Structural insight into the substrate specificity of DNA Polymerase mu

Nat Struct Mol Biol. 2007 Jan;14(1):45-53. doi: 10.1038/nsmb1180. Epub 2006 Dec 10.


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 A 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' 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Amino Acid Substitution
  • Animals
  • Binding Sites
  • Crystallography, X-Ray
  • DNA / chemistry
  • DNA / metabolism
  • DNA Repair
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / metabolism*
  • Dideoxynucleotides
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Substrate Specificity
  • Thymine Nucleotides / metabolism


  • DNA-Binding Proteins
  • Dideoxynucleotides
  • Thymine Nucleotides
  • DNA
  • DNA polymerase mu
  • DNA-Directed DNA Polymerase
  • 2',3'-dideoxythymidine triphosphate

Associated data

  • PDB/2IHM