2FMP

DNA Polymerase beta with a terminated gapped DNA substrate and ddCTP with sodium in the catalytic site

2FMP の概要

• エントリーDOI: 10.2210/pdb2fmp/pdb
• 関連するPDBエントリー: 2FMQ 2FMS
• 分子名称: 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... (8 entities in total)
• 機能のキーワード: nucleotidyl transferase, transferase-dna complex, transferase/dna
• 由来する生物種: Homo sapiens (human)
• 細胞内の位置: Nucleus: P06746
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 48282.28

構造登録者

Batra, V.K.,Beard, W.A.,Shock, D.D.,Krahn, J.M.,Pedersen, L.C.,Wilson, S.H. (登録日: 2006-01-09, 公開日: 2006-04-25, 最終更新日: 2023-08-30)

主引用文献

Batra, V.K.,Beard, W.A.,Shock, D.D.,Krahn, J.M.,Pedersen, L.C.,Wilson, S.H.
Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
Structure, 14:757-766, 2006

PubMed Abstract: The molecular details of the nucleotidyl transferase reaction have remained speculative, as strategies to trap catalytic intermediates for structure determination utilize substrates lacking the primer terminus 3'-OH and catalytic Mg2+, resulting in an incomplete and distorted active site geometry. Since the geometric arrangement of these essential atoms will impact chemistry, structural insight into fidelity strategies has been hampered. Here, we present a crystal structure of a precatalytic complex of a DNA polymerase with bound substrates that include the primer 3'-OH and catalytic Mg2+. This catalytic intermediate was trapped with a nonhydrolyzable deoxynucleotide analog. Comparison with two new structures of DNA polymerase beta lacking the 3'-OH or catalytic Mg2+ is described. These structures provide direct evidence that both atoms are required to achieve a proper geometry necessary for an in-line nucleophilic attack of O3' on the alphaP of the incoming nucleotide.

PubMed: 16615916
DOI: 10.1016/j.str.2006.01.011

実験手法

X-RAY DIFFRACTION (1.65 Å)