Summary information and primary citation
- PDB-id
-
1bsu;
DSSR-derived features in text and
JSON formats; DNAproDB
- Class
- hydrolase-DNA
- Method
- X-ray (2.0 Å)
- Summary
- Structural and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease
- Reference
-
Martin AM, Sam MD, Reich NO, Perona JJ (1999): "Structural
and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease." Nat.Struct.Biol.,
6, 269-277. doi: 10.1038/6707.
- Abstract
- Specific recognition by EcoRV endonuclease of its
cognate, sharply bent GATATC site at the center TA step
occurs solely via hydrophobic interaction with thymine
methyl groups. Mechanistic kinetic analyses of base
analog-substituted DNAs at this position reveal that direct
readout provides 5 kcal mol(-1) toward specificity, with an
additional 6-10 kcal mol(-1) arising from indirect readout.
Crystal structures of several base analog complexes show
that the major-groove hydrophobic contacts are crucial to
forming required divalent metal-binding sites, and that
indirect readout operates in part through the
sequence-dependent free-energy cost of unstacking the
center base-pair step of the DNA.
