Summary information and primary citation

PDB-id
1bsu; SNAP-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.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js

List of 2 5mC-amino acid contacts

No. 1 C.5CM906: other-contacts is-WC-paired is-in-duplex [+]:Acg/cgT
No. 2 D.5CM806: other-contacts is-WC-paired is-in-duplex [-]:cgT/Acg