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PDBsum entry 3ebc
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Hydrolase/DNA
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PDB id
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3ebc
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References listed in PDB file
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Key reference
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Title
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Early interrogation and recognition of DNA sequence by indirect readout.
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Authors
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E.J.Little,
A.C.Babic,
N.C.Horton.
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Ref.
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Structure, 2008,
16,
1828-1837.
[DOI no: ]
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PubMed id
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Abstract
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Control of replication, transcription, recombination and repair requires
proteins capable of finding particular DNA sequences in a background of a large
excess of nonspecific sequences. Such recognition can involve direct readout,
with direct contacts to the bases of DNA, or in some cases through the less
well-characterized indirect readout mechanisms. In order to measure the relative
contributions of direct and indirect readout by a sequence specific
endonuclease, HincII, a mutant enzyme deficient in a direct contact, was
characterized, and surprisingly showed no loss of sequence specificity. The
three dimensional crystal structure shows the loss of most of the direct readout
contacts to the DNA, possibly capturing an early stage in target site
recognition using predominately indirect readout to prescreen sites before full
sequence interrogation.
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Figure 1.
Figure 1. DNA Binding and Distortion by Wild-Type HincII
(A) Two views of the structure of wild-type HincII (two subunits
shown as black or white ribbons) bound to cognate DNA (shown in
space filling with the recognition site DNA in light brown and
the center two base pairs of the YR step in cyan and magenta,
respectively, with flanking DNA in dark brown).
(B) Cartoon
depiction of B form DNA (left) with that of the center YR step
of the HincII DNA recognition sequence bound to wild-type HincII
(right), in which the DNA bases of the same strand are unstacked
and the purine bases from opposing strands exhibit greater
stacking surface area (dashed lines) forming the cross-strand
purine stack (CSPS).
(C) Numbering of the HincII
recognition sequence used throughout the text.
(D) Hydrogen
bonds between the side chain of N141 in wild-type HincII and
bound cognate DNA.
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Figure 4.
Figure 4. Protein DNA Contacts in Wild-Type and N141A
HincII/DNA Structures
(A) Stereo view of the contacts to
the DNA by residues 138–141 of N141A HincII. Colored by atom
type: N-blue, O-red, P-orange, C-green in protein, pink in DNA
of the recognition site and yellow in flanking base pairs. A
water molecule is shown as a red sphere. Dashes indicate
hydrogen bonds.
(B) Stereo view of the contacts to the DNA
by residues 138–141 of wild-type HincII. Colored as in (A).
Dashes indicate hydrogen bonds.
(C) Stereo view of the
contacts to the DNA at Thy 2′ and Gua 1′ of N141A HincII.
Colored as in (A). Methyl groups are shown as green or pink
spheres; water molecule is shown as a red sphere. Dashes
indicate hydrogen bonds or van der Waals interactions.
(D)
Stereo view of the contacts to the DNA at Thy 2′ and Gua 1′
of wild-type HincII. Colored as in (A). Methyl groups are shown
as green or pink spheres. Dashes indicate hydrogen bonds or van
der Waals interactions.
(E) Cartoon of protein-DNA contacts
to bases in the major groove in the N141A HincII/DNA structure.
Water molecule is shown as a red circle.
(F) Cartoon of
protein-DNA contacts to bases in the major groove in the
wild-type HincII/DNA structure. Dashes indicate hydrogen bonds
or van der Waals interactions.
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The above figures are
reprinted
from an Open Access publication published by Cell Press:
Structure
(2008,
16,
1828-1837)
copyright 2008.
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