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- EMDB-64926: Cryo-EM structure of glycogen phosphorylase from Dorea longicaten... -

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Basic information

Entry
Database: EMDB / ID: EMD-64926
TitleCryo-EM structure of glycogen phosphorylase from Dorea longicatena (monomer form)
Map datasharp map
Sample
  • Complex: Monomeric structure of DlGP
    • Protein or peptide: Alpha-1,4 glucan phosphorylase
Keywordsglycogen phosphorylase / TRANSFERASE
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 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsTakai M / Tanino H / Shobu K / Fukuda Y / Inoue T
Funding support Japan, 1 items
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
DepositionJun 4, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64926.png

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Map

FileDownload / File: emd_64926.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.0596913 - 1.5600059
Average (Standard dev.)0.00034062142 (±0.023128511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64926_msk_1.map
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Mask #2

Fileemd_64926_msk_2.map
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Mask #3

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Half map: half map B

Fileemd_64926_half_map_1.map
Annotationhalf map B
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Half map: half map A

Fileemd_64926_half_map_2.map
Annotationhalf map A
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Sample components

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Entire : Monomeric structure of DlGP

EntireName: Monomeric structure of DlGP
Components
  • Complex: Monomeric structure of DlGP
    • Protein or peptide: Alpha-1,4 glucan phosphorylase

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Supramolecule #1: Monomeric structure of DlGP

SupramoleculeName: Monomeric structure of DlGP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Dorea longicatena (bacteria)

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Macromolecule #1: Alpha-1,4 glucan phosphorylase

MacromoleculeName: Alpha-1,4 glucan phosphorylase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: glycogen phosphorylase
Source (natural)Organism: Dorea longicatena (bacteria)
Molecular weightTheoretical: 88.22425 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH ENLYFQGMNF SEKLQQTLGK AIKDASNEEI YAALLNTVKE AAADKGRNIS EKGRKVYYIS AEFLIGKLLS NNLINLGVY DEVRELLAAN GKDICEIEEV EPEPSLGNGG LGRLAACFLD SIATLGLEGD GIGLNYHLGL FKQVFENHKQ K ETPNPWIQ ...String:
MGSSHHHHHH ENLYFQGMNF SEKLQQTLGK AIKDASNEEI YAALLNTVKE AAADKGRNIS EKGRKVYYIS AEFLIGKLLS NNLINLGVY DEVRELLAAN GKDICEIEEV EPEPSLGNGG LGRLAACFLD SIATLGLEGD GIGLNYHLGL FKQVFENHKQ K ETPNPWIQ NTSWLTDTGI GFDVPFKDFS LHSKLYDIDV TGYENGTNKL HLFDIESVNE NIVGDGISFD KNDIRENLTL FL YPDDSDK QGELLRIYQQ YFMVSNGAQF ILKECEEKGY SLEELDKHVV IQINDTHPSM VIPELIRLLT ARGISMDKAI EIV TNTCAY TNHTILAEAL EKWPIDYLEA VVPHLMPIIR ELAARVAAKY DNKDVQIIDE WNRVHMARMD MHYGFSVNGV AALH TEILK NVELKPFYDI YPEKFNNKTN GITFRRWLMH CDKKLVEWMD KYGVSEFRKD ASKLEGLLAQ IDNEEALNEL LDVKQ QNKT ALKEYLEKES GVVLNDNAIF DIQIKRLHEY KRQQMNVLYI IYKYLDIKAG NKPKRPITMI FGAKAAPAYI IAKDII HVI LCLQELLKND PEVAPYLQVV MVENYNVTMA EKLIPACEVS EQISLASKEA SGTGNM(LLP)FML NGAVTLGTED GAN VEIHQL VGDENIYIFG ESSDQVIEHY AKSDYVAADY YINDKDIRKW VDFIISPEML KIGDVRTLLE IHAELIQKDW FMTL LDVKD YIQTKERVFA DYEDRMTWAK KMIVNIAKAG FFSSDRTIAE YNRDIWHV

UniProtKB: Alpha-1,4 glucan phosphorylase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
150.0 mMsodium chlorideNaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters droplet, 0 seconds delay before blotting, 1.5 seconds blot, 0 second delay before plunging..

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6822 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

Particle selectionNumber selected: 1476535
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: NONE
Startup modelType of model: INSILICO MODEL / Details: Predicted by ColabFold
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 348670
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9vbl:
Cryo-EM structure of glycogen phosphorylase from Dorea longicatena (monomer form)

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