6DT1

Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate

6DT1 の概要

• エントリーDOI: 10.2210/pdb6dt1/pdb
• 分子名称: DNA ligase, ADENOSINE MONOPHOSPHATE, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(DOC))-3'), ... (11 entities in total)
• 機能のキーワード: ligase-dna complex, ligase, ligase/dna
• 由来する生物種: Enterobacteria phage T4 (Bacteriophage T4); 詳細
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 143640.85

構造登録者

Shi, K.,Aihara, H. (登録日: 2018-06-14, 公開日: 2018-09-19, 最終更新日: 2023-10-11)

主引用文献

Shi, K.,Bohl, T.E.,Park, J.,Zasada, A.,Malik, S.,Banerjee, S.,Tran, V.,Li, N.,Yin, Z.,Kurniawan, F.,Orellana, K.,Aihara, H.
T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.
Nucleic Acids Res., 46:10474-10488, 2018

PubMed Abstract: DNA ligases play essential roles in DNA replication and repair. Bacteriophage T4 DNA ligase is the first ATP-dependent ligase enzyme to be discovered and is widely used in molecular biology, but its structure remained unknown. Our crystal structure of T4 DNA ligase bound to DNA shows a compact α-helical DNA-binding domain (DBD), nucleotidyl-transferase (NTase) domain, and OB-fold domain, which together fully encircle DNA. The DBD of T4 DNA ligase exhibits remarkable structural homology to the core DNA-binding helices of the larger DBDs from eukaryotic and archaeal DNA ligases, but it lacks additional structural components required for protein interactions. T4 DNA ligase instead has a flexible loop insertion within the NTase domain, which binds tightly to the T4 sliding clamp gp45 in a novel α-helical PIP-box conformation. Thus, T4 DNA ligase represents a prototype of the larger eukaryotic and archaeal DNA ligases, with a uniquely evolved mode of protein interaction that may be important for efficient DNA replication.

PubMed: 30169742
DOI: 10.1093/nar/gky776

実験手法

X-RAY DIFFRACTION (2.75 Å)