The Closed Structure of an Archaeal DNA Ligase from Pyrococcus furiosus

Hirokazu Nishida, Shinichi Kiyonari, Yoshizumi Ishino, Kosuke Morikawa

Research output: Contribution to journalArticle

41 Citations (Scopus)

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 Å 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.

Original languageEnglish
Pages (from-to)956-967
Number of pages12
JournalJournal of Molecular Biology
Volume360
Issue number5
DOIs
Publication statusPublished - Jul 28 2006

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Archaeal DNA
Pyrococcus furiosus
DNA Ligases
Catalytic Domain
mRNA guanylyltransferase
DNA
Adenosine Monophosphate
Ligases
Nucleotidyltransferases
Enzymes
Nucleotide Motifs
Double-Stranded DNA Breaks
Static Electricity
Adenosine Triphosphate
Phosphates
Genome

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Cite this

The Closed Structure of an Archaeal DNA Ligase from Pyrococcus furiosus. / Nishida, Hirokazu; Kiyonari, Shinichi; Ishino, Yoshizumi; Morikawa, Kosuke.

In: Journal of Molecular Biology, Vol. 360, No. 5, 28.07.2006, p. 956-967.

Research output: Contribution to journalArticle

Nishida, Hirokazu ; Kiyonari, Shinichi ; Ishino, Yoshizumi ; Morikawa, Kosuke. / The Closed Structure of an Archaeal DNA Ligase from Pyrococcus furiosus. In: Journal of Molecular Biology. 2006 ; Vol. 360, No. 5. pp. 956-967.
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