1BUA

STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE

Summary for 1BUA

• Entry DOI: 10.2210/pdb1bua/pdb
• Descriptor: DNA (5'-D(*AP*AP*AP*GP*AP*CP*IP*TP*CP*TP*T)-3'), ENDONUCLEASE ECORV (3 entities in total)
• Functional Keywords: endonuclease ecorv (e.c.3.1.21.4)-dna complex, hydrolase-dna complex, hydrolase/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 63802.73

Authors

Perona, J.J.,Martin, A.M. (deposition date: 1998-09-03, release date: 1998-09-09, Last modification date: 2023-08-02)

Primary citation

Martin, A.M.,Sam, M.D.,Reich, N.O.,Perona, J.J.
Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease.
Nat.Struct.Biol., 6:269-276, 1999

PubMed 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.

PubMed: 10074946
DOI: 10.1038/6707

Experimental method

X-RAY DIFFRACTION (2.15 Å)