Summary information and primary citation
- PDB-id
-
1k3w;
DSSR-derived features in text and
JSON formats
- Class
- hydrolase-DNA
- Method
- X-ray (1.42 Å)
- Summary
- Crystal structure of a trapped reaction intermediate of
the DNA repair enzyme endonuclease viii with DNA
- Reference
-
Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE,
Kycia JH, Rieger RA, Grollman AP, Shoham G (2002):
"Structural
analysis of an Escherichia coli endonuclease VIII
covalent reaction intermediate." EMBO J.,
21, 789-800. doi: 10.1093/emboj/21.4.789.
- Abstract
- 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.