Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis.
It is generally assumed that an enzyme-substrate (ES) complex contains all components necessary for catalysis and that conversion to products occurs by rearrangement of atoms, protons, and electrons. However, we find that DNA synthesis does not occur in a fully assembled DNA polymerase-DNA-deoxynucleoside triphosphate complex with two canonical metal ions bound. Using time-resolved x-ray crystallography, we show that the phosphoryltransfer reaction takes place only after the ES complex captures a third divalent cation that is not coordinated by the enzyme. Binding of the third cation is incompatible with the basal ES complex and requires thermal activation of the ES for entry. It is likely that the third cation provides the ultimate boost over the energy barrier to catalysis of DNA synthesis.
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Yang
Y
Gao
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. wei.yang@nih.gov.
Wei
W
Yang
D055162:Biocatalysis; D002413:Cations, Divalent / Q000737:chemistry; D018360:Crystallography, X-Ray; D004247:DNA / Q000096:biosynthesis*; D004261:DNA Replication; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000648:ultrastructure; D008274:Magnesium / Q000737:chemistry*; D008345:Manganese / Q000737:chemistry; D009711:Nucleotides / Q000737:chemistry; D000099270:Y-Family DNA Polymerases
D002413:Cations, Divalent; D004247:DNA; D004259:DNA-Directed DNA Polymerase; D008274:Magnesium; D008345:Manganese; D009711:Nucleotides; C112338:Rad30 protein; D000099270:Y-Family DNA Polymerases