DNA polymerase structure

Sicily. T. A. (1999). DNA polymerases Structural diversity and common mechanisms. J. Biol. Chem. 274, 17395-17398. 

Ahn,J., Wemeburg, B. G., and Tsai, M. D. (1997). DNA polymerase [ Structure-fidelity relationship from pre-steady-state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant. Biochemistry 36, 1100-1107. 

Yang, W. (2003). Damage repair DNA polymerases Y. Curr. Opin. Struct. Biol. 13, 23-30. Zhao, Y., Jeruzalmi, D., Moarefi, I., Leighton, L., Lasken, R., and Kuriyan,J. (1999). Crystal structure of an archaebacterial DNA polymerase. Structure Fold Des. 7, 1189-1199. 

Fig. 4.1.2. A. Structure of Thermits aquaticus (Taq) DNA polymerase bound to the DNA primer-template complex. B. "Open and closed conformation after dNTP binding of Taq DNA polymerase. Structures were built on PDB entries 3KTQ and 4KTQ. 

Taking together, DNA polymerase structural data indicate a high degree of shape complementary between the active sites of the enzymes and the nucleotide substrates, suggesting that geometrical constraints are at least one cause of DNA polymerase fidelity. 

Figure 27.11. DNA Polymerase Structure. The first DNA polymerase structure determined was that of a fragment of E. coli DNA polymerase I called the Klenow fragment. Like other DNA polymerases, the polymerase unit resembles a right hand with fingers (blue), palm (yellow), and thumb (red). The Klenow fragment also includes an exonuclease domain.

Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., and Aggarwal, A.K. (2008) Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Revl DNA polymerase. Structure, 16, 239-245. 

DNA Polymerase Structure-Function Relationships Elucidated with B[a]P-Derived Lesions 335... 

In the rest of this chapter we reflect on what we have observed in our models of Pol IV and UmuC(V), and compare this to the X-ray structures for other Y-family DNA polymerases. Our laboratory has focused on the relationship between DNA polymerase structure and function for B[a]P-N2-dG adducts, which will be described below, although much of this analysis is unpublished [116]. 

Lee, C.H., Chandani, S., and Loechler, E.L. (2006) Homology modeling of four lesion-bypass DNA polymerases structure and lesion bypass findings suggest that E. coli pol IV and human Pol k are orthologs, and E. coli pol V and human Pol r are orthologs. 

DNA Polymerases Enzymes Catalyzing Polynucleotide Chain Elongation Discovery of DNA Polymerase Structure and Activities of DNA Polymerase I... 

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