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- EMDB-67418: R583A mutant of glycogen phosphorylase from