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Nature Structural & Molecular Biology 14, 45–53 (1 January 2007) | doi:10.1038/nsmb1180

Structural insight into the substrate specificity of DNA Polymerase |[mu]|

Andrea F Moon , Miguel Garcia-Diaz , Katarzyna Bebenek , Bryan J Davis , Xuejun Zhong , Dale A Ramsden , Thomas A Kunkel & Lars C Pedersen

DNA polymerase |[mu]| (Pol |[mu]|) is a family X enzyme with unique substrate specificity that contributes to its specialized role in nonhomologous DNA end joining (NHEJ). To investigate Pol |[mu]|'s unusual substrate specificity, we describe the 2.4 |[Aring]| crystal structure of the polymerase domain of murine Pol |[mu]| bound to gapped DNA with a correct dNTP at the active site. This structure reveals substrate interactions with side chains in Pol |[mu]| that differ from other family X members. For example, a single amino acid substitution, H329A, has little effect on template-dependent synthesis by Pol |[mu]| from a paired primer terminus, but it reduces both template-independent and template-dependent synthesis during NHEJ of intermediates whose 3|[prime]| ends lack complementary template strand nucleotides. These results provide insight into the substrate specificity and differing functions of four closely related mammalian family X DNA polymerases.