EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Molecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis.
ジャーナル・号・ページ	Nat Commun, Vol. 15, Issue 1, Page 8, Year 2024
掲載日	2024年1月2日
著者	Jingjing Hong / Tingting Li / Yulin Chao / Yidan Xu / Zhini Zhu / Zixuan Zhou / Weijie Gu / Qianhui Qu / Dianfan Li /
PubMed 要旨	The secretion and quality control of glycosylphosphatidylinositol-anchored proteins (GPI-APs) necessitates post-attachment remodeling initiated by the evolutionarily conserved PGAP1, which deacylates ...The secretion and quality control of glycosylphosphatidylinositol-anchored proteins (GPI-APs) necessitates post-attachment remodeling initiated by the evolutionarily conserved PGAP1, which deacylates the inositol in nascent GPI-APs. Impairment of PGAP1 activity leads to developmental diseases in humans and fatality and infertility in animals. Here, we present three PGAP1 structures (2.66-2.84 Å), revealing its 10-transmembrane architecture and product-enzyme interaction details. PGAP1 holds GPI-AP acyl chains in an optimally organized, guitar-shaped cavity with apparent energetic penalties from hydrophobic-hydrophilic mismatches. However, abundant glycan-mediated interactions in the lumen counterbalance these repulsions, likely conferring substrate fidelity and preventing off-target hydrolysis of bulk membrane lipids. Structural and biochemical analyses uncover a serine hydrolase-type catalysis with atypical features and imply mechanisms for substrate entrance and product release involving a drawing compass movement of GPI-APs. Our findings advance the mechanistic understanding of GPI-AP remodeling.
リンク	Nat Commun / PubMed:38167496 / PubMed Central
手法	EM (単粒子)
解像度	2.66 - 2.84 Å
構造データ	36995 8k9q EMDB-36995, PDB-8k9q: Cryo-EM structure of the GPI inositol-deacylase (PGAP1/Bst1) from Chaetomium thermophilum 手法: EM (単粒子) / 解像度: 2.84 Å 36996 8k9r EMDB-36996, PDB-8k9r: Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum 手法: EM (単粒子) / 解像度: 2.68 Å 36997 8k9t EMDB-36997, PDB-8k9t: Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum 手法: EM (単粒子) / 解像度: 2.66 Å
化合物	ChemComp-Y01: CHOLESTEROL HEMISUCCINATE / コレステリルヘミスクシナ-ト ChemComp-D39: (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid / 1-パルミトイル-2-オレオイルホスファチジルセリン ChemComp-MAN: alpha-D-mannopyranose / α-D-マンノピラノ-ス ChemComp-05E: 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate ChemComp-PA1: 2-amino-2-deoxy-alpha-D-glucopyranose / α-D-グルコサミン ChemComp-L9H: [(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] octadecanoate ChemComp-PLM: PALMITIC ACID / パルミチン酸 ChemComp-CLR: CHOLESTEROL / コレステロ-ル ChemComp-80Y: 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate ChemComp-LYI: [(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z},11~{Z},14~{Z})-icosa-5,8,11,14-tetraenoate
由来	Thermochaetoides thermophila (菌類) synthetic construct (人工物) chaetomium thermophilum (strain dsm 1495 / cbs 144.50 / imi 039719) (菌類) psychromonas sp. b3m02 (バクテリア) homo sapiens (ヒト)
キーワード	MEMBRANE PROTEIN / Bst1 / Glycosylphosphatidylinositol / GPI anchoring / GPI-AP / GPI-AP remodelase / Integral membrane enzyme / Lipase / Lipid remodeling / Membrane enzyme / Nanodisc / PGAP1 / Transmembrane enzyme / Triad enzyme / TGP / Thermostable green fluorescence protein / Triad enzyme.