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Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: Determinants of affinity and sequence specificity

Academic Article
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Overview

authors

  • Wuttke, D. S.
  • Foster, M. P.
  • Case, David A.
  • Gottesfeld, Joel
  • Wright, Peter

publication date

  • October 1997

journal

  • Journal of Molecular Biology  Journal

abstract

  • The high resolution solution structure of a protein containing the three amino-terminal zinc fingers of Xenopus laevis transcription factor IIIA (TFIIIA) bound to its cognate DNA duplex was determined by nuclear magnetic resonance spectroscopy. The protein, which is designated zf1-3, binds with all three fingers in the DNA major groove, with a number of amino acids making base-specific contacts. The DNA structure is close to B-form. Although the mode of interaction of zf1-3 with DNA is similar to that of zif268 and other structurally characterized zinc finger complexes, the TFIIIA complex exhibits several novel features. Each zinc finger contacts four to five base-pairs and the repertoire of known base contact residues is extended to include a tryptophan at position +2 of the helix (finger 1) and arginine at position +10 (finger 3). Sequence-specific base contacts are made over virtually the entire length of the finger 3 helix. Lysine and histidine side-chains involved in base recognition are dynamically disordered in the solution structure; in the case of lysine, in particular, this could significantly decrease the entropic cost of DNA binding. The TGEKP(N) linker sequences, which are highly flexible in the unbound protein, adopt ordered conformations on DNA binding. The linkers appear to play an active structural role in stabilization of the protein-DNA complex. Substantial protein-protein contact surfaces are formed between adjacent fingers. As a consequence of these protein-protein interactions, the orientation of finger 1 in the major groove differs from that of the other fingers. Contributions to high affinity binding by zf1-3 come from both direct protein-DNA contacts and from indirect protein-protein interactions associated with structural organization of the linkers and formation of well-packed interfaces between adjacent zinc fingers in the DNA complex. The structures provide a molecular level explanation for the large body of footprinting and mutagenesis data available for the TFIIIA-DNA complex.

subject areas

  • Amino Acid Sequence
  • Animals
  • Carbon Isotopes
  • DNA
  • DNA-Binding Proteins
  • Hydrogen Bonding
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Sequence Data
  • Nitrogen Isotopes
  • Nucleic Acid Conformation
  • Oligodeoxyribonucleotides
  • Protein Conformation
  • Transcription Factor TFIIIA
  • Transcription Factors
  • Xenopus laevis
  • Zinc Fingers
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Research

keywords

  • NMR structure
  • TFIIIA
  • protein-DNA recognition
  • zinc finger
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Identity

International Standard Serial Number (ISSN)

  • 0022-2836

Digital Object Identifier (DOI)

  • 10.1006/jmbi.1997.1291

PubMed ID

  • 9367756
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Additional Document Info

start page

  • 183

end page

  • 206

volume

  • 273

issue

  • 1

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