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PDBsum entry 1q1a
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Gene regulation
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PDB id
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1q1a
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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 the yeast hst2 protein deacetylase in ternary complex with 2'-O-Acetyl ADP ribose and histone peptide.
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Authors
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K.Zhao,
X.Chai,
R.Marmorstein.
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Ref.
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Structure, 2003,
11,
1403-1411.
[DOI no: ]
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PubMed id
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Abstract
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Sir2 proteins are NAD(+)-dependant protein deactylases that have been implicated
in playing roles in gene silencing, DNA repair, genome stability, longevity,
metabolism, and cell physiology. To define the mechanism of Sir2 activity, we
report the 1.5 A crystal structure of the yeast Hst2 (yHst2) Sir2 protein in
ternary complex with 2'-O-acetyl ADP ribose and an acetylated histone H4
peptide. The structure captures both ligands meeting within an enclosed tunnel
between the small and large domains of the catalytic protein core and permits
the assignment of a detailed catalytic mechanism for the Sir2 proteins that is
consistent with solution and enzymatic studies. Comparison of the ternary
complex with the yHst2/NAD(+) complex, also reported here, and nascent yHst2
structure also reveals that NAD(+) binding accompanies intramolecular loop
rearrangement for more stable NAD(+) and acetyl-lysine binding, and that
acetyl-lysine peptide binding induces a trimer-monomer protein transition
involving nonconserved Sir2 residues.
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Figure 4.
Figure 4. The yHst2-Histone H4 Interface(A) Stereo view of
yHst2-histone H4 interactions within the ternary complex.
Hydrogen bonds are indicated with a dashed line. Residues that
mediate van der Waals interactions are also shown.(B) Summary of
yHst2-histone H4 interactions. Hydrogen bonds are indicated with
a dashed line, and van der Waals interactions are indicated with
a half-moon symbol. For clarity, histone H4 side chains that do
no participate in direct protein-peptide interactions are not
shown. The residues highlighted in cyan and red highlight
interactions with acetly-lysine peptide substrate that are
conserved and nonconserved, respectively, with the
protein-peptide interactions observed in the Af2-Sir2/p53
peptide structure.(C) The p53 peptide (purple) from the
Af2-Sir2/p53 peptide structure and the "pseudosubstrate" from
the nascent yHst2 structure (yellow) are overlayed with the
histone H4 peptide (green) onto a surface representation of
yHst2 from the ternary complex. Protein residues that make
conserved interactions between the three substrates are
indicated in blue, and protein residues that mediate variable
interactions are indicated in red.(D) Backbone overlay of
yHst2/NAD^+ (gray) and nascent yHst2 (cyan) homotrimers with the
yHst2/2'-O-acetyl ADP ribose/histone H4 monomer (red). The
ADP-ribose is highlighted in yellow, the histone H4 peptide is
highlighted in green, and the C-terminal domain of nascent yHst2
is highlighted in purple.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2003,
11,
1403-1411)
copyright 2003.
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Secondary reference #1
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Title
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Structure and autoregulation of the yeast hst2 homolog of sir2.
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Authors
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K.Zhao,
X.Chai,
A.Clements,
R.Marmorstein.
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Ref.
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Nat Struct Biol, 2003,
10,
864-871.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4. The acetyl-lysine substrate-binding site and trimer
formation by yeast Hst2. (a) Detailed view of the
intermolecular interactions between yHst2 and the N-terminal
extended loop from a symmetry-related molecule (indicated with a
prime designation). Residues that mediate interactions are cyan,
the N-terminal extended loop is green and the  13
helix is yellow. (b) Superposition with the p53 acetyl-lysine
substrate (red) extracted from the Af2 Sir2-p53 peptide complex.
(c) 2F[o] - F[c] electron density map contoured at 1  showing
the N-terminal loop comprising residues 1 -7 of yHst2. (d)
Schematic representation of the trimer with the N-terminal
extended loop and 13
helix in yellow. (e) Detailed view of the trimer interface.
Symmetry-related residues are indicated with a prime designation.
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Figure 5.
Figure 5. Solution oligomerization and kinetic properties of
yeast Hst2 proteins. (a) Equilibrium sedimentation data for
untagged native yHst2 fit with data from nine curves (three
protein concentrations at three centrifugation speeds). A
representative run at a centrifugation speed of 21,425g and
three protein concentrations of 1.75, 2.0 and 2.25 mg ml-1 is
shown. The plots represent a monomer-trimer model for which all
nine curves were fit to a single dissociation constant. Bottom
panels, experimental data (  )
with calculated fits (lines). Top panels, residuals of the fits.
The monomer-trimer K[d] parameters calculated for yHst2 and
His-yHst2 were 1.12  10^-8
M (  2.08
10^-9
M) and 3.44 10^-9
M (4.94 10^-9-2.40
10^-9
M), respectively; the monomer-dimer K[d] parameter calculated
for yHst2-  N7
was 6.46 10^-6
M ( 1.75
10^-6
M). (b) Kinetic analysis of yHst2 and truncation mutants.
Initial velocity pattern is shown in the double reciprocal plot
in which 1/velocity is plotted against 1/[fluorogenic
acetyl-lysine substrate] for the proteins yHst2 (cyan  ),
yHst2- N7
(green  )
and yHst2- C64
(  ).
(c) Inhibition of yHst2 and truncation mutants by acetylated
histone H4 peptide. K[m,app] is determined at various histone H4
peptide concentrations and plotted against the concentration of
H4. Linear fits for the proteins His[6]-tagged yHst2 (cyan ),
untagged yHst2 (  diamond
) and untagged yHst2- 7
(green )
are shown.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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