4J9M

Human DNA polymerase eta-DNA ternary complex: misincorporation G opposite T after an A at the primer 3' end (AA/G)

Summary for 4J9M

• Entry DOI: 10.2210/pdb4j9m/pdb
• Related: 3MR2 4DL2 4DL3 4J9K 4J9L 4J9N 4J9O 4J9P 4J9Q 4J9R 4J9S
• Descriptor: DNA polymerase eta, DNA, MAGNESIUM ION, ... (8 entities in total)
• Functional Keywords: immunoglobulin, a to g transition, misincorporation, wobble base pair, dna polymerase, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: Q9Y253
• Total number of polymer chains: 3
• Total formula weight: 55746.90

Authors

Zhao, Y.,Gregory, M.,Biertumpfel, C.,Hua, Y.,Hanaoka, F.,Yang, W. (deposition date: 2013-02-16, release date: 2013-05-01, Last modification date: 2023-09-20)

Primary citation

Zhao, Y.,Gregory, M.T.,Biertumpfel, C.,Hua, Y.J.,Hanaoka, F.,Yang, W.
Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta.
Proc.Natl.Acad.Sci.USA, 110:8146-8151, 2013

PubMed 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.

PubMed: 23630267
DOI: 10.1073/pnas.1303126110

Experimental method

X-RAY DIFFRACTION (2.25 Å)