Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: Recognition of pyrimidine-purine and purine-purine steps

Andrew A. Napoli, Catherine L. Lawson, Richard Ebright, Helen Berman

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex, typically introducing a sharp DNA kink, with a roll angle of ∼40° and a twist angle of ∼20°, between positions 6 and 7 of the DNA half-site, 5′-A1A2A3T4G5T 6G7A8T9C10T 11-3′ ("primary kink"). In previous work, we showed that CAP recognizes the nucleotide immediately 5′ to the primary-kink site, T6, through an "indirect-readout" mechanism involving sequence effects on energetics of primary-kink formation. Here, to understand further this example of indirect readout, we have determined crystal structures of CAP-DNA complexes containing each possible nucleotide at position 6. The structures show that CAP can introduce a DNA kink at the primary-kink site with any nucleotide at position 6. The DNA kink is sharp with the consensus pyrimidine-purine step T6G7 and the non-consensus pyrimidine-purine step C6G7 (roll angles of ∼42°, twist angles of ∼16°), but is much less sharp with the non-consensus purine-purine steps A6G7 and G6G7 (roll angles of ∼20°, twist angles of ∼17°). We infer that CAP discriminates between consensus and non-consensus pyrimidine-purine steps at positions 6-7 solely based on differences in the energetics of DNA deformation, but that CAP discriminates between the consensus pyrimidine-purine step and non-consensus purine-purine steps at positions 6-7 both based on differences in the energetics of DNA deformation and based on qualitative differences in DNA deformation. The structures further show that CAP can achieve a similar, ∼46° per DNA half-site, overall DNA bend through a sharp DNA kink, a less sharp DNA kink, or a smooth DNA bend. Analysis of these and other crystal structures of CAP-DNA complexes indicates that there is a large, ∼28° per DNA half-site, out-of-plane component of CAP-induced DNA bending in structures not constrained by end-to-end DNA lattice interactions and that lattice contacts involving CAP tend to involve residues in or near biologically functional surfaces.

Original languageEnglish (US)
Pages (from-to)173-183
Number of pages11
JournalJournal of molecular biology
Volume357
Issue number1
DOIs
StatePublished - Mar 17 2006

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Cyclic AMP Receptor Protein
DNA
Nucleotides
pyrimidine
purine

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Keywords

  • Catabolite activator protein (CAP)
  • Indirect readout
  • Protein-DNA interaction
  • Protein-induced DNA bending
  • cAMP receptor protein (CRP)

Cite this

@article{95f58e01523d4ce8998d8dd1e06b5aef,
title = "Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: Recognition of pyrimidine-purine and purine-purine steps",
abstract = "The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex, typically introducing a sharp DNA kink, with a roll angle of ∼40° and a twist angle of ∼20°, between positions 6 and 7 of the DNA half-site, 5′-A1A2A3T4G5T 6G7A8T9C10T 11-3′ ({"}primary kink{"}). In previous work, we showed that CAP recognizes the nucleotide immediately 5′ to the primary-kink site, T6, through an {"}indirect-readout{"} mechanism involving sequence effects on energetics of primary-kink formation. Here, to understand further this example of indirect readout, we have determined crystal structures of CAP-DNA complexes containing each possible nucleotide at position 6. The structures show that CAP can introduce a DNA kink at the primary-kink site with any nucleotide at position 6. The DNA kink is sharp with the consensus pyrimidine-purine step T6G7 and the non-consensus pyrimidine-purine step C6G7 (roll angles of ∼42°, twist angles of ∼16°), but is much less sharp with the non-consensus purine-purine steps A6G7 and G6G7 (roll angles of ∼20°, twist angles of ∼17°). We infer that CAP discriminates between consensus and non-consensus pyrimidine-purine steps at positions 6-7 solely based on differences in the energetics of DNA deformation, but that CAP discriminates between the consensus pyrimidine-purine step and non-consensus purine-purine steps at positions 6-7 both based on differences in the energetics of DNA deformation and based on qualitative differences in DNA deformation. The structures further show that CAP can achieve a similar, ∼46° per DNA half-site, overall DNA bend through a sharp DNA kink, a less sharp DNA kink, or a smooth DNA bend. Analysis of these and other crystal structures of CAP-DNA complexes indicates that there is a large, ∼28° per DNA half-site, out-of-plane component of CAP-induced DNA bending in structures not constrained by end-to-end DNA lattice interactions and that lattice contacts involving CAP tend to involve residues in or near biologically functional surfaces.",
keywords = "Catabolite activator protein (CAP), Indirect readout, Protein-DNA interaction, Protein-induced DNA bending, cAMP receptor protein (CRP)",
author = "Napoli, {Andrew A.} and Lawson, {Catherine L.} and Richard Ebright and Helen Berman",
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Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex : Recognition of pyrimidine-purine and purine-purine steps. / Napoli, Andrew A.; Lawson, Catherine L.; Ebright, Richard; Berman, Helen.

