title: Structural analysis of HMGD-DNA complexes reveals influence of intercalation on sequence selectivity and DNA bending.
abstract: The ubiquitous, eukaryotic, high-mobility group box (HMGB) chromosomal proteins promote many chromatin-mediated cellular activities through their non-sequence-specific binding and bending of DNA. Minor-groove DNA binding by the HMG box results in substantial DNA bending toward the major groove owing to electrostatic interactions, shape complementarity, and DNA intercalation that occurs at two sites. Here, the structures of the complexes formed with DNA by a partially DNA intercalation-deficient mutant of Drosophila melanogaster HMGD have been determined by X-ray crystallography at a resolution of 2.85 Å. The six proteins and 50 bp of DNA in the crystal structure revealed a variety of bound conformations. All of the proteins bound in the minor groove, bridging DNA molecules, presumably because these DNA regions are easily deformed. The loss of the primary site of DNA intercalation decreased overall DNA bending and shape complementarity. However, DNA bending at the secondary site of intercalation was retained and most protein-DNA contacts were preserved. The mode of binding resembles the HMGB1 box A-cisplatin-DNA complex, which also lacks a primary intercalating residue. This study provides new insights into the binding mechanisms used by HMG boxes to recognize varied DNA structures and sequences as well as modulate DNA structure and DNA bending.
authors.affiliation: Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; Molecular Biology Program, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA. Electronic address: mair.churchill@ucdenver.edu.
authors.forename: Mair E A
authors.initials: MEA
authors.lastname: Churchill
authors.affiliation: Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
authors.forename: Janet
authors.initials: J
authors.lastname: Klass
authors.affiliation: Molecular Biology Program, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Zoetewey
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D029721:Drosophila Proteins / Q000737:chemistry* / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000737:chemistry / Q000235:genetics; D006609:High Mobility Group Proteins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
chemical_list: D029721:Drosophila Proteins; D006609:High Mobility Group Proteins; C106685:HmgD protein, Drosophila; D050505:Mutant Proteins; D004247:DNA
references.citation: EMBO J. 1993 Apr;12(4):1311-9
references.pmid: 8467791
references.citation: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references.pmid: 8744570
references.citation: Prog Nucleic Acid Res Mol Biol. 1996;54:35-100
references.pmid: 8768072
references.citation: J Mol Biol. 2001 Sep 21;312(3):481-99
references.pmid: 11563911
references.citation: Acta Crystallogr D Biol Crystallogr. 1996 Jul 1;52(Pt 4):842-57
references.pmid: 15299650
references.citation: Curr Biol. 2005 Jan 11;15(1):68-72
references.pmid: 15649368
references.citation: Immunol Rev. 2007 Dec;220:35-46
references.pmid: 17979838
references.citation: Cell. 1995 Jun 2;81(5):705-14
references.pmid: 7774012
references.citation: J Biol Chem. 2004 May 14;279(20):20935-40
references.pmid: 15014079
references.citation: Methods Enzymol. 1997;277:525-45
references.pmid: 18488323
references.citation: Biochemistry. 1995 Dec 26;34(51):16596-607
references.pmid: 8527432
references.citation: Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3
references.pmid: 15299374
references.citation: J Mol Graph Model. 2001;19(3-4):325-30, 388-90
references.pmid: 11449571
references.citation: Acta Crystallogr D Biol Crystallogr. 1999 Apr;55(Pt 4):941-4
references.pmid: 10089342
references.citation: EMBO J. 1999 Dec 1;18(23):6610-8
references.pmid: 10581235
references.citation: Biochim Biophys Acta. 2010 Jan-Feb;1799(1-2):101-13
references.pmid: 20123072
references.citation: Nucleic Acids Res. 2008 Jul;36(12):4009-21
references.pmid: 18515834
references.citation: J Mol Biol. 2001 May 25;309(1):79-88
references.pmid: 11491303
references.citation: Nucleic Acids Res. 2003 Jun 1;31(11):2852-64
references.pmid: 12771212
references.citation: Nucleic Acids Res. 1979 Dec 11;7(7):1815-35
references.pmid: 537911
references.citation: J Mol Biol. 2002 Oct 18;323(2):263-84
references.pmid: 12381320
