Protein-DNA interactions: A structural analysis

被引:362
作者
Jones, S
van Heyningen, P
Berman, HM
Thornton, JM
机构
[1] UCL, Dept Biochem & Mol Biol, Biomol Struct & Modelling Unit, London WC1E 6BT, England
[2] Rutgers State Univ, Dept Chem, Piscataway, NJ 08855 USA
[3] Univ London Birkbeck Coll, Dept Crystallog, London WC1E 7HX, England
关键词
protein-DNA complex; motif; binding modes; interface; DNA distortion;
D O I
10.1006/jmbi.1999.2659
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
A detailed analysis of the DNA-binding sites of 26 proteins is presented using data from the Nucleic Acid Database (NDB) and the Protein Data Bank (PDB). Chemical and physical properties of the protein-DNA interface, such as polarity, size, shape, and packing, were analysed. The DNA-binding sites shared common features, comprising many discontinuous sequence segments forming hydrophilic surfaces capable of direct and water-mediated hydrogen bonds. These interface sites were compared to those of protein-protein binding sites, revealing them to be more polar, with many more intermolecular hydrogen bonds and buried water molecules than the protein-protein interface sites. By looking at the number and positioning of protein residue-DNA base interactions in a series of interaction footprints, three modes of DNA binding were identified (single-headed, double-headed and enveloping). Six of the eight enzymes in the data set bound in the enveloping mode, with the protein presenting a large interface area effectively wrapped around the DNA. A comparison of structural parameters of the DNA revealed that some values for the bound DNA (including twist, slide and roll) were intermediate of those observed for the unbound B-DNA and A-DNA. The distortion of bound DNA was evaluated by calculating a root-mean-square deviation on fitting to a canonical B-DNA structure. Major distortions were commonly caused by specific kinks in the DNA sequence, some resulting in the overall bending of the helix. The helix bending affected the dimensions of the grooves in the DNA, allowing the binding of protein elements that would otherwise be unable to make contact. From this structural analysis a preliminary set of rules that govern the bending of the DNA in protein-DNA complexes, are proposed. (C) 1999 Academic Press.
引用
收藏
页码:877 / 896
页数:20
相关论文
共 82 条
  • [41] NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions
    Luscombe, NM
    Laskowski, RA
    Thornton, JM
    [J]. NUCLEIC ACIDS RESEARCH, 1997, 25 (24) : 4940 - 4945
  • [42] New tools and resources for analysing protein structures and their interactions
    Luscombe, NM
    Laskowski, RA
    Westhead, DR
    Milburn, D
    Jones, S
    Karmirantzou, M
    Thornton, JM
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 : 1132 - 1138
  • [43] CRYSTAL-STRUCTURE OF MYOD BHLH DOMAIN-DNA COMPLEX - PERSPECTIVES ON DNA RECOGNITION AND IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION
    MA, PCM
    ROULD, MA
    WEINTRAUB, H
    PABOT, CO
    [J]. CELL, 1994, 77 (03) : 451 - 459
  • [44] DNA RECOGNITION BY GAL4 - STRUCTURE OF A PROTEIN DNA COMPLEX
    MARMORSTEIN, R
    CAREY, M
    PTASHNE, M
    HARRISON, SC
    [J]. NATURE, 1992, 356 (6368) : 408 - 414
  • [45] STRUCTURE OF THE DNA-ECO RI ENDONUCLEASE RECOGNITION COMPLEX AT 3 A RESOLUTION
    MCCLARIN, JA
    FREDERICK, CA
    WANG, BC
    GREENE, P
    BOYER, HW
    GRABLE, J
    ROSENBERG, JM
    [J]. SCIENCE, 1986, 234 (4783) : 1526 - 1541
  • [46] SATISFYING HYDROGEN-BONDING POTENTIAL IN PROTEINS
    MCDONALD, IK
    THORNTON, JM
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1994, 238 (05) : 777 - 793
  • [47] RAPID COMPARISON OF PROTEIN STRUCTURES
    MCLACHLAN, AD
    [J]. ACTA CRYSTALLOGRAPHICA SECTION A, 1982, 38 (NOV): : 871 - 873
  • [48] DISTINCTIVE DNA CONFORMATION WITH ENLARGED MAJOR GROOVE IS FOUND IN ZN-FINGER DNA AND OTHER PROTEIN-DNA COMPLEXES
    NEKLUDOVA, L
    PABO, CO
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994, 91 (15) : 6948 - 6952
  • [49] STRUCTURE OF BAM-HI ENDONUCLEASE BOUND TO DNA - PARTIAL FOLDING AND UNFOLDING ON DNA-BINDING
    NEWMAN, M
    STRZELECKA, T
    DORNER, LF
    SCHILDKRAUT, I
    AGGARWAL, AK
    [J]. SCIENCE, 1995, 269 (5224) : 656 - 663
  • [50] Enzymatic C5-cytosine methylation of DNA: Mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes
    OGara, M
    Klimasauskas, S
    Roberts, RJ
    Cheng, XD
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1996, 261 (05) : 634 - 645