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PDBsum entry 1nk2
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DNA binding protein/DNA
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PDB id
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1nk2
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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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Interactions of the vnd/nk-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.
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Authors
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J.M.Gruschus,
D.H.Tsao,
L.H.Wang,
M.Nirenberg,
J.A.Ferretti.
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Ref.
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Biochemistry, 1997,
36,
5372-5380.
[DOI no: ]
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PubMed id
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Abstract
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The interactions responsible for the nucleotide sequence-specific binding of the
vnd/NK-2 homeodomain of Drosophila melanogaster to its consensus DNA binding
site have been identified. A three-dimensional structure of the vnd/NK-2
homeodomain-DNA complex is presented, with emphasis on the structure of regions
of observed protein-DNA contacts. This structure is based on protein-DNA
distance restraints derived from NMR data, along with homology modeling,
solvated molecular dynamics, and results from methylation and ethylation
interference experiments. Helix III of the homeodomain binds in the major groove
of the DNA and the N-terminal arm binds in the minor groove, in analogy with
other homeodomain-DNA complexes whose structures have been reported. The
vnd/NK-2 homeodomain recognizes the unusual DNA consensus sequence 5'-CAAGTG-3'.
The roles in sequence specificity and strength of binding of individual amino
acid residues that make contact with the DNA are described. We show, based
primarily on the observed protein-DNA contacts, that the interaction of Y54 with
the DNA is the major determinant of this uncommon nucleotide binding specificity
in the vnd/NK-2 homeodomain-DNA complex.
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Secondary reference #1
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Title
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Interactions of the vnd/nk-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.
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Authors
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J.M.Gruschus,
D.H.Tsao,
L.H.Wang,
M.Nirenberg,
J.A.Ferretti.
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Ref.
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Biochemistry, 1997,
36,
5372-5380.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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The three-Dimensional solution structure of the nk-2 homeodomain from drosophila.
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Authors
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D.H.Tsao,
J.M.Gruschus,
L.H.Wang,
M.Nirenberg,
J.A.Ferretti.
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Ref.
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J Mol Biol, 1995,
251,
297-307.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. Superposition of the polypeptide backbone of the 30 structures of NK-2 homeodomain protein generated with
DSPACE and refined with X-PLOR. The colors are representative of the r.m.s.d. of the 30 structures, where blue indicates
very well defined, green/yellow indicate intermediate and magenta indicates very well defined.
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Figure 3.
Figure 3. Superposition of the polypeptide backbone for
residues 8 to 53 and the well-ordered side-chains which
form the hydrophobic core in NK-2. Helix I and II are in
the front part of the Figure, and helix III is at the back.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #3
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Title
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Elongation of helix III of the nk-2 homeodomain upon binding to DNA: a secondary structure study by nmr.
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Authors
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D.H.Tsao,
J.M.Gruschus,
L.H.Wang,
M.Nirenberg,
J.A.Ferretti.
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Ref.
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Biochemistry, 1994,
33,
15053-15060.
[DOI no: ]
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PubMed id
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