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	Structural and mechanistic diversity of glycogen phosphorylases from gut bacteria.
ジャーナル・号・ページ	Proc Natl Acad Sci U S A, Vol. 123, Issue 7, Page e2518513123, Year 2026
掲載日	2026年2月17日
著者	Keigo Shobu / Mayu Takai / Hiroki Tanino / Yohta Fukuda / Tsuyoshi Inoue /
PubMed 要旨	Glycogen phosphorylase (GP) plays a central role in glycogen metabolism. While the structure and regulation of mammalian GPs have been extensively studied, the corresponding mechanisms in gut ...Glycogen phosphorylase (GP) plays a central role in glycogen metabolism. While the structure and regulation of mammalian GPs have been extensively studied, the corresponding mechanisms in gut bacterial GPs remain poorly understood. Here, we investigate GPs from (GP), (GP), and (GP), which represent three phylogenetic clades of GPs, using enzymatic assays, cryo-electron microscopy (cryo-EM), and X-ray crystallography. We find that GP forms a unique pentamer that undergoes adenosine monophosphate (AMP)-dependent assembly into a dimer-of-pentamer, which inhibits activity by restricting substrate access to the catalytic site. GP exists in equilibrium among monomers, dimers, and tetramers, with AMP promoting tetramer dissociation and enhancing catalytic efficiency. In contrast, GP remains predominantly monomeric and is unresponsive to AMP. These findings uncover structural and regulatory diversity among gut bacterial GPs. Notably, the oligomeric states of GPs modulate substrate accessibility and enzyme activation, suggesting a distinct mode of allosteric regulation beyond the canonical T-to-R transition model. Because bacterial GPs contribute to the generation of glucose, their regulation may influence the composition of gut-derived metabolites that affect host glucose homeostasis and insulin sensitivity. Our study provides mechanistic insight into the structural and functional diversity of gut bacterial GPs and lays a foundation for future exploration of microbiome-mediated metabolic interactions.
リンク	Proc Natl Acad Sci U S A / PubMed:41662519 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	2.63 - 4.03 Å
構造データ	62853 9l6i EMDB-62853, PDB-9l6i: Glycogen phosphorylase from Segatella copri 手法: EM (単粒子) / 解像度: 2.98 Å 63736 9m9p EMDB-63736, PDB-9m9p: Glycogen phosphorylase dimer from E. coli 手法: EM (単粒子) / 解像度: 2.93 Å 63749 9ma8 EMDB-63749, PDB-9ma8: Glycogen phosphorylase from Segatella copri bound to glycogen-chain A and E 手法: EM (単粒子) / 解像度: 3.85 Å 63814 9u3a EMDB-63814, PDB-9u3a: Glycogen phosphorylase from Segatella copri in complex with AMP 手法: EM (単粒子) / 解像度: 2.98 Å 63816 9u3k EMDB-63816, PDB-9u3k: Glycogen phosphorylase from Segatella copri pentamer in complex with AMP chains D and E 手法: EM (単粒子) / 解像度: 3.32 Å 64377 9uoe EMDB-64377, PDB-9uoe: Glycogen phosphorylase tetramer from E. coli 手法: EM (単粒子) / 解像度: 2.63 Å 64393 9upe EMDB-64393, PDB-9upe: Glycogen phosphorylase dimer from E. coli in complex with AMP. 手法: EM (単粒子) / 解像度: 3.72 Å 64491 9utg EMDB-64491, PDB-9utg: Glycogen phosphorylase from Segatella copri decamer in complex with AMP 手法: EM (単粒子) / 解像度: 3.58 Å 64514 9uup EMDB-64514, PDB-9uup: Glycogen phosphorylase from Segatella copri bound to glycogen-pentamer 手法: EM (単粒子) / 解像度: 4.03 Å 64926 9vbl EMDB-64926, PDB-9vbl: Cryo-EM structure of glycogen phosphorylase from Dorea longicatena (monomer form) 手法: EM (単粒子) / 解像度: 3.39 Å 64927 9vbm EMDB-64927, PDB-9vbm: Cryo-EM structure of glycogen phosphorylase from Dorea longicatena (dimer form) 手法: EM (単粒子) / 解像度: 3.19 Å EMDB-64931: Cryo-EM map of glycogen phosphorylase from Dorea longicatena (monomer form with extra density) 手法: EM (単粒子) / 解像度: 3.3 Å 65039 9vfv EMDB-65039, PDB-9vfv: Glycogen phosphorylase tetramer from E. coli in complex with AMP 手法: EM (単粒子) / 解像度: 3.14 Å EMDB-65042: Glycogen phosphorylase dimer from E. coli in complex with glycogen 手法: EM (単粒子) / 解像度: 3.46 Å 67417 20yr EMDB-67417, PDB-20yr: R583A mutant of glycogen phosphorylase from Segatella copri 手法: EM (単粒子) / 解像度: 3.0 Å 67418 20ys EMDB-67418, PDB-20ys: R583A mutant of glycogen phosphorylase from Segatella copri in the presence of AMP 手法: EM (単粒子) / 解像度: 2.96 Å PDB-9maq: Glycogen phosphorylase from D. longicatena 手法: X-RAY DIFFRACTION / 解像度: 3.8 Å PDB-9ukq: Crystal structure of glycogen phosphorylase from Escherichia coli 手法: X-RAY DIFFRACTION / 解像度: 3.5 Å PDB-9ukr: Crystal structure of glycogen phosphorylase from E. coli in complex with AMP 手法: X-RAY DIFFRACTION / 解像度: 3.55 Å PDB-9v16: Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant in complex with AMP 手法: X-RAY DIFFRACTION / 解像度: 3.45 Å PDB-9v17: Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant 手法: X-RAY DIFFRACTION / 解像度: 3.7 Å
化合物	ChemComp-G1P: 1-O-phosphono-alpha-D-glucopyranose / グルコ-ス-1-りん酸 ChemComp-PO4: PHOSPHATE ION / ホスファ-ト ChemComp-AMP: ADENOSINE MONOPHOSPHATE / AMP / AMPYM ChemComp-HOH*: WATER
由来	segatella copri (バクテリア) escherichia coli bl21(de3) (大腸菌) dorea longicatena (バクテリア) dorea longicatena dsm 13814 (バクテリア) escherichia coli k12 (大腸菌) escherichia coli k-12 (大腸菌)
キーワード	TRANSFERASE / glycogen phosphorylase / STRUCTURAL PROTEIN / glycogen metabolism / cryo-EM / gut bacteria