Summary information and primary citation
- PDB-id
-
1bss;
DSSR-derived features in text and
JSON formats
- Class
- hydrolase-DNA
- Method
- X-ray (2.15 Å)
- Summary
- Ecorv-t93a-DNA-ca2+
- Reference
-
Horton NC, Newberry KJ, Perona JJ (1998): "Metal
ion-mediated substrate-assisted catalysis in type II
restriction endonucleases."
Proc.Natl.Acad.Sci.USA, 95,
13489-13494. doi: 10.1073/pnas.95.23.13489.
- Abstract
- The 2.15-A resolution cocrystal structure of EcoRV
endonuclease mutant T93A complexed with DNA and Ca2+ ions
reveals two divalent metals bound in one of the active
sites. One of these metals is ligated through an
inner-sphere water molecule to the phosphate group located
3' to the scissile phosphate. A second inner-sphere water
on this metal is positioned approximately in-line for
attack on the scissile phosphate. This structure
corroborates the observation that the pro-SP phosphoryl
oxygen on the adjacent 3' phosphate cannot be modified
without severe loss of catalytic efficiency. The structural
equivalence of key groups, conserved in the active sites of
EcoRV, EcoRI, PvuII, and BamHI endonucleases, suggests that
ligation of a catalytic divalent metal ion to this
phosphate may occur in many type II restriction enzymes.
Together with previous cocrystal structures, these data
allow construction of a detailed model for the
pretransition state configuration in EcoRV. This model
features three divalent metal ions per active site and
invokes assistance in the bond-making step by a conserved
lysine, which stabilizes the attacking hydroxide ion
nucleophile.
