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PDBsum entry 1tc3
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DNA binding protein/DNA
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PDB id
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1tc3
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the specific DNA-Binding domain of tc3 transposase of c.Elegans in complex with transposon DNA.
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Authors
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G.Van pouderoyen,
R.F.Ketting,
A.Perrakis,
R.H.Plasterk,
T.K.Sixma.
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Ref.
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EMBO J, 1997,
16,
6044-6054.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the complex between the N-terminal DNA-binding domain
of Tc3 transposase and an oligomer of transposon DNA has been determined. The
specific DNA-binding domain contains three alpha-helices, of which two form a
helix-turn-helix (HTH) motif. The recognition of transposon DNA by the
transposase is mediated through base-specific contacts and complementarity
between protein and sequence-dependent deformations of the DNA. The HTH motif
makes four base-specific contacts with the major groove, and the N-terminus
makes three base-specific contacts with the minor groove. The DNA oligomer
adopts a non-linear B-DNA conformation, made possible by a stretch of seven G:C
base pairs at one end and a TATA sequence towards the other end. Extensive
contacts (seven salt bridges and 16 hydrogen bonds) of the protein with the DNA
backbone allow the protein to probe and recognize the sequence-dependent DNA
deformation. The DNA-binding domain forms a dimer in the crystals. Each monomer
binds a separate transposon end, implying that the dimer plays a role in
synapsis, necessary for the simultaneous cleavage of both transposon termini.
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Figure 2.
Figure 2 Protein -DNA contacts. (A) A schematic view with
ribbons drawn through the C  s
of the Tc3A DNA-binding domain (yellow) and through the
phosphate backbone of the DNA strands (blue and magenta). (B)
Sketch summarizing the hydrogen bonding (indicated by green
dotted lines, base-specific H-bonds by green solid lines) and
salt bridging contacts (blue lines) between the Tc3A domain and
the DNA. Gray boxes indicate residues involved in base-specific
contacts. Hydrogen bonds are at a maximum distance of 3.5 Å and
salt bridges at a maximum of 4.0 Å (Barlow and Thorton, 1983).
(C) and (D) Stereo views (Kraulis, 1991) of the HTH DNA contacts
in the major groove, and the N-terminus of Tc3A bound in the
minor groove of DNA, respectively. Hydrogen bonds are indicated
with green dotted lines.
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Figure 4.
Figure 4 The Tc3A domain bound to DNA. The protein is shown in
an electrostatic surface representation with positively and
negatively charged regions in blue and red respectively
(GRASP-scale -10 to +10). DNA is shown in stick representation,
with carbons in white, nitrogens in blue, oxygens in red and
phosphors in yellow.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(1997,
16,
6044-6054)
copyright 1997.
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