Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural and mechanistic diversity of glycogen phosphorylases from gut bacteria.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 123, Issue 7, Page e2518513123, Year 2026
Publish date	Feb 17, 2026
Authors	Keigo Shobu / Mayu Takai / Hiroki Tanino / Yohta Fukuda / Tsuyoshi Inoue /
PubMed Abstract	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.
External links	Proc Natl Acad Sci U S A / PubMed:41662519 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.63 - 4.03 Å
Structure data	62853 9l6i EMDB-62853, PDB-9l6i: Glycogen phosphorylase from Segatella copri Method: EM (single particle) / Resolution: 2.98 Å 63736 9m9p EMDB-63736, PDB-9m9p: Glycogen phosphorylase dimer from E. coli Method: EM (single particle) / Resolution: 2.93 Å 63749 9ma8 EMDB-63749, PDB-9ma8: Glycogen phosphorylase from Segatella copri bound to glycogen-chain A and E Method: EM (single particle) / Resolution: 3.85 Å 63814 9u3a EMDB-63814, PDB-9u3a: Glycogen phosphorylase from Segatella copri in complex with AMP Method: EM (single particle) / Resolution: 2.98 Å 63816 9u3k EMDB-63816, PDB-9u3k: Glycogen phosphorylase from Segatella copri pentamer in complex with AMP chains D and E Method: EM (single particle) / Resolution: 3.32 Å 64377 9uoe EMDB-64377, PDB-9uoe: Glycogen phosphorylase tetramer from E. coli Method: EM (single particle) / Resolution: 2.63 Å 64393 9upe EMDB-64393, PDB-9upe: Glycogen phosphorylase dimer from E. coli in complex with AMP. Method: EM (single particle) / Resolution: 3.72 Å 64491 9utg EMDB-64491, PDB-9utg: Glycogen phosphorylase from Segatella copri decamer in complex with AMP Method: EM (single particle) / Resolution: 3.58 Å 64514 9uup EMDB-64514, PDB-9uup: Glycogen phosphorylase from Segatella copri bound to glycogen-pentamer Method: EM (single particle) / Resolution: 4.03 Å 64926 9vbl EMDB-64926, PDB-9vbl: Cryo-EM structure of glycogen phosphorylase from Dorea longicatena (monomer form) Method: EM (single particle) / Resolution: 3.39 Å 64927 9vbm EMDB-64927, PDB-9vbm: Cryo-EM structure of glycogen phosphorylase from Dorea longicatena (dimer form) Method: EM (single particle) / Resolution: 3.19 Å EMDB-64931: Cryo-EM map of glycogen phosphorylase from Dorea longicatena (monomer form with extra density) Method: EM (single particle) / Resolution: 3.3 Å 65039 9vfv EMDB-65039, PDB-9vfv: Glycogen phosphorylase tetramer from E. coli in complex with AMP Method: EM (single particle) / Resolution: 3.14 Å EMDB-65042: Glycogen phosphorylase dimer from E. coli in complex with glycogen Method: EM (single particle) / Resolution: 3.46 Å 67417 20yr EMDB-67417, PDB-20yr: R583A mutant of glycogen phosphorylase from Segatella copri Method: EM (single particle) / Resolution: 3.0 Å 67418 20ys EMDB-67418, PDB-20ys: R583A mutant of glycogen phosphorylase from Segatella copri in the presence of AMP Method: EM (single particle) / Resolution: 2.96 Å PDB-9maq: Glycogen phosphorylase from D. longicatena Method: X-RAY DIFFRACTION / Resolution: 3.8 Å PDB-9ukq: Crystal structure of glycogen phosphorylase from Escherichia coli Method: X-RAY DIFFRACTION / Resolution: 3.5 Å PDB-9ukr: Crystal structure of glycogen phosphorylase from E. coli in complex with AMP Method: X-RAY DIFFRACTION / Resolution: 3.55 Å PDB-9v16: Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant in complex with AMP Method: X-RAY DIFFRACTION / Resolution: 3.45 Å PDB-9v17: Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant Method: X-RAY DIFFRACTION / Resolution: 3.7 Å
Chemicals	ChemComp-G1P: 1-O-phosphono-alpha-D-glucopyranose ChemComp-PO4: PHOSPHATE ION ChemComp-AMP: ADENOSINE MONOPHOSPHATE / AMPYM ChemComp-HOH*: WATER
Source	segatella copri (bacteria) escherichia coli bl21(de3) (bacteria) dorea longicatena (bacteria) dorea longicatena dsm 13814 (bacteria) escherichia coli k12 (bacteria) escherichia coli k-12 (bacteria)
Keywords	TRANSFERASE / glycogen phosphorylase / STRUCTURAL PROTEIN / glycogen metabolism / cryo-EM / gut bacteria