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PDBsum entry 2hdd
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Transcription/DNA
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PDB id
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2hdd
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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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Engrailed (gln50-->Lys) homeodomain-Dna complex at 1.9 a resolution: structural basis for enhanced affinity and altered specificity.
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Authors
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L.Tucker-Kellogg,
M.A.Rould,
K.A.Chambers,
S.E.Ades,
R.T.Sauer,
C.O.Pabo.
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Ref.
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Structure, 1997,
5,
1047-1054.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: The homeodomain is one of the key DNA-binding motifs used in
eukaryotic gene regulation, and homeodomain proteins play critical roles in
development. The residue at position 50 of many homeodomains appears to
determine the differential DNA-binding specificity, helping to distinguish among
binding sites of the form TAATNN. However, the precise role(s) of residue 50 in
the differential recognition of alternative sites has not been clear. None of
the previously determined structures of homeodomain-DNA complexes has shown
evidence for a stable hydrogen bond between residue 50 and a base, and there has
been much discussion, based in part on NMR studies, about the potential
importance of water-mediated contacts. This study was initiated to help clarify
some of these issues. RESULTS: The crystal structure of a complex containing the
engrailed Gln50-->Lys variant (QK50) with its optimal binding site TAATCC
(versus TAATTA for the wild-type protein) has been determined at 1.9 A
resolution. The overall structure of the QK50 variant is very similar to that of
the wild-type complex, but the sidechain of Lys50 projects directly into the
major groove and makes several hydrogen bonds to the O6 and N7 atoms of the
guanines at base pairs 5 and 6. Lys50 also makes an additional water-mediated
contact with the guanine at base pair 5 and has an alternative conformation that
allows a hydrogen bond with the O4 of the thymine at base pair 4. CONCLUSIONS:
The structural context provided by the folding and docking of the engrailed
homeodomain allows Lys50 to make remarkably favorable contacts with the guanines
at base pairs 5 and 6 of the binding site. Although many different residues
occur at position 50 in different homeodomains, and although numerous position
50 variants have been constructed, the most striking examples of altered
specificity usually involve introducing or removing a lysine sidechain from
position 50. This high-resolution structure also confirms the critical role of
Asn51 in homeodomain-DNA recognition and further clarifies the roles of water
molecules near residues 50 and 51.
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Figure 3.
Figure 3. Major groove contacts of the QK50-TAATCC complex.
Three residues make base contacts in the major groove: Asn51
makes a pair of hydrogen bonds with the adenine at bp 3 (red);
lle47 makes hydrophobic contacts with the methyl group of the
thymine at bp 4 (purple); the primary conformation of Lys50
(yellow) makes hydrogen bonds with the O6 of the guanine at bp 5
and with the O6 and N7 atoms of the guanine at bp 6; the
secondary conformation of Lys50 (green) makes hydrogen bonds
with the O6 of the guanine at bp 5 and with the O4 of the
thymine at bp 4. Hydrogen bonds are shown as dashed lines and
van der Waals contacts are indicated with dotted spheres. For
clarity, water molecules have been omitted in this figure.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1997,
5,
1047-1054)
copyright 1997.
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