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PDBsum entry 1mpg
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.2.21
- DNA-3-methyladenine glycosylase Ii.
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Reaction:
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Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine, and 7-methyladenine.
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DOI no:
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Cell
86:321-329
(1996)
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PubMed id:
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Structural basis for the excision repair of alkylation-damaged DNA.
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J.Labahn,
O.D.Schärer,
A.Long,
K.Ezaz-Nikpay,
G.L.Verdine,
T.E.Ellenberger.
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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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Selected figure(s)
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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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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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Y.G.Mok,
R.Uzawa,
J.Lee,
G.M.Weiner,
B.F.Eichman,
R.L.Fischer,
and
J.H.Huh
(2010).
Domain structure of the DEMETER 5-methylcytosine DNA glycosylase.
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Proc Natl Acad Sci U S A,
107,
19225-19230.
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F.Faucher,
S.Duclos,
V.Bandaru,
S.S.Wallace,
and
S.Doublié
(2009).
Crystal structures of two archaeal 8-oxoguanine DNA glycosylases provide structural insight into guanine/8-oxoguanine distinction.
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Structure,
17,
703-712.
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PDB codes:
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F.Faucher,
S.M.Robey-Bond,
S.S.Wallace,
and
S.Doublié
(2009).
Structural characterization of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase in its apo form and in complex with 8-oxodeoxyguanosine.
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J Mol Biol,
387,
669-679.
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PDB codes:
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P.C.Anderson,
and
V.Daggett
(2009).
The R46Q, R131Q and R154H polymorphs of human DNA glycosylase/beta-lyase hOgg1 severely distort the active site and DNA recognition site but do not cause unfolding.
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J Am Chem Soc,
131,
9506-9515.
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B.R.Bowman,
S.Lee,
S.Wang,
and
G.L.Verdine
(2008).
Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA.
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Structure,
16,
1166-1174.
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PDB codes:
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C.S.Chen,
E.Korobkova,
H.Chen,
J.Zhu,
X.Jian,
S.C.Tao,
C.He,
and
H.Zhu
(2008).
A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli.
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Nat Methods,
5,
69-74.
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G.M.Lingaraju,
M.Kartalou,
L.B.Meira,
and
L.D.Samson
(2008).
Substrate specificity and sequence-dependent activity of the Saccharomyces cerevisiae 3-methyladenine DNA glycosylase (Mag).
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DNA Repair (Amst),
7,
970-982.
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L.R.Rutledge,
H.F.Durst,
and
S.D.Wetmore
(2008).
Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases.
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Phys Chem Chem Phys,
10,
2801-2812.
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S.Adhikari,
P.V.Manthena,
A.Uren,
and
R.Roy
(2008).
Expression, purification and characterization of codon-optimized human N-methylpurine-DNA glycosylase from Escherichia coli.
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Protein Expr Purif,
58,
257-262.
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S.Adhikari,
S.J.Kennel,
G.Roy,
P.S.Mitra,
S.Mitra,
and
R.Roy
(2008).
Discrimination of lesion removal of N-methylpurine-DNA glycosylase revealed by a potent neutralizing monoclonal antibody.
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DNA Repair (Amst),
7,
31-39.
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A.H.Metz,
T.Hollis,
and
B.F.Eichman
(2007).
DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG).
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EMBO J,
26,
2411-2420.
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PDB codes:
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B.Dalhus,
I.H.Helle,
P.H.Backe,
I.Alseth,
T.Rognes,
M.Bjørås,
and
J.K.Laerdahl
(2007).
Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats.
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Nucleic Acids Res,
35,
2451-2459.
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G.Mao,
X.Pan,
B.B.Zhu,
Y.Zhang,
F.Yuan,
J.Huang,
M.A.Lovell,
M.P.Lee,
W.R.Markesbery,
G.M.Li,
and
L.Gu
(2007).
Identification and characterization of OGG1 mutations in patients with Alzheimer's disease.
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Nucleic Acids Res,
35,
2759-2766.
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I.Leiros,
M.P.Nabong,
K.Grøsvik,
J.Ringvoll,
G.T.Haugland,
L.Uldal,
K.Reite,
I.K.Olsbu,
I.Knaevelsrud,
E.Moe,
O.A.Andersen,
N.K.Birkeland,
P.Ruoff,
A.Klungland,
and
S.Bjelland
(2007).
Structural basis for enzymatic excision of N1-methyladenine and N3-methylcytosine from DNA.
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EMBO J,
26,
2206-2217.
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PDB codes:
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S.Adhikari,
A.Uren,
and
R.Roy
(2007).
N-terminal extension of N-methylpurine DNA glycosylase is required for turnover in hypoxanthine excision reaction.
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J Biol Chem,
282,
30078-30084.
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Y.Mishina,
and
C.He
(2006).
Oxidative dealkylation DNA repair mediated by the mononuclear non-heme iron AlkB proteins.
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J Inorg Biochem,
100,
670-678.
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Y.Mishina,
E.M.Duguid,
and
C.He
(2006).
Direct reversal of DNA alkylation damage.
