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- PDB-9maq: Glycogen phosphorylase from D. longicatena -

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Basic information

Entry
Database: PDB / ID: 9maq
TitleGlycogen phosphorylase from D. longicatena
ComponentsAlpha-1,4 glucan phosphorylase
KeywordsSTRUCTURAL PROTEIN / glycogen metabolism / cryo-EM / gut bacteria
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Phosphorylase pyridoxal-phosphate attachment site. / Glycosyl transferase, family 35 / Carbohydrate phosphorylase
Similarity search - Domain/homology
Alpha-1,4 glucan phosphorylase
Similarity search - Component
Biological speciesDorea longicatena DSM 13814 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsTakai, M. / Fukuda, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural and mechanistic diversity of glycogen phosphorylases from gut bacteria.
Authors: Keigo Shobu / Mayu Takai / Hiroki Tanino / Yohta Fukuda / Tsuyoshi Inoue /
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.
History
DepositionMar 14, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2026Group: Database references / Category: citation / citation_author
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Revision 1.2Mar 25, 2026Group: Database references / Category: citation / citation_author
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Revision 1.3Apr 1, 2026Group: Database references / Category: citation / citation_author
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,4 glucan phosphorylase
B: Alpha-1,4 glucan phosphorylase


Theoretical massNumber of molelcules
Total (without water)172,4762
Polymers172,4762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-15 kcal/mol
Surface area53150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.969, 122.851, 136.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Alpha-1,4 glucan phosphorylase


Mass: 86238.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dorea longicatena DSM 13814 (bacteria) / Gene: glgP, malP_2, ERS852423_02459, GT528_00800 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A174FL20, glycogen phosphorylase
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Potassium thiocyanate, 28 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 28, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.8→49.29 Å / Num. obs: 17775 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.104 / Rrim(I) all: 0.27 / Net I/σ(I): 10.1
Reflection shellResolution: 3.8→4.25 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 5 / Num. unique obs: 4958 / CC1/2: 0.939 / Rpim(I) all: 0.262 / Rrim(I) all: 0.687 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
REFMAC5.5refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→48.56 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 859 4.85 %
Rwork0.2014 --
obs0.2046 17716 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12128 0 0 0 12128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412366
X-RAY DIFFRACTIONf_angle_d0.67816728
X-RAY DIFFRACTIONf_dihedral_angle_d7.0471638
X-RAY DIFFRACTIONf_chiral_restr0.0441856
X-RAY DIFFRACTIONf_plane_restr0.0052148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.040.34221190.26312761X-RAY DIFFRACTION100
4.04-4.350.28751440.23052769X-RAY DIFFRACTION100
4.35-4.790.29321340.20672789X-RAY DIFFRACTION100
4.79-5.480.27641410.19292789X-RAY DIFFRACTION100
5.48-6.90.24621680.21692801X-RAY DIFFRACTION100
6.9-48.560.22421530.16012948X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 26.8738 Å / Origin y: -62.6178 Å / Origin z: 36.1385 Å
111213212223313233
T0.6357 Å20.0742 Å20.0114 Å2-0.8002 Å2-0.046 Å2--0.7055 Å2
L0.4414 °2-0.5914 °20.3223 °2-1.5988 °2-0.6496 °2--0.6084 °2
S-0.165 Å °-0.1872 Å °0.0398 Å °0.4037 Å °0.1989 Å °0.0658 Å °-0.0914 Å °-0.2994 Å °-0.0204 Å °
Refinement TLS groupSelection details: all

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