Structure of DNase I at 2.0 A resolution suggests a mechanism for binding to and cutting DNA.
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.
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D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D055598:Chemical Phenomena; D002621:Chemistry; D004247:DNA / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000378:metabolism; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D013942:Thymine Nucleotides / Q000378:metabolism
D010710:Phosphates; D013942:Thymine Nucleotides; C019111:thymidine 3',5'-diphosphate; D004247:DNA; D003850:Deoxyribonuclease I; D002118:Calcium