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- PDB-9ukq: Crystal structure of glycogen phosphorylase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 9ukq
TitleCrystal structure of glycogen phosphorylase from Escherichia coli
ComponentsGlycogen phosphorylase
KeywordsTRANSFERASE / glycogen phosphorylase
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / protein homodimerization activity / 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
Glycogen phosphorylase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTakai, M. / Shobu, K. / 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
DepositionApr 18, 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: Glycogen phosphorylase
B: Glycogen phosphorylase
C: Glycogen phosphorylase
D: Glycogen phosphorylase
E: Glycogen phosphorylase
F: Glycogen phosphorylase


Theoretical massNumber of molelcules
Total (without water)562,1866
Polymers562,1866
Non-polymers00
Water00
1
A: Glycogen phosphorylase
B: Glycogen phosphorylase
C: Glycogen phosphorylase
D: Glycogen phosphorylase


Theoretical massNumber of molelcules
Total (without water)374,7914
Polymers374,7914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Glycogen phosphorylase
F: Glycogen phosphorylase

E: Glycogen phosphorylase
F: Glycogen phosphorylase


Theoretical massNumber of molelcules
Total (without water)374,7914
Polymers374,7914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)134.769, 205.603, 264.075
Angle α, β, γ (deg.)90.00, 104.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glycogen phosphorylase


Mass: 93697.672 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: glgP, glgY, b3428, JW3391 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC86, 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein conc: 10.4mg/mL; 0.1M MES pH 6.0, 9% (v/v) 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: Nov 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→47.69 Å / Num. obs: 86898 / % possible obs: 99.1 % / Redundancy: 3.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.083 / Rrim(I) all: 0.157 / Net I/σ(I): 6.2
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.949 / Num. unique obs: 4462 / CC1/2: 0.596 / Rpim(I) all: 0.576 / Rrim(I) all: 1.112 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→46.21 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 4436 5.11 %
Rwork0.2307 --
obs0.2329 86855 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38963 0 0 0 38963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00339842
X-RAY DIFFRACTIONf_angle_d0.66554047
X-RAY DIFFRACTIONf_dihedral_angle_d5.1195359
X-RAY DIFFRACTIONf_chiral_restr0.0455872
X-RAY DIFFRACTIONf_plane_restr0.0057028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.540.37491600.35862781X-RAY DIFFRACTION100
3.54-3.580.34841590.33632717X-RAY DIFFRACTION100
3.58-3.630.34731480.31892794X-RAY DIFFRACTION100
3.63-3.670.37021470.31482727X-RAY DIFFRACTION100
3.67-3.720.33261440.31232802X-RAY DIFFRACTION100
3.72-3.770.34991430.31042718X-RAY DIFFRACTION100
3.77-3.820.38871550.31112752X-RAY DIFFRACTION100
3.82-3.880.34021370.2922760X-RAY DIFFRACTION100
3.88-3.940.33021440.28992790X-RAY DIFFRACTION100
3.94-4.010.32111340.27752743X-RAY DIFFRACTION100
4.01-4.080.32651620.27892773X-RAY DIFFRACTION100
4.08-4.150.30141640.26162704X-RAY DIFFRACTION100
4.15-4.230.28671540.26672774X-RAY DIFFRACTION100
4.23-4.320.26611330.25662745X-RAY DIFFRACTION100
4.32-4.410.31751760.24862751X-RAY DIFFRACTION99
4.41-4.510.31681430.2492767X-RAY DIFFRACTION100
4.51-4.620.25921470.23322730X-RAY DIFFRACTION100
4.62-4.750.29171630.23442754X-RAY DIFFRACTION99
4.75-4.890.26351400.2322770X-RAY DIFFRACTION99
4.89-5.050.23441250.22042754X-RAY DIFFRACTION99
5.05-5.230.25911340.22362745X-RAY DIFFRACTION99
5.23-5.440.25631380.22552764X-RAY DIFFRACTION99
5.44-5.680.31151440.23082785X-RAY DIFFRACTION99
5.68-5.980.2921540.23472743X-RAY DIFFRACTION99
5.98-6.350.28311330.24322745X-RAY DIFFRACTION99
6.36-6.840.30021390.23322756X-RAY DIFFRACTION98
6.84-7.530.25761840.20762665X-RAY DIFFRACTION98
7.53-8.610.20861580.17262719X-RAY DIFFRACTION98
8.62-10.830.1481230.13382741X-RAY DIFFRACTION97
10.83-46.210.19681510.14922650X-RAY DIFFRACTION93

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