In: Journal of molecular biology, Vol. 357, No. 1, 17.03.2006, p. 173-183.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex

T2 - Recognition of pyrimidine-purine and purine-purine steps

AU - Napoli, Andrew A.

AU - Lawson, Catherine L.

AU - Ebright, Richard

AU - Berman, Helen

PY - 2006/3/17

Y1 - 2006/3/17

N2 - The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex, typically introducing a sharp DNA kink, with a roll angle of ∼40° and a twist angle of ∼20°, between positions 6 and 7 of the DNA half-site, 5′-A1A2A3T4G5T 6G7A8T9C10T 11-3′ ("primary kink"). In previous work, we showed that CAP recognizes the nucleotide immediately 5′ to the primary-kink site, T6, through an "indirect-readout" mechanism involving sequence effects on energetics of primary-kink formation. Here, to understand further this example of indirect readout, we have determined crystal structures of CAP-DNA complexes containing each possible nucleotide at position 6. The structures show that CAP can introduce a DNA kink at the primary-kink site with any nucleotide at position 6. The DNA kink is sharp with the consensus pyrimidine-purine step T6G7 and the non-consensus pyrimidine-purine step C6G7 (roll angles of ∼42°, twist angles of ∼16°), but is much less sharp with the non-consensus purine-purine steps A6G7 and G6G7 (roll angles of ∼20°, twist angles of ∼17°). We infer that CAP discriminates between consensus and non-consensus pyrimidine-purine steps at positions 6-7 solely based on differences in the energetics of DNA deformation, but that CAP discriminates between the consensus pyrimidine-purine step and non-consensus purine-purine steps at positions 6-7 both based on differences in the energetics of DNA deformation and based on qualitative differences in DNA deformation. The structures further show that CAP can achieve a similar, ∼46° per DNA half-site, overall DNA bend through a sharp DNA kink, a less sharp DNA kink, or a smooth DNA bend. Analysis of these and other crystal structures of CAP-DNA complexes indicates that there is a large, ∼28° per DNA half-site, out-of-plane component of CAP-induced DNA bending in structures not constrained by end-to-end DNA lattice interactions and that lattice contacts involving CAP tend to involve residues in or near biologically functional surfaces.

AB - The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex, typically introducing a sharp DNA kink, with a roll angle of ∼40° and a twist angle of ∼20°, between positions 6 and 7 of the DNA half-site, 5′-A1A2A3T4G5T 6G7A8T9C10T 11-3′ ("primary kink"). In previous work, we showed that CAP recognizes the nucleotide immediately 5′ to the primary-kink site, T6, through an "indirect-readout" mechanism involving sequence effects on energetics of primary-kink formation. Here, to understand further this example of indirect readout, we have determined crystal structures of CAP-DNA complexes containing each possible nucleotide at position 6. The structures show that CAP can introduce a DNA kink at the primary-kink site with any nucleotide at position 6. The DNA kink is sharp with the consensus pyrimidine-purine step T6G7 and the non-consensus pyrimidine-purine step C6G7 (roll angles of ∼42°, twist angles of ∼16°), but is much less sharp with the non-consensus purine-purine steps A6G7 and G6G7 (roll angles of ∼20°, twist angles of ∼17°). We infer that CAP discriminates between consensus and non-consensus pyrimidine-purine steps at positions 6-7 solely based on differences in the energetics of DNA deformation, but that CAP discriminates between the consensus pyrimidine-purine step and non-consensus purine-purine steps at positions 6-7 both based on differences in the energetics of DNA deformation and based on qualitative differences in DNA deformation. The structures further show that CAP can achieve a similar, ∼46° per DNA half-site, overall DNA bend through a sharp DNA kink, a less sharp DNA kink, or a smooth DNA bend. Analysis of these and other crystal structures of CAP-DNA complexes indicates that there is a large, ∼28° per DNA half-site, out-of-plane component of CAP-induced DNA bending in structures not constrained by end-to-end DNA lattice interactions and that lattice contacts involving CAP tend to involve residues in or near biologically functional surfaces.

KW - Catabolite activator protein (CAP)

KW - Indirect readout

KW - Protein-DNA interaction

KW - Protein-induced DNA bending

KW - cAMP receptor protein (CRP)

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