Author:
Urs Usha K.,Murali Ramachandran,Krishna Murthy H. M.
Abstract
Thermus aquaticus DNA polymerase I consists of the polymerase, the structure-specific nuclease and the vestigial editing nuclease domains. Three-dimensional structures of the native enzyme and its complex with DNA have already been reported. The structure of a complex with an inhibitory antibody has also been determined. The structure of the native enzyme in a different crystal form determined at 2.6 Å is reported here. Optimized anomalous diffraction measurements made at the holmium L
III edge were valuable in validating solutions obtained through molecular replacement. The structure of the polymerase domain is similar to those reported previously, while the relative orientation of the structure-specific nuclease domain is significantly different from those of the native enzyme and the DNA complex; it is, however, identical to that observed in the structure of the Fab complex. In the structures of the native enzyme and of the DNA complex reported previously, the active site of the structure-specific nuclease domain is too far from that of the polymerase domain, making it difficult to propose a structural model for the in vivo primer-excision and nick-translation activities of the enzyme. In the present structure, the two active sites are considerably closer. Taken together, the reported structure of the native enzyme, that of the Fab complex and the present structure imply that the different orientation of the structure-specific nuclease domain is probably a consequence of intrinsically high relative mobility between these two domains in this enzyme.
Publisher
International Union of Crystallography (IUCr)
Subject
General Medicine,Structural Biology
Cited by
11 articles.
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1. Conformational Dynamics of Thermus aquaticus DNA Polymerase I during Catalysis;Journal of Molecular Biology;2014-08
2. A Model for Transition of 5′-Nuclease Domain of DNA Polymerase I from Inert to Active Modes;PLoS ONE;2011-01-14
3. In defence of our science – validation now!;Acta Crystallographica Section F Structural Biology and Crystallization Communications;2010-01-28
4. In defence of our science – validation now!;Acta Crystallographica Section D Biological Crystallography;2010-01-22
5. Retraction of articles by H. M. Krishna Murthyet al.;Acta Crystallographica Section D Biological Crystallography;2010-01-22