Nature 382, 278 - 281 (18 July 1996); doi:10.1038/382278a0

Structure of Taq polymerase with DNA at the polymerase active site

Soo Hyun Eom^*, Jimin Wang^* & Thomas A. Steitz^*†‡

Departments of ^* Molecular Biophysics & Biochemistry and ^† Chemistry
^‡ Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8114, USA

THE DNA polymerase from Thermus aquaticus (Taq polymerase) is homologous to Escherichia coli DNA polymerase I (Pol I) and likewise has domains responsible for DNA polymerase and 5' nuclease activities^1,2. The structures of the polymerase domains of Taq polymerase and of the Klenow fragment (KF) of Pol I are almost identical, whereas the structure of a vestigial editing 3'–5' exonuclease domain of Taq polymerase that lies between the other two domains is dramatically altered, resulting in the absence of this activity in the thermostable enzyme². The structures have been solved for editing complexes between KF and single-stranded DNA^3,4 and for duplex DNA with a 3' overhanging single strand⁵, but not for a complex containing duplex DNA at the polymerase active-site. Here we present the co-crystal structure of Taq polymerase with a blunt-ended duplex DNA bound to the polymerase active-site cleft; the DNA neither bends nor goes through the large polymerase cleft, and the structural form of the bound DNA is between the B and A forms. A wide minor groove allows access to protein side chains that hydrogen-bond to the N3 of purines and the O2 of pyrimidines at the blunt-end terminus. Part of the DNA bound to the polymerase site shares a common binding site with DNA bound to the exonuclease site, but they are translated relative to each other by several ångströms along their helix axes.

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