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PDBsum entry 1j5k
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Transcription/DNA
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PDB id
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1j5k
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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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Molecular basis of sequence-Specific single-Stranded DNA recognition by kh domains: solution structure of a complex between hnrnp k kh3 and single-Stranded DNA.
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Authors
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D.T.Braddock,
J.L.Baber,
D.Levens,
G.M.Clore.
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Ref.
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EMBO J, 2002,
21,
3476-3485.
[DOI no: ]
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PubMed id
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Abstract
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To elucidate the basis of sequence-specific single-stranded (ss) DNA recognition
by K homology (KH) domains, we have solved the solution structure of a complex
between the KH3 domain of the transcriptional regulator heterogeneous nuclear
ribonucleoprotein K (hnRNP K) and a 10mer ssDNA. We show that hnRNP K KH3
specifically recognizes a tetrad of sequence 5'd-TCCC. The complex is stabilized
by a dense network of methyl-oxygen hydrogen bonds involving the methyl groups
of three isoleucine residues and the O2 and N3 atoms of the two central cytosine
bases. Comparison with the recently solved structure of a specific protein-ssDNA
complex involving the KH3 and KH4 domains of the far upstream element (FUSE)
binding protein FBP suggests that the amino acid located five residues
N-terminal of the invariant GXXG motif, which is characteristic of all KH
domains, plays a crucial role in discrimination of the first two bases of the
tetrad.
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Figure 2.
Figure 2 ssDNA binding by hnRNP K KH3. (A) Overall complex. The
protein is displayed as a molecular surface (left) and as a
backbone tube (right); hydrophobic, uncharged hydrophilic,
positively charged and negatively charged residues located in
the ssDNA binding site are depicted in green, magenta, blue and
red, respectively; the ssDNA heavy atoms are in gold. (B)
Detailed stereoview showing the hydrogen-bonding interactions of
the methyl groups of Ile29, Ile36 and Ile49 with the O2 and N3
atoms of the cytosine bases. Nucleotide numbering is in italics.
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Figure 4.
Figure 4 Discrimination of the first two first bases of the
ssDNA recognition site by KH domains of hnRNP K and FBP. (A)
hnRNP K KH3 recognizes TC, (B) FBP KH3 recognizes TT and (C) FBP
KH4 recognizes TA. The protein backbone and side chains are
shown in red and green, respectively, and the DNA in light blue.
The numbering scheme employed is that of the hnRNP K KH3−ssDNA
complex. Dashed lines indicate intermolecular hydrogen bonds.
The residue at position 25 plays a key role in selection of the
first two bases of the site. The coordinates of the FBP KH3/KH4
complex (accession code 1J4W) are taken from Braddock et al.
(2002).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
3476-3485)
copyright 2002.
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