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PDBsum entry 2h4f
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References listed in PDB file
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Key reference
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Title
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Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide.
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Authors
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K.G.Hoff,
J.L.Avalos,
K.Sens,
C.Wolberger.
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Ref.
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Structure, 2006,
14,
1231-1240.
[DOI no: ]
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PubMed id
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Abstract
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Sirtuin proteins comprise a unique class of NAD+-dependent protein deacetylases.
Although several structures of sirtuins have been determined, the mechanism by
which NAD+ cleavage occurs has remained unclear. We report the structures of
ternary complexes containing NAD+ and acetylated peptide bound to the bacterial
sirtuin Sir2Tm and to a catalytic mutant (Sir2Tm(H116Y)). NAD+ in these
structures binds in a conformation different from that seen in previous
structures, exposing the alpha face of the nicotinamide ribose to the carbonyl
oxygen of the acetyl lysine substrate. The NAD+ conformation is identical in
both structures, suggesting that proper coenzyme orientation is not dependent on
contacts with the catalytic histidine. We also present the structure of
Sir2Tm(H116A) bound to deacteylated peptide and 3'-O-acetyl ADP ribose. Taken
together, these structures suggest a mechanism for nicotinamide cleavage in
which an invariant phenylalanine plays a central role in promoting formation of
the O-alkylamidate reaction intermediate and preventing nicotinamide exchange.
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Figure 1.
Figure 1. Structure of the Ternary Complex of Sir2Tm Bound
to Acetylated Peptide and NAD^+
(A) Overall structure of
Sir2Tm bound to an acetylated peptide corresponding to residues
372–389 of the p53 protein (yellow) and β-NAD^+ (gray). The
Sir2Tm Rossmann fold domain, the α-helical subdomain and Zn
binding subdomain, and the Zn atom are colored teal, blue, and
gold, respectively.
(B) Electron density for the sirtuin
substrates. The 2F[o] − F[c] electron density map contoured at
1σ is shown surrounding the acetylated p53 peptide (yellow) and
β-NAD^+ bound to the active site of Sir2Tm.
(C)
Stereodiagram of NAD^+ (white) in the active site of Sir2Tm
(teal) bound to acetylated peptide (yellow). Active site
residues that make contact with NAD^+ are shown as lines, the
acetyl lysine substrate and NAD^+ are shown as sticks, and water
contacts are shown as dashed, gray sticks.
(D) Schematic
representation of Sir2Tm contacts with NAD^+ and acetyl lysine.
Sir2Tm residues are shown as ovals containing the amino acid
designation and number; invariant residues shaded in blue,
waters are shown as red circles, and the acetyl lysine side
chain is designated as Ac-K and shaded yellow. Hydrogen bonds
between NAD^+ and backbone amides and carbonyls are shown as
blue and red dashes, respectively. Hydrogen bonds to amino acid
side chains are represented as green dashes, and van der Waals
interactions are indicated by yellow semicircles.
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Figure 2.
Figure 2. Comparison of NAD^+ and NAD^+-Analog Bound
Sirtuin Structures
Structural alignment of
Sir2Tm-acetylated p53 peptide-NAD^+ (blue), Hst2Sc-acetylated
histone H4 peptide-carba-NAD^+ (green), and Sir2Af2-NAD^+ (pink)
based on atoms in the adenine ring, adenine ribose,
nicotinamide, and the catalytic histidine. Acetyl lysine and
active site residues for the corresponding structures are
indicated.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2006,
14,
1231-1240)
copyright 2006.
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