6RCE

Pmar-Lig_PreS3

6RCE の概要

• エントリーDOI: 10.2210/pdb6rce/pdb
• 分子名称: DNA (5'-D(*TP*TP*CP*CP*GP*AP*CP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3'), DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*C)-3'), DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3'), ... (7 entities in total)
• 機能のキーワード: dna ligase, atp-dependent, ligase-dna co-crystal structure, determinants in dna binding, dna binding protein
• 由来する生物種: Prochlorococcus marinus; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 63186.17

構造登録者

Leiros, H.K.S.,Williamson, A. (登録日: 2019-04-11, 公開日: 2019-07-10, 最終更新日: 2024-01-24)

主引用文献

Williamson, A.,Leiros, H.S.
Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation.
Nucleic Acids Res., 47:7147-7162, 2019

PubMed Abstract: DNA ligases join adjacent 5' phosphate (5'P) and 3' hydroxyl (3'OH) termini of double-stranded DNA via a three-step mechanism requiring a nucleotide cofactor and divalent metal ion. Although considerable structural detail is available for the first two steps, less is known about step 3 where the DNA-backbone is joined or about the cation role at this step. We have captured high-resolution structures of an adenosine triphosphate (ATP)-dependent DNA ligase from Prochlorococcus marinus including a Mn-bound pre-ternary ligase-DNA complex poised for phosphodiester bond formation, and a post-ternary intermediate retaining product DNA and partially occupied AMP in the active site. The pre-ternary structure unambiguously identifies the binding site of the catalytic metal ion and confirms both its role in activating the 3'OH terminus for nucleophilic attack on the 5'P group and stabilizing the pentavalent transition state. The post-ternary structure indicates that DNA distortion and most enzyme-AMP contacts remain after phosphodiester bond formation, implying loss of covalent linkage to the DNA drives release of AMP, rather than active site rearrangement. Additionally, comparisons of this cyanobacterial DNA ligase with homologs from bacteria and bacteriophage pose interesting questions about the structural origin of double-strand break joining activity and the evolution of these ATP-dependent DNA ligase enzymes.

PubMed: 31312841
DOI: 10.1093/nar/gkz596

実験手法

X-RAY DIFFRACTION (1.946 Å)