PDBsum entry 4j9m

Transferase/DNA

PDB id: 4j9m

Contents

Protein chain

429 a.a.

DNA/RNA

Ligands

XG4

GOL ×2

Metals

_MG ×2

_NA

Waters ×188

References listed in PDB file

Key reference

• Title: Mechanism of somatic hypermutation at the wa motif by human DNA polymerase η.
• Authors: Y.Zhao, M.T.Gregory, C.Biertümpfel, Y.J.Hua, F.Hanaoka, W.Yang.
• Ref.: Proc Natl Acad Sci U S A, 2013, 110, 8146-8151. [DOI no: 10.1073/pnas.1303126110]
• PubMed id: 23630267

Abstract

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.