1JVA

CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES

1JVA の概要

• エントリーDOI: 10.2210/pdb1jva/pdb
• 関連するPDBエントリー: 1EF0 1VDE
• 分子名称: VMA1-DERIVED HOMING ENDONUCLEASE X10SSS (2 entities in total)
• 機能のキーワード: protein-splicing, vma1-derived endonuclease, intein, thiazolidine intermediate, vde, hydrolase
• 由来する生物種: Saccharomyces cerevisiae (baker's yeast)
• 細胞内の位置: Endomembrane system: P17255
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 106300.29

構造登録者

Mizutani, R.,Satow, Y. (登録日: 2001-08-29, 公開日: 2002-08-29, 最終更新日: 2023-10-25)

主引用文献

Mizutani, R.,Nogami, S.,Kawasaki, M.,Ohya, Y.,Anraku, Y.,Satow, Y.
Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides.
J.Mol.Biol., 316:919-929, 2002

PubMed Abstract: Protein splicing excises an internal intein segment from a protein precursor precisely, and concomitantly ligates flanking N and C-extein polypeptides at the respective sides of the precursor. Here, a series of precursor recombinants bearing 11 N-extein and ten C-extein residues is prepared for the intein of the Saccharomyces cerevisiae VMA1-derived homing endonuclease referred to as VDE and as PI-SceI. The recombinant with replacements of C284S, H362N, N737S, and C738S is chosen as a spliceable precursor model and is then subjected to a 2.1A resolution crystallographic analysis. The crystal structure shows that the introduced extein polypeptides are located in the vicinity of the splicing site, and that each of their peptide bonds is in the trans conformation. The S284 O(gamma) atom located at a distance of 3.1A from the G283 C atom in the N-terminal junction suggests that a nucleophilic attack of the C284 S(gamma) atom on the G283 C atom forms a tetrahedral intermediate containing a five-membered thiazolidine ring. The tetrahedral intermediate is supposedly resolved into a thioester acyl group upon the cleavage of the linkage between the G283 C and C284 N atoms, and this thioester acyl formation completes the initial steps of Nright arrowS acyl shift at the junction between the N-extein and intein. The S738 O(gamma) atom in the C-terminal junction is placed in close proximity to the S284 O(gamma) atom at a distance of 3.6A, and is well suited for another nucleophilic attack on the resultant thioester acyl group that is then subjected to the transesterification in the next step. The reaction steps proposed for the acyl shift are driven entirely by protonation and deprotonation, in which proton ingress and egress is balanced within the splicing site.

PubMed: 11884132
DOI: 10.1006/jmbi.2001.5357

実験手法

X-RAY DIFFRACTION (2.1 Å)