ジャーナル: Proc Natl Acad Sci U S A / 年: 2015 タイトル: Structural and functional insights into Escherichia coli α2-macroglobulin endopeptidase snap-trap inhibition. 著者: Irene Garcia-Ferrer / Pedro Arêde / Josué Gómez-Blanco / Daniel Luque / Stephane Duquerroy / José R Castón / Theodoros Goulas / F Xavier Gomis-Rüth / 要旨: The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2- ...The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2-macroglobulin (α2M). Escherichia coli α2M (ECAM) is a ∼ 180-kDa multidomain membrane-anchored pan-peptidase inhibitor, which is cleaved by host endopeptidases in an accessible bait region. Structural studies by electron microscopy and crystallography reveal that this cleavage causes major structural rearrangement of more than half the 13-domain structure from a native to a compact induced form. It also exposes a reactive thioester bond, which covalently traps the peptidase. Subsequently, peptidase-laden ECAM is shed from the membrane and may dimerize. Trapped peptidases are still active except against very large substrates, so inhibition potentially prevents damage of large cell envelope components, but not host digestion. Mechanistically, these results document a novel monomeric "snap trap."
解像度: 2.7→48 Å / Num. all: 28350 / Num. obs: 28350 / % possible obs: 99.4 % / 冗長度: 6.4 % / Biso Wilson estimate: 86 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.3
反射 シェル
解像度: 2.7→2.77 Å / 冗長度: 6.6 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.9 / % possible all: 95.3
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解析
ソフトウェア
名称
バージョン
分類
XDS
データ削減
XSCALE
データスケーリング
SHELXDE
位相決定
Coot
モデル構築
BUSTER
2.11.5
精密化
精密化
構造決定の手法: 単一同系置換・異常分散 開始モデル: dataset of a Se-Met crystal collected at the selenium absorption peak and a native dataset to higher resolution 解像度: 2.7→47.98 Å / Cor.coef. Fo:Fc: 0.9405 / Cor.coef. Fo:Fc free: 0.8812 / SU R Cruickshank DPI: 0.404 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.398 / SU Rfree Blow DPI: 0.268 / SU Rfree Cruickshank DPI: 0.273