Watching DNA Polymerase η Make a Phosphodiester Bond

• NAKAMURA Teruya

  Graduate School of Pharmaceutical Sciences, Kumamoto University

• YAMAGATA Yuriko

  Graduate School of Pharmaceutical Sciences, Kumamoto University

• YANG Wei

  Laboratory of Molecular Biology, NIDDK, NIH

Bibliographic Information

Other Title

• DNAポリメラーゼηによるリン酸ジエステル結合の形成過程の観察
• DNA ポリメラーゼe ニ ヨル リンサン ジエステル ケツゴウ ノ ケイセイ カテイ ノ カンサツ

Abstract

A number of structural and kinetic studies of DNA polymerases have proposed the catalytic mechanism of the nucleotidyl-transfer reaction. However, the actual process has never been visualized. Here we show the nucleotidyl-transfer reaction process catalyzed by human DNA polymerase η using time-resolved protein crystallography. In sequence, the nucleophile 3′-OH is deprotonated, the deoxyribose at the primer end converts from C2′-endo to C3′-endo, and the nucleophile and the α-phosphate of dATP approach each other to form the new bond. A third Mg²⁺ ion, which arrives with the new bond and stabilizes the intermediate state, may be an unappreciated feature of the two-metal-ion mechanism.<br>

Journal

• Seibutsu Butsuri

  Seibutsu Butsuri 53 (5), 254-257, 2013

  The Biophysical Society of Japan General Incorporated Association

Keywords

• Time resolved protein crystallography
• DNA polymerase
• Nucleotidyl transfer reaction

Details

• CRID: 1390001206534336640
• NII Article ID: 10031191847
• NII Book ID: AN00129693
• DOI: 10.2142/biophys.53.254
• COI: 1:CAS:528:DC%2BC3sXhsFCht7%2FJ
• ISSN: 13474219
• ISSN: 05824052
• NDL BIB ID: 024919348
• Web Site: https://ndlsearch.ndl.go.jp/books/R000000004-I024919348
• Web Site: https://www.jstage.jst.go.jp/article/biophys/53/5/53_254/_pdf
• Web Site: https://search.jamas.or.jp/link/ui/2014048358
• Text Lang: ja
• Data Source:
  • JaLC
  • NDL
  • Crossref
  • CiNii Articles
  • KAKEN
• Abstract License Flag: Disallowed