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PDBsum entry 2nqh
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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 apurinic-Apyrimidinic site binding and excision by endonuclease IV.
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Authors
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E.D.Garcin,
D.J.Hosfield,
S.A.Desai,
B.J.Haas,
M.Björas,
R.P.Cunningham,
J.A.Tainer.
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Ref.
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Nat Struct Mol Biol, 2008,
15,
515-522.
[DOI no: ]
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PubMed id
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Abstract
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Escherichia coli endonuclease IV is an archetype for an abasic or
apurinic-apyrimidinic endonuclease superfamily crucial for DNA base excision
repair. Here biochemical, mutational and crystallographic characterizations
reveal a three-metal ion mechanism for damage binding and incision. The 1.10-A
resolution DNA-free and the 2.45-A resolution DNA-substrate complex structures
capture substrate stabilization by Arg37 and reveal a distorted Zn3-ligand
arrangement that reverts, after catalysis, to an ideal geometry suitable to hold
rather than release cleaved DNA product. The 1.45-A resolution DNA-product
complex structure shows how Tyr72 caps the active site, tunes its dielectric
environment and promotes catalysis by Glu261-activated hydroxide, bound to two
Zn2+ ions throughout catalysis. These structural, mutagenesis and biochemical
results suggest general requirements for abasic site removal in contrast to
features specific to the distinct endonuclease IV alpha-beta triose phosphate
isomerase (TIM) barrel and APE1 four-layer alpha-beta folds of the
apurinic-apyrimidinic endonuclease families.
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Figure 2.
(a) Stereoview of DNA-free structure with coordination of the
active-site phosphate and three Zn^2+ ions. Omit map is
contoured at 2  (light
blue) and 4 (dark
blue) for the bound phosphate group. (b) AP DNA complex
stereoview showing the three–metal ion active site (green
spheres), residues Arg37, Tyr72 and Gln261 (pink), and bound DNA
substrate with both the AP-site sugar and phosphate moieties and
the cognate nucleotide (orange) flipped out from the DNA base
stack. The 2F[o] - F[c] electron density map is contoured at 1
(blue
mesh). (c) Stereoview of DNA substrate complex binding to
active-site metal ions. Omit map (contoured at 2 ,
pink mesh) shows the intact phosphodiester bond (black arrow)
that constrains the Zn[3] to Cyt6 O[3]' distance to 2.7 Å.
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Figure 3.
The structure of the Y72A mutant reveals cleaved AP DNA
(a) and ordered water molecules (b) adjacent to the cleaved AP
site (3 light
blue and 4 dark
blue contoured omit maps). Panels a and b are drawn in
stereoview. (c) The structures of wild-type (left) and Y72A
mutant (right) Endo IV bound to AP DNA product are virtually
superimposable. Removal of the Tyr72 side chain allows increased
solvation of the active site.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2008,
15,
515-522)
copyright 2008.
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