references.citation: J Mol Biol. 2004 Oct 15;343(2):371-93
references.pmid: 15451667
references.citation: EMBO J. 1997 May 15;16(10):2665-70
references.pmid: 9184213
references.citation: FEBS Lett. 1997 Sep 15;414(3):514-20
references.pmid: 9323026
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10320-5
references.pmid: 18650382
references.citation: EMBO J. 1995 Mar 15;14(6):1264-75
references.pmid: 7720717
references.citation: Nature. 1999 Jun 17;399(6737):708-12
references.pmid: 10385126
references.citation: Biochemistry. 1979 Aug 21;18(17):3739-48
references.pmid: 476083
references.citation: Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21
references.pmid: 9757107
references.citation: EMBO J. 1994 Dec 15;13(24):6115-24
references.pmid: 7813448
references.citation: J Biol Chem. 1998 Feb 20;273(8):4424-35
references.pmid: 9468494
references.citation: Nucleic Acids Res. 2009 Jun;37(10):3153-64
references.pmid: 19304746
references.citation: Nucleic Acids Res. 2003 Sep 1;31(17):5108-21
references.pmid: 12930962
references.citation: Nature. 1995 Aug 31;376(6543):791-5
references.pmid: 7651541
references.citation: Eur J Biochem. 1987 Jan 2;162(1):111-8
references.pmid: 3816775
references.citation: J Mol Biol. 1999 Nov 26;294(2):373-87
references.pmid: 10610765
references.citation: Structure. 1994 Jul 15;2(7):609-27
references.pmid: 7922039
references.citation: Methods Enzymol. 1997;276:307-26
references.pmid: 27754618
references.citation: BMC Mol Biol. 2008 Apr 01;9:32
references.pmid: 18380906
references.citation: J Mol Biol. 2006 Jun 30;360(1):90-104
references.pmid: 16813837
references.citation: Trends Biochem Sci. 2001 Mar;26(3):167-74
references.pmid: 11246022
references.citation: Nucleic Acids Res. 2008 Jun;36(11):3655-66
references.pmid: 18474528
references.citation: Methods Enzymol. 1999;304:99-133
references.pmid: 10372358
references.citation: EMBO J. 1996 Sep 16;15(18):4959-69
references.pmid: 8890169
references.citation: Nat Rev Immunol. 2005 Apr;5(4):331-42
references.pmid: 15803152
references.citation: Biochemistry. 2000 Nov 28;39(47):14426-35
references.pmid: 11087395
references.citation: Mol Cell Biol. 2005 Nov;25(22):9886-96
references.pmid: 16260604
references.citation: EMBO J. 1996 Feb 1;15(3):548-61
references.pmid: 8599938
references.citation: Mol Cell Biol. 2001 Oct;21(19):6598-605
references.pmid: 11533247
references.citation: EMBO J. 2001 Jul 2;20(13):3506-17
references.pmid: 11432837
references.citation: Methods Enzymol. 1997;277:505-24
references.pmid: 18488322
references.citation: Protein Eng. 1999 Mar;12(3):235-42
references.pmid: 10235624
references.citation: Mol Cell Biol. 1999 Oct;19(10):6532-42
references.pmid: 10490593
references.citation: Cell. 2006 Apr 21;125(2):275-86
references.pmid: 16630816
references.citation: Acta Crystallogr D Biol Crystallogr. 1999 Sep;55(Pt 9):1594-7
references.pmid: 10489457
references.citation: Nucleic Acids Res. 2009 Mar;37(4):1107-14
references.pmid: 19129233
references.citation: Protein Sci. 2001 Mar;10(3):504-18
references.pmid: 11344319
references.citation: Biophys J. 2005 Jul;89(1):353-64
references.pmid: 15833996
references.citation: Proteins. 1998 Feb 1;30(2):113-35
references.pmid: 9489920
references.citation: Mol Cell Biol. 2005 Jun;25(11):4413-25
references.pmid: 15899848
references.citation: Biochemistry. 2000 Aug 15;39(32):9725-36
references.pmid: 10933789
references.citation: EMBO J. 2002 Dec 16;21(24):6865-73
references.pmid: 12486007
references.citation: J Biomol Struct Dyn. 1989 Feb;6(4):655-67
references.pmid: 2619933
references.citation: J Mol Biol. 2003 Aug 22;331(4):795-813
references.pmid: 12909011
references.citation: EMBO J. 1996 Sep 16;15(18):4981-91
references.pmid: 8890171
references.citation: Mol Cell. 2005 Apr 1;18(1):109-21
references.pmid: 15808513
references.citation: J Biol Chem. 1994 Jun 24;269(25):17136-40
references.pmid: 8006019
references.citation: Genes Dev. 1998 Feb 15;12(4):462-72
references.pmid: 9472015
references.citation: Structure. 2000 Apr 15;8(4):R83-9
references.pmid: 10801483
references.citation: EMBO J. 1995 Mar 15;14(6):1198-208
references.pmid: 7720710
references.citation: EMBO J. 1993 Jun;12(6):2503-12
references.pmid: 8508775
references.citation: Biochemistry. 2009 Mar 17;48(10):2125-34
references.pmid: 19236006
references.citation: Mol Cell Biol. 1998 Aug;18(8):4471-87
references.pmid: 9671457