Mechanism of somatic hypermutation at the WA motif by human DNA polymerase η

Proc Natl Acad Sci U S A. 2013 May 14;110(20):8146-51. doi: 10.1073/pnas.1303126110. Epub 2013 Apr 29.


Somatic hypermutation is programmed base substitutions in the variable regions of Ig genes for high-affinity antibody generation. Two motifs, RGYW and WA (R, purine; Y, pyrimidine; W, A or T), have been found to be somatic hypermutation hotspots. Overwhelming evidence suggests that DNA polymerase η (Pol η) is responsible for converting the WA motif to WG by misincorporating dGTP opposite the templating T. To elucidate the molecular mechanism, crystal structures and kinetics of human Pol η substituting dGTP for dATP in four sequence contexts, TA, AA, GA, and CA, have been determined and compared. The T:dGTP wobble base pair is stabilized by Gln-38 and Arg-61, two uniquely conserved residues among Pol η. Weak base paring of the W (T:A or A:T) at the primer end and their distinct interactions with Pol η lead to misincorporation of G in the WA motif. Between two WA motifs, our kinetic and structural data indicate that A-to-G mutation occurs more readily in the TA context than AA. Finally, Pol η can extend the T:G mispair efficiently to complete the mutagenesis.

Keywords: A-to-G transition; immunoglobulin; π–cation stacking.

Publication types

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

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Amino Acid Motifs
  • Cations
  • DNA-Directed DNA Polymerase / chemistry*
  • Deoxyguanine Nucleotides / chemistry
  • Humans
  • Immunoglobulins / chemistry
  • Kinetics
  • Mutagenesis, Site-Directed
  • Mutation
  • Nucleic Acid Conformation
  • Somatic Hypermutation, Immunoglobulin*


  • Cations
  • Deoxyguanine Nucleotides
  • Immunoglobulins
  • deoxyguanosine triphosphate
  • Adenosine Triphosphate
  • DNA-Directed DNA Polymerase
  • Rad30 protein

Associated data

  • PDB/4J9K
  • PDB/4J9L
  • PDB/4J9M
  • PDB/4J9N
  • PDB/4J9O
  • PDB/4J9P
  • PDB/4J9Q
  • PDB/4J9R
  • PDB/4J9S