Structure of DNase I at 2.0 A resolution suggests a mechanism for binding to and cutting DNA

Nature. 1986 Jun;321(6070):620-5. doi: 10.1038/321620a0.

Abstract

Bovine pancreatic deoxyribonuclease I (DNase I), an endonuclease that degrades double-stranded DNA in a nonspecific but sequence-dependent manner, has been used as a biochemical tool in various reactions, in particular as a probe for the structure of chromatin and for the helical periodicity of DNA on the nucleosome and in solution. Limited digestion by DNase I, termed DNase I 'footprinting', is routinely used to detect protected regions in DNA-protein complexes. Recently, we have solved the three-dimensional structure of this glycoprotein (relative molecular mass 30,400) by X-ray structure analysis at 2.5 A resolution and have subsequently refined it crystallographically at 2.0 A. Based on the refined structure and the binding of Ca2+-thymidine 3',5'-diphosphate (Ca-pTp) at the active site, we propose a mechanism of action and present a model for the interaction of DNase I with double-stranded DNA that involves the binding of an exposed loop region in the minor groove of B-DNA and electrostatic interactions of phosphates from both strands with arginine and lysine residues on either side of this loop. We explain DNase I cleavage patterns in terms of this model and discuss the consequences of the extended DNase I-DNA contact region for the interpretation of DNase I footprinting results.

MeSH terms

  • Binding Sites
  • Calcium / metabolism
  • Chemical Phenomena
  • Chemistry
  • DNA / metabolism*
  • Deoxyribonuclease I / metabolism*
  • Models, Molecular
  • Nucleic Acid Conformation
  • Phosphates / metabolism
  • Protein Conformation
  • Structure-Activity Relationship
  • Thymine Nucleotides / metabolism

Substances

  • Phosphates
  • Thymine Nucleotides
  • thymidine 3',5'-diphosphate
  • DNA
  • Deoxyribonuclease I
  • Calcium