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PDBsum entry 2hap
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Gene regulation/DNA
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PDB id
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2hap
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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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Structure of hap1-18-Dna implicates direct allosteric effect of protein-Dna interactions on transcriptional activation.
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Authors
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D.A.King,
L.Zhang,
L.Guarente,
R.Marmorstein.
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Ref.
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Nat Struct Biol, 1999,
6,
22-27.
[DOI no: ]
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PubMed id
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Abstract
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HAP1 is a yeast transcriptional activator that binds with equal affinity to the
dissimilar upstream activation sequences UAS1 and UAS(CYC7), but activates
transcription differentially when bound to each site. HAP1-18 harbors an amino
acid change in the DNA binding domain. While binding UAS1 poorly, HAP1-18 binds
UAS(CYC7) with wild-type properties and activates transcription at elevated
levels relative to HAP1. We have determined the structure of HAP1-18-UAS(CYC7)
and have compared it to HAP1-UAS(CYC7). Unexpectedly, the single amino acid
substitution in HAP1-18 nucleates a significantly altered hydrogen bond
interface between the protein and DNA resulting in DNA conformational changes
and an ordering of one N-terminal arm of the protein dimer along the DNA minor
groove. These observations, together with a large subset of transcriptionally
defective mutations in the HAP1 DNA-binding domain that map to the HAP1-DNA
interface, suggest that protein-DNA interactions may have direct allosteric
effects on transcriptional activation.
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Figure 2.
Figure 2. Alignment of HAP1 and HAP1-18 and the protein−DNA
interface. a, Allignment of the HAP1 and HAP1-18 DNA
complexes showing the entire UAS[CYC7] DNA target and the C  trace
of the protein dimers. The HAP1 and HAP1-18 complexes are shown
in grey and red respectively. The superposition was carried out
by aligning the C atoms
of each of the protein dimers to one another C r.m.s.
deviation is 0.51 Å). The location of the S63R
substitution of each protein subunit is shown in blue and the
left subunit is numbered according to the discrete domains
labeled in Fig. 1. The half sites are highlighted in green. b,
Interactions between the left subunit of HAP-18 and UAS[CYC7].
For reference, the DNA target of the HAP1 complex is shown in
grey while the DNA of the HAP1-18 complex is shown in red with
the DNA half sites highlighted in pink. The left subunit's
N-terminal arm, Zn[2]Cys[6] domain and linker are shown as a
ribbon with the two zinc atoms shown as yellow balls. Side
chains of residues making different interactions as compared to
the wild-type protein are shown in green while side chains
making conserved interactions in both complexes are shown in
yellow. Hydrogen bonds are shown as dashed lines. c,
Interactions between the right subunit of HAP1-18 and UAS[
CYC7]. For reference the DNA of both NCS-related molecules of
the HAP1 complex are shown in light and dark grey while the DNA
of the HAP1-18 complex is shown in red.
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Figure 3.
Figure 3. Location of positive control mutations in the HAP1
structure. The two HAP1 subunits are shown in blue and aqua.
The DNA is shown in red with the half sites highlighted in
green. The most common side chain rotamer of each positive
control mutation is modeled onto the HAP1−DNA complex^8 and
shown in yellow, and the HAP1-18 mutation is shown in green .
Point mutations all evoke the positive control phenotype except
PC3, which requires a double mutation at amino acids 98 and 101.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(1999,
6,
22-27)
copyright 1999.
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