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PDBsum entry 1abk
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References listed in PDB file
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Key reference
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Title
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Atomic structure of the DNA repair [4fe-4s] enzyme endonuclease III.
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Authors
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C.F.Kuo,
D.E.Mcree,
C.L.Fisher,
S.F.O'Handley,
R.P.Cunningham,
J.A.Tainer.
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Ref.
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Science, 1992,
258,
434-440.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the DNA repair enzyme endonuclease III, which
recognizes and cleaves DNA at damaged bases, has been solved to 2.0 angstrom
enzyme is
elongated and bilobal with a deep cleft separating two similarly sized domains:
a novel, sequence-continuous, six-helix domain (residues 22 to 132) and a
Greek-key, four-helix domain formed by the amino-terminal and three
carboxyl-terminal helices (residues 1 to 21 and 133 to 211) together with the
cluster. The cluster is bound entirely within the carboxyl-terminal
loop with a ligation pattern (Cys-X6-Cys-X2-Cys-X5-Cys) distinct from all other
proteins. Sequence conservation and the positive electrostatic
potential of conserved regions identify a surface suitable for binding duplex
B-DNA across the long axis of the enzyme, matching a 46 angstrom length of
cluster appears to involve
positioning conserved basic residues for interaction with the DNA phosphate
backbone. The crystallographically identified inhibitor binding region, which
recognizes the damaged base thymine glycol, is a seven-residue beta-hairpin
(residues 113 to 119). Location and side chain orientation at the base of the
inhibitor binding site implicate Glu112 in the N-glycosylase mechanism and
Lys120 in the beta-elimination mechanism. Overall, the structure reveals an
clusters and provides a
structural basis for studying recognition of damaged DNA and the N-glycosylase
and apurinic/apyrimidinic-lyase mechanisms.
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Secondary reference #1
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Title
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Crystallization and crystallographic characterization of the iron-Sulfur-Containing DNA-Repair enzyme endonuclease III from escherichia coli.
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Authors
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C.F.Kuo,
D.E.Mcree,
R.P.Cunningham,
J.A.Tainer.
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Ref.
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J Mol Biol, 1992,
227,
347-351.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Crystallization of endonuclease III by ialy-
sis; miroseeding, and macroseeding methods. (a) De nowo
rystallization by ialysis: the dialysis was carried out as
escribed in the text. The crystals emerged within several
ours. These crystals tended to nucleate along the side
nd bot,tom f the well and are hllow at the ends (0.7 mm
x 0.2 m x OS! mm). (b) Microseeding: crystals appeared
long the tract of straking and had solid rather than
hollow ends 0.15 mm x 0.1 mm x 0.1 mm). Crystals
ith clean surfaces and suitable morphology were chosen
s seeds for macroseeding. (c) Macroseeding: microcrystals
btained from microseeding were used to seed a fresh
rotein drop as described in the text. The use of higher
ionic srength buffer (200 mw-NaCl) as the transferring
olution is critical to avoid microcrystalline contamina-
ion nd obtain large single crystals (1.2 mm x 0.5 mm x
.3 mm).
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The above figure is
reproduced from the cited reference
with permission from Elsevier
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