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Chem Rev,
106,
215-232.
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B.I.Lee,
K.H.Kim,
S.J.Park,
S.H.Eom,
H.K.Song,
and
S.W.Suh
(2004).
Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair.
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EMBO J,
23,
2029-2038.
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PDB code:
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F.Coste,
M.Ober,
T.Carell,
S.Boiteux,
C.Zelwer,
and
B.Castaing
(2004).
Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase.
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J Biol Chem,
279,
44074-44083.
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PDB codes:
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K.Hashiguchi,
J.A.Stuart,
N.C.de Souza-Pinto,
and
V.A.Bohr
(2004).
The C-terminal alphaO helix of human Ogg1 is essential for 8-oxoguanine DNA glycosylase activity: the mitochondrial beta-Ogg1 lacks this domain and does not have glycosylase activity.
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Nucleic Acids Res,
32,
5596-5608.
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R.C.Manuel,
K.Hitomi,
A.S.Arvai,
P.G.House,
A.J.Kurtz,
M.L.Dodson,
A.K.McCullough,
J.A.Tainer,
and
R.S.Lloyd
(2004).
Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase.
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J Biol Chem,
279,
46930-46939.
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PDB codes:
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Y.Choi,
J.J.Harada,
R.B.Goldberg,
and
R.L.Fischer
(2004).
An invariant aspartic acid in the DNA glycosylase domain of DEMETER is necessary for transcriptional activation of the imprinted MEDEA gene.
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Proc Natl Acad Sci U S A,
101,
7481-7486.
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B.F.Eichman,
E.J.O'Rourke,
J.P.Radicella,
and
T.Ellenberger
(2003).
Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases.
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EMBO J,
22,
4898-4909.
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PDB codes:
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E.M.Duguid,
Y.Mishina,
and
C.He
(2003).
How do DNA repair proteins locate potential base lesions? a chemical crosslinking method to investigate O6-alkylguanine-DNA alkyltransferases.
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Chem Biol,
10,
827-835.
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G.L.Verdine,
and
D.P.Norman
(2003).
Covalent trapping of protein-DNA complexes.
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Annu Rev Biochem,
72,
337-366.
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J.C.Fromme,
and
G.L.Verdine
(2003).
Structure of a trapped endonuclease III-DNA covalent intermediate.
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EMBO J,
22,
3461-3471.
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PDB codes:
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J.C.Fromme,
S.D.Bruner,
W.Yang,
M.Karplus,
and
G.L.Verdine
(2003).
Product-assisted catalysis in base-excision DNA repair.
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Nat Struct Biol,
10,
204-211.
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PDB codes:
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A.B.Guliaev,
B.Hang,
and
B.Singer
(2002).
Structural insights by molecular dynamics simulations into differential repair efficiency for ethano-A versus etheno-A adducts by the human alkylpurine-DNA N-glycosylase.
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Nucleic Acids Res,
30,
3778-3787.
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A.C.Drohat,
K.Kwon,
D.J.Krosky,
and
J.T.Stivers
(2002).
3-Methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member.
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Nat Struct Biol,
9,
659-664.
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PDB code:
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D.O.Zharkov,
G.Golan,
R.Gilboa,
A.S.Fernandes,
S.E.Gerchman,
J.H.Kycia,
R.A.Rieger,
A.P.Grollman,
and
G.Shoham
(2002).
Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.
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EMBO J,
21,
789-800.
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PDB codes:
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F.Dantzer,
L.Luna,
M.Bjørås,
and
E.Seeberg
(2002).
Human OGG1 undergoes serine phosphorylation and associates with the nuclear matrix and mitotic chromatin in vivo.
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Nucleic Acids Res,
30,
2349-2357.
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H.Terato,
A.Masaoka,
K.Asagoshi,
A.Honsho,
Y.Ohyama,
T.Suzuki,
M.Yamada,
K.Makino,
K.Yamamoto,
and
H.Ide
(2002).
Novel repair activities of AlkA (3-methyladenine DNA glycosylase II) and endonuclease VIII for xanthine and oxanine, guanine lesions induced by nitric oxide and nitrous acid.
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Nucleic Acids Res,
30,
4975-4984.
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K.S.Yan,
and
M.M.Zhou
(2002).
TAGging the target for damage control.
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Nat Struct Biol,
9,
638-640.
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C.J.Norbury,
and
I.D.Hickson
(2001).
Cellular responses to DNA damage.
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Annu Rev Pharmacol Toxicol,
41,
367-401.
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H.Yang,
I.T.Phan,
S.Fitz-Gibbon,
M.K.Shivji,
R.D.Wood,
W.M.Clendenin,
E.C.Hyman,
and
J.H.Miller
(2001).
A thermostable endonuclease III homolog from the archaeon Pyrobaculum aerophilum.
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Nucleic Acids Res,
29,
604-613.
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O.D.Schärer,
and
J.Jiricny
(2001).
Recent progress in the biology, chemistry and structural biology of DNA glycosylases.
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Bioessays,
23,
270-281.
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X.Li,
and
A.L.Lu
(2001).
