2CFM

ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS

2CFM の概要

• エントリーDOI: 10.2210/pdb2cfm/pdb
• 分子名称: THERMOSTABLE DNA LIGASE, MAGNESIUM ION, ADENOSINE MONOPHOSPHATE, ... (4 entities in total)
• 機能のキーワード: ligase, protein-nucleotide complex, cell cycle, cell division, dna damage, dna recombination, dna repair, dna replication, nucleotide-binding
• 由来する生物種: PYROCOCCUS FURIOSUS
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 64991.08

構造登録者

Nishida, H.,Ishino, Y.,Morikawa, K. (登録日: 2006-02-22, 公開日: 2006-07-12, 最終更新日: 2024-11-06)

主引用文献

Nishida, H.,Kiyonari, S.,Ishino, Y.,Morikawa, K.
The Closed Structure of an Archaeal DNA Ligase from Pyrococcus Furiosus.
J.Mol.Biol., 360:956-, 2006

PubMed Abstract: DNA ligases join single-strand breaks in double-stranded DNA, and are essential to maintain genome integrity in DNA metabolism. Here, we report the 1.8 A resolution structure of Pyrococcus furiosus DNA ligase (PfuLig), which represents the first full-length atomic view of an ATP-dependent eukaryotic-type DNA ligase. The enzyme comprises the N-terminal DNA-binding domain, the middle adenylation domain, and the C-terminal OB-fold domain. The architecture of each domain resembles those of human DNA ligase I, but the domain arrangements differ strikingly between the two enzymes. The closed conformation of the two "catalytic core" domains at the carboxyl terminus in PfuLig creates a small compartment, which holds a non-covalently bound AMP molecule. This domain rearrangement results from the "domain-connecting" role of the helical extension conserved at the C termini in archaeal and eukaryotic DNA ligases. The DNA substrate in the human open-ligase is replaced by motif VI in the Pfu closed-ligase. Both the shapes and electrostatic distributions are similar between motif VI and the DNA substrate, suggesting that motif VI in the closed state mimics the incoming substrate DNA. Two basic residues (R531 and K534) in motif VI reside within the active site pocket and interact with the phosphate group of the bound AMP. The crystallographic and functional analyses of mutant enzymes revealed that these two residues within the RxDK sequence play essential and complementary roles in ATP processing. This sequence is also conserved exclusively among the covalent nucleotidyltransferases, even including mRNA-capping enzymes with similar helical extensions at the C termini.

PubMed: 16820169
DOI: 10.1016/J.JMB.2006.05.062

実験手法

X-RAY DIFFRACTION (1.8 Å)