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PDBsum entry 1mpg
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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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Structural basis for the excision repair of alkylation-Damaged DNA.
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Authors
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J.Labahn,
O.D.Schärer,
A.Long,
K.Ezaz-Nikpay,
G.L.Verdine,
T.E.Ellenberger.
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Ref.
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Cell, 1996,
86,
321-329.
[DOI no: ]
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PubMed id
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Abstract
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Base-excision DNA repair proteins that target alkylation damage act on a variety
of seemingly dissimilar adducts, yet fail to recognize other closely related
lesions. The 1.8 A crystal structure of the monofunctional DNA glycosylase AlkA
(E. coli 3-methyladenine-DNA glycosylase II) reveals a large hydrophobic cleft
unusually rich in aromatic residues. An Asp residue projecting into this cleft
is essential for catalysis, and it governs binding specificity for
mechanism-based inhibitors. We propose that AlkA recognizes electron-deficient
methylated bases through pi-donor/acceptor interactions involving the
electron-rich aromatic cleft. Remarkably, AlkA is similar in fold and active
site location to the bifunctional glycosylase/lyase endonuclease III, suggesting
the two may employ fundamentally related mechanisms for base excision.
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Figure 3.
Figure 3. Overall Shape and Domain Structure of AlkA(A and
B) Course of the AlkA polypeptide chain, with elements of
secondary structure assigned and colored accordingly (blue = β
sheet, red/orange = α helix, WHITE = nonrepetitive elements).
The arrow in (A) shows the location of the proposed enzyme
active site. The view in (B) is related to that in (A) by
rotation of  vert,
similar 180°.(C) The AlkA protein consists of three domains:
an Image -terminal mixed α-β structure (Domain 1, blue); a
central seven-helix bundle (Domain 2, red; αD through αJ), and
a C-terminal domain of four α helices (Domain 3, yellow; αC
and αK through αM). A paucity of intersubunit contacts allows
some movement of domain 3 with respect to the rest of the
protein. The conserved helix-hairpin-helix motif, consisting of
helices αI and αJ and the intervening β turn, is located on
one side of this interdomain cleft.(D) The solvent-accessible
surface of AlkA, colored according to electrostatic potential
(blue, positively charged; red, negatively charged), reveals a
cleft at the junction of domains 2 and 3, which is unusually
rich in aromatic residues. Jutting into the cleft is the
catalytically essential residue Asp-238. The neighboring Asp
residue at position 237, which lies at the periphery of the
aromatic cleft, is not essential for glycosylase activity. A
number of lysines and arginines (blue), which could potentially
interact with DNA backbone phosphates, decorate the protein
surface around the aromatic cleft. This figure was created using
the program GRASP ([33]).
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Figure 4.
Figure 4. Detail of the Proposed Active Site of the AlkA
ProteinThe cleft, viewed along the direction of the arrow in
Figure 3D, is rich in electron-donating aromatic side chains,
which are well suited to recognize electron-deficient methylated
bases through π–donor/acceptor interactions. The
catalytically essential Asp-238 (green) lies at the bottom of
the cleft, where it is poised to participate in the reaction
chemistry, and to interact with mechanism-based oligonucleotide
inhibitors.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(1996,
86,
321-329)
copyright 1996.
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Secondary reference #1
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Title
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Three-Dimensional structure of a DNA repair enzyme, 3-Methyladenine DNA glycosylase ii, From escherichia coli.
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Authors
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Y.Yamagata,
M.Kato,
K.Odawara,
Y.Tokuno,
Y.Nakashima,
N.Matsushima,
K.Yasumura,
K.Tomita,
K.Ihara,
Y.Fujii,
Y.Nakabeppu,
M.Sekiguchi,
S.Fujii.
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Ref.
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Cell, 1996,
86,
311-319.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Overall Structure of AlkA(a) Ribbon diagram of
AlkA drawn with the program MOLSCRIPT ([20]). AlkA is composed
of three domains: domain I in purple, domain II in green, and
domain III in yellow.(b) Schematic topology (TOPS) diagram
([11]) of c
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Figure 2.
Figure 2. Domain I Similar to TBP and AlkA Dimer(a)
Superimposition of domain I of AlkA and one-half of TBP (1tbp;
[8]. Domain I of AlkA is shown as thick bonds between Cα atoms,
one-half of TBP as thin bonds.(b) AlkA dimer found in the
crystal structure. The dimer interface contains salt bridges,
hydrogen bonds, and van der Waals interactions involving α2 and
β1 in domain I and loops connecting α8 to α9 in domain II. An
area of about 1300 Å^2 of the 13500 Å^2 available
surface of each monomer is buried upon dimer formation.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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