Crystal structure of yeast DNA polymerase ε catalytic domain

Rinku Jain, Kanagalaghatta R. Rajashankar, Angeliki Buku, Robert E. Johnson, Louise Prakash, Satya Prakash, Aneel K. Aggarwal

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

DNA polymerase e (Pole) is a multi-subunit polymerase that contributes to genomic stability via its roles in leading strand replication and the repair of damaged DNA. Here we report the ternary structure of the Pole catalytic subunit (Pol2) bound to a nascent G:C base pair (Pol2G:C). Pol2G:C has a typical B-family polymerase fold and embraces the template-primer duplex with the palm, fingers, thumb and exonuclease domains. The overall arrangement of domains is similar to the structure of Pol2T:A reported recently, but there are notable differences in their polymerase and exonuclease active sites. In particular, we observe Ca2+ ions at both positions A and B in the polymerase active site and also observe a Ca2+ at position B of the exonuclease site. We find that the contacts to the nascent G:C base pair in the Pol2G:C structure are maintained in the Pol2T:A structure and reflect the comparable fidelity of Pol2 for nascent purine-pyrimidine and pyrimidine-purine base pairs. We note that unlike that of Pol3, the shape of the nascent base pair binding pocket in Pol2 is modulated from the major grove side by the presence of Tyr431. Together with Pol2 T:A, our results provide a framework for understanding the structural basis of high fidelity DNA synthesis by Pol2.

Original languageEnglish (US)
Article numbere94835
JournalPLoS One
Volume9
Issue number4
DOIs
StatePublished - Apr 14 2014

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Exonucleases
DNA-directed DNA polymerase
DNA-Directed DNA Polymerase
crystal structure
active sites
Base Pairing
Yeast
Catalytic Domain
Yeasts
Crystal structure
pyrimidines
purines
yeasts
calcium
DNA
groves
protein subunits
DNA repair
Genomic Instability
Thumb

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Jain, R., Rajashankar, K. R., Buku, A., Johnson, R. E., Prakash, L., Prakash, S., & Aggarwal, A. K. (2014). Crystal structure of yeast DNA polymerase ε catalytic domain. PLoS One, 9(4), [e94835]. https://doi.org/10.1371/journal.pone.0094835

Crystal structure of yeast DNA polymerase ε catalytic domain. / Jain, Rinku; Rajashankar, Kanagalaghatta R.; Buku, Angeliki; Johnson, Robert E.; Prakash, Louise; Prakash, Satya; Aggarwal, Aneel K.

In: PLoS One, Vol. 9, No. 4, e94835, 14.04.2014.

Research output: Contribution to journalArticle

Jain, R, Rajashankar, KR, Buku, A, Johnson, RE, Prakash, L, Prakash, S & Aggarwal, AK 2014, 'Crystal structure of yeast DNA polymerase ε catalytic domain', PLoS One, vol. 9, no. 4, e94835. https://doi.org/10.1371/journal.pone.0094835
Jain, Rinku ; Rajashankar, Kanagalaghatta R. ; Buku, Angeliki ; Johnson, Robert E. ; Prakash, Louise ; Prakash, Satya ; Aggarwal, Aneel K. / Crystal structure of yeast DNA polymerase ε catalytic domain. In: PLoS One. 2014 ; Vol. 9, No. 4.
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