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- EMDB-63816: Glycogen phosphorylase from Segatella copri pentamer in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-63816
TitleGlycogen phosphorylase from Segatella copri pentamer in complex with AMP chains D and E
Map data
Sample
  • Complex: glycogen phosphorylase
    • Protein or peptide: Alpha-glucan family phosphorylase
  • Ligand: ADENOSINE MONOPHOSPHATE
Keywordsglycogen metabolism / cryo-EM / gut bacteria / STRUCTURAL PROTEIN
Function / homology
Function and homology information


glycogen phosphorylase activity / pyridoxal phosphate binding / carbohydrate metabolic process
Similarity search - Function
Alpha-glucan phosphorylase / Glycogen phosphorylase, domain of unknown function DUF3417 / : / Protein of unknown function (DUF3417) / Glycosyl transferase, family 35 / Carbohydrate phosphorylase
Similarity search - Domain/homology
Alpha-glucan family phosphorylase
Similarity search - Component
Biological speciesSegatella copri (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsShobu 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
DepositionMar 18, 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_63816.png

Downloads & links

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Map

FileDownload / File: emd_63816.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 588 pix.
= 488.04 Å		0.83 Å/pix.
x 588 pix.
= 488.04 Å		0.83 Å/pix.
x 588 pix.
= 488.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.174
Minimum - Maximum-0.6158662 - 1.0549225
Average (Standard dev.)-0.00009413936 (±0.025445761)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions588588588
Spacing588588588
CellA=B=C: 488.03998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63816_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #1

Fileemd_63816_half_map_2.map
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Histogram (log scale)

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Sample components

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Entire : glycogen phosphorylase

EntireName: glycogen phosphorylase
Components
  • Complex: glycogen phosphorylase
    • Protein or peptide: Alpha-glucan family phosphorylase
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: glycogen phosphorylase

SupramoleculeName: glycogen phosphorylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Segatella copri (bacteria)

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Macromolecule #1: Alpha-glucan family phosphorylase

MacromoleculeName: Alpha-glucan family phosphorylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Segatella copri (bacteria)
Molecular weightTheoretical: 98.795938 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKIKADYANA PQWKETTIKS SLPKELKCLD EIAHNMWWAW NYEGRDLFKS LDPDLYEKCN ANPVLLLERL SYDRKEAIVK DKETMAKVK NVYKMFREYM DVKPNAKRPS VAYFCMEYGI NQVVKIYSGG LGMLAGDYLK EASDSNVDMC AVGFLYRYGY F KQSLSMDG ...String:
MKIKADYANA PQWKETTIKS SLPKELKCLD EIAHNMWWAW NYEGRDLFKS LDPDLYEKCN ANPVLLLERL SYDRKEAIVK DKETMAKVK NVYKMFREYM DVKPNAKRPS VAYFCMEYGI NQVVKIYSGG LGMLAGDYLK EASDSNVDMC AVGFLYRYGY F KQSLSMDG QQIANYDAQN FNSLPIERVY DENGNPLVVD VPYTNYQVHA YVWQMNVGRI KLYLLDTDND MNSEFDRPIT YS LYGGDWE NRLKQEILLG IGGILTLKKL GIKKEIYHCN EGHAALCNLQ RLCDYIEEDG LNFNQALELV RASSLYTVHT PVP AGHDYF DEALFGKYMG GYPQRLGISW DEFIGMGREN ADDHNERFCL STFACNTCQE VNGVSKLHGW VSQQMFSNIW KGYF PEENH VGYVTNGVHF PTWTATEWRK LYDTYFDKNF MNDQSNEEIW HAIYKVSDAE IWNTRMTLKK KLVAYIREKF TQTWL KNQG DPARVVSLLE RINPNALMIG FCRRFATYKR AHLLFTDLER LSKIVNDPEH PVLFFFSGKA HPADGAGQGL IKKIFE ISQ RPEFLGKIIF LEDYDMTLAR RLVSGVDIWM NTPTRPLEAS GTSGE(LLP)AEMN GVVNLSVLDG WWVEGYREGA GWA LPEKRT YQNQGYQDQL DAATIYNLLE NDIIPMYYNK NKEGFSKEWI QVVKNSIATI APHYTMKRQL DDYYDKFYNK EAAR FKKLS ANDNALAKEI ALWKESVAER WDGIHVVSKD DCMLMAAETG QKIKVQYVID EQGLNDAVGL ELVVLKEQPE DGKQV YAVY PFKMVGHEGN NFTFEAEIEP INAGSFKTGV RMYPKNDKLP HRQDFCYVKW LN

UniProtKB: Alpha-glucan family phosphorylase

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Macromolecule #2: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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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

Concentration4.58 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMTris
5.0 mMAMPadenosine monophosphate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.007 kPa / Details: 10 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters droplet, 5 seconds delay before blotting, 3 seconds blot, 0 second delay before plunging..

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6271 / 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

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9l6i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60006
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: UCSF ChimeraX
Output model

PDB-9u3k:
Glycogen phosphorylase from Segatella copri pentamer in complex with AMP chains D and E

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