kimura S, Yokoyama S, Takano Y, Kikuchi T, Sato N. Biochem Biophys Res Commun 379 765-770 (2009)
  21. Molecular characterization of Sp110 gene in pigs. Li LZ, Wang QS, Han LX, Wang JK, Shao SY, Wang L, Liu D, Yang XQ. Mol Genet Genomics 291 1431-1442 (2016)
  22. PML Body Component Sp100A Is a Cytosolic Responder to IFN and Activator of Antiviral ISGs. Dong H, Wu W, Li J, Ma Y, Deng X, Guo D, Xu P. mBio 13 e0204422 (2022)


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