1DQ3

CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI

1DQ3 の概要

• エントリーDOI: 10.2210/pdb1dq3/pdb
• 分子名称: ENDONUCLEASE, ZINC ION (3 entities in total)
• 機能のキーワード: endonuclease, pi-pfui, intein-encoded, hydrolase
• 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: 53225.85

構造登録者

Ichiyanagi, K.,Ishino, Y.,Morikawa, K. (登録日: 1999-12-30, 公開日: 2000-07-05, 最終更新日: 2024-02-07)

主引用文献

Ichiyanagi, K.,Ishino, Y.,Ariyoshi, M.,Komori, K.,Morikawa, K.
Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI.
J.Mol.Biol., 300:889-901, 2000

PubMed Abstract: Inteins possess two different enzymatic activities, self-catalyzed protein splicing and site-specific DNA cleavage. These endonucleases, which are classified as part of the homing endonuclease family, initiate the mobility of their genetic elements into homologous alleles. They recognize long asymmetric nucleotide sequences and cleave both DNA strands in a monomer form. We present here the 2.1 A crystal structure of the archaeal PI-PfuI intein from Pyroccocus furiosus. The structure reveals a unique domain, designated here as the Stirrup domain, which is inserted between the Hint domain and an endonuclease domain. The horseshoe-shaped Hint domain contains a catalytic center for protein splicing, which involves both N and C-terminal residues. The endonuclease domain, which is inserted into the Hint domain, consists of two copies of substructure related by an internal pseudo 2-fold axis. In contrast with the I-CreI homing endonuclease, PI-PfuI possibly has two asymmetric catalytic sites at the center of a putative DNA-binding cleft formed by a pair of four-stranded beta-sheets. DNase I footprinting experiments showed that PI-PfuI covers more than 30 bp of the substrate asymmetrically across the cleavage site. A docking model of the DNA-enzyme complex suggests that the endonuclease domain covers the 20 bp DNA duplex encompassing the cleavage site, whereas the Stirrup domain could make an additional contact with another upstream 10 bp region. For the double-strand break, the two strands in the DNA duplex were cleaved by PI-PfuI with different efficiencies. We suggest that the cleavage of each strand is catalyzed by each of the two non-equivalent active sites.

PubMed: 10891276
DOI: 10.1006/jmbi.2000.3873

実験手法

X-RAY DIFFRACTION (2.1 Å)