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PDBsum entry 1k3w
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Hydrolase/DNA
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PDB id
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1k3w
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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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Structural analysis of an escherichia coli endonuclease VIII covalent reaction intermediate.
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Authors
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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,
G.Shoham.
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Ref.
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EMBO J, 2002,
21,
789-800.
[DOI no: ]
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PubMed id
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Abstract
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Endonuclease VIII (Nei) of Escherichia coli is a DNA repair enzyme that excises
oxidized pyrimidines from DNA. Nei shares with formamidopyrimidine-DNA
glycosylase (Fpg) sequence homology and a similar mechanism of action: the
latter involves removal of the damaged base followed by two sequential
beta-elimination steps. However, Nei differs significantly from Fpg in substrate
specificity. We determined the structure of Nei covalently crosslinked to a
13mer oligodeoxynucleotide duplex at 1.25 A resolution. The crosslink is derived
from a Schiff base intermediate that precedes beta-elimination and is stabilized
by reduction with NaBH(4). Nei consists of two domains connected by a hinge
region, creating a DNA binding cleft between domains. DNA in the complex is
sharply kinked, the deoxyribitol moiety is bound covalently to Pro1 and everted
from the duplex into the active site. Amino acids involved in substrate binding
and catalysis are identified. Molecular modeling and analysis of amino acid
conservation suggest a site for recognition of the damaged base. Based on
structural features of the complex and site-directed mutagenesis studies, we
propose a catalytic mechanism for Nei.
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Figure 4.
Figure 4 Scheme of Nei−DNA interactions. Nucleotides are
numbered beginning from Tg^0, positive towards the 5'-end, with
superscript in parentheses for the complementary strand. Only
the central 9 bp are shown. Hydrogen bonds are shown as arrows
pointing towards their respective acceptors. Leu70, Tyr71 and
Pro253 form van der Waals contacts with nearby DNA residues.
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Figure 8.
Figure 8 Central region of the DNA duplex in the Nei−DNA
complex. Protein residues that fill the void in DNA created by
Tg eversion are shown as solid (cyan) spheres. DNA is presented
as a ball-and-stick model with dotted van der Waals radii; dRbl
in red, the remaining DNA in yellow.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
789-800)
copyright 2002.
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