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PDBsum entry 1k82
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Hydrolase/DNA
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PDB id
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1k82
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Contents |
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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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Structure of formamidopyrimidine-Dna glycosylase covalently complexed to DNA.
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Authors
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R.Gilboa,
D.O.Zharkov,
G.Golan,
A.S.Fernandes,
S.E.Gerchman,
E.Matz,
J.H.Kycia,
A.P.Grollman,
G.Shoham.
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Ref.
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J Biol Chem, 2002,
277,
19811-19816.
[DOI no: ]
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PubMed id
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Abstract
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Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises
oxidized purines from damaged DNA. The Schiff base intermediate formed during
this reaction between Escherichia coli Fpg and DNA was trapped by reduction with
sodium borohydride, and the structure of the resulting covalently cross-linked
complex was determined at a 2.1-A resolution. Fpg is a bilobal protein with a
wide, positively charged DNA-binding groove. It possesses a conserved zinc
finger and a helix-two turn-helix motif that participate in DNA binding. The
absolutely conserved residues Lys-56, His-70, Asn-168, and Arg-258 form hydrogen
bonds to the phosphodiester backbone of DNA, which is sharply kinked at the
lesion site. Residues Met-73, Arg-109, and Phe-110 are inserted into the DNA
helix, filling the void created by nucleotide eversion. A deep hydrophobic
pocket in the active site is positioned to accommodate an everted base.
Structural analysis of the Fpg-DNA complex reveals essential features of damage
recognition and the catalytic mechanism of Fpg.
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Figure 4.
Fig. 4. Schematic representation of Fpg-DNA interactions.
The central nucleotides of the modified and complementary
strands are 8-oxoG0 and C^(0), respectively. Nucleotides are
numbered as shown with those in the complementary strand in
parentheses.
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Figure 6.
Fig. 6. Scheme of principal steps in the sequence of
reactions catalyzed by Fpg, showing catalytically important
amino acid residues. Nucleophilic attack at C1' and protonation
at O4' (a) lead to base displacement and deoxyribose ring
opening. A Schiff base involving Pro-1 is formed with O4'
stabilized by hydrogen bonding to Glu-2. b, following
abstraction of the 2' proton of deoxyribose by a general base,
Lys-56 protonates the 3'-phosphate leading to  -elimination
(c). Deprotonation of C4', now vinilogous to C1', is followed by
protonation of the 5'-phosphate by Arg-258 and the second -elimination
event (c).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2002,
277,
19811-19816)
copyright 2002.
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