Molecular cloning and functional analysis of the MutY homolog of Deinococcus radiodurans.
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J Bacteriol,
183,
6151-6158.
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X.Liu,
and
R.Roy
(2001).
Mutation at active site lysine 212 to arginine uncouples the glycosylase activity from the lyase activity of human endonuclease III.
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Biochemistry,
40,
13617-13622.
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A.Gogos,
D.Jantz,
S.Sentürker,
D.Richardson,
M.Dizdaroglu,
and
N.D.Clarke
(2000).
Assignment of enzyme substrate specificity by principal component analysis of aligned protein sequences: an experimental test using DNA glycosylase homologs.
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Proteins,
40,
98.
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A.J.Doherty,
and
S.W.Suh
(2000).
Structural and mechanistic conservation in DNA ligases.
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Nucleic Acids Res,
28,
4051-4058.
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A.Memisoglu,
and
L.Samson
(2000).
Contribution of base excision repair, nucleotide excision repair, and DNA recombination to alkylation resistance of the fission yeast Schizosaccharomyces pombe.
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J Bacteriol,
182,
2104-2112.
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A.Y.Lau,
M.D.Wyatt,
B.J.Glassner,
L.D.Samson,
and
T.Ellenberger
(2000).
Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG.
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Proc Natl Acad Sci U S A,
97,
13573-13578.
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PDB codes:
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C.V.Privezentzev,
M.Saparbaev,
A.Sambandam,
M.M.Greenberg,
and
J.Laval
(2000).
AlkA protein is the third Escherichia coli DNA repair protein excising a ring fragmentation product of thymine.
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Biochemistry,
39,
14263-14268.
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F.A.Quiocho,
G.Hu,
and
P.D.Gershon
(2000).
Structural basis of mRNA cap recognition by proteins.
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Curr Opin Struct Biol,
10,
78-86.
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H.Yang,
S.Fitz-Gibbon,
E.M.Marcotte,
J.H.Tai,
E.C.Hyman,
and
J.H.Miller
(2000).
Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum.
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J Bacteriol,
182,
1272-1279.
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J.J.Tsai-Wu,
H.T.Su,
Y.L.Wu,
S.M.Hsu,
and
C.H.Wu
(2000).
Nuclear localization of the human mutY homologue hMYH.
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J Cell Biochem,
77,
666-677.
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J.Y.Lee,
C.Chang,
H.K.Song,
J.Moon,
J.K.Yang,
H.K.Kim,
S.T.Kwon,
and
S.W.Suh
(2000).
Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.
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EMBO J,
19,
1119-1129.
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PDB codes:
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M.Saparbaev,
J.C.Mani,
and
J.Laval
(2000).
Interactions of the human, rat, Saccharomyces cerevisiae and Escherichia coli 3-methyladenine-DNA glycosylases with DNA containing dIMP residues.
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Nucleic Acids Res,
28,
1332-1339.
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M.Sugahara,
T.Mikawa,
T.Kumasaka,
M.Yamamoto,
R.Kato,
K.Fukuyama,
Y.Inoue,
and
S.Kuramitsu
(2000).
Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8.
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EMBO J,
19,
3857-3869.
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PDB code:
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R.Roy,
T.Biswas,
J.C.Lee,
and
S.Mitra
(2000).
Mutation of a unique aspartate residue abolishes the catalytic activity but not substrate binding of the mouse N-methylpurine-DNA glycosylase (MPG).
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J Biol Chem,
275,
4278-4282.
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S.D.Bruner,
D.P.Norman,
J.C.Fromme,
and
G.L.Verdine
(2000).
Structural and mechanistic studies on repair of 8-oxoguanine in mammalian cells.
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Cold Spring Harb Symp Quant Biol,
65,
103-111.
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T.C.Umland,
S.Q.Wei,
R.Craigie,
and
D.R.Davies
(2000).
Structural basis of DNA bridging by barrier-to-autointegration factor.
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Biochemistry,
39,
9130-9138.
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PDB code:
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T.Hollis,
Y.Ichikawa,
and
T.Ellenberger
(2000).
DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
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EMBO J,
19,
758-766.
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PDB code:
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X.Li,
and
A.L.Lu
(2000).
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PDB codes:
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M.Tani,
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Genomic structure and chromosomal localization of the mouse Ogg1 gene that is involved in the repair of 8-hydroxyguanine in DNA damage.
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Specific binding of a designed pyrrolidine abasic site analog to multiple DNA glycosylases.
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Biochemistry,
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MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily.
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Nat Struct Biol,
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PDB codes:
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A.E.Hodel,
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Specific protein recognition of an mRNA cap through its alkylated base.
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PDB codes:
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Structure of translation factor eIF4E bound to m7GDP and interaction with 4E-binding protein.
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PDB code:
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Nick sensing by vaccinia virus DNA ligase requires a 5' phosphate at the nick and occupancy of the adenylate binding site on the enzyme.
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Repair of O6-benzylguanine by the Escherichia coli Ada and Ogt and the human O6-alkylguanine-DNA alkyltransferases.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
|
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