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PDBsum entry 2d5v
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Transcription/DNA
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PDB id
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2d5v
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References listed in PDB file
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Key reference
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Title
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Dna recognition mechanism of the onecut homeodomain of transcription factor hnf-6.
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Authors
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D.Iyaguchi,
M.Yao,
N.Watanabe,
J.Nishihira,
I.Tanaka.
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Ref.
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Structure, 2007,
15,
75-83.
[DOI no: ]
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PubMed id
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Abstract
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Hepatocyte nuclear factor-6 (HNF-6), a liver-enriched transcription factor,
controls the development of various tissues, such as the pancreas and liver, and
regulates the expression of several hepatic genes. This protein belongs to the
ONECUT class of homeodomain proteins and contains a bipartite DNA-binding domain
composed of a single cut domain and a characteristic homeodomain. This
transcription factor has two distinct modes of DNA binding and transcriptional
activation that use different coactivators depending on the target gene. The
crystal structure of the bipartite DNA-binding domain of HNF-6alpha complexed
with the HNF-6-binding site of the TTR promoter revealed the DNA recognition
mechanism of this protein. Comparing our structure with the DNA-free structure
of HNF-6 or the structure of Oct-1, we discuss characteristic features
associated with DNA binding and the structural basis for the dual mode of action
of this protein, and we suggest a strategy for variability of transcriptional
activation of the target gene.
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Figure 5.
Figure 5. Protein-DNA Contacts
Schematic diagram of
protein-DNA contacts. Residues from the cut domain are shown in
light blue, and the homeodomain is shown in yellow. The bases,
phosphates, and sugars contacted by each domain are indicated in
the corresponding colors. The bases contacted by both domains
are shown in red. Solid black lines indicate hydrogen bonds. van
der Waals interactions are indicated as dashed blue lines. Water
molecules are shown as green spheres.
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Figure 6.
Figure 6. Detailed View of the Homeodomain-DNA Interactions
Interactions of Asn-143, Met-146, Asn-147, and Arg-150 with
DNA are shown. Dashed red lines indicate hydrogen bonds. van der
Waals interactions are indicated as dashed blue lines. Water
molecules are shown as green spheres. Residue numbers and base
numbers are labeled.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2007,
15,
75-83)
copyright 2007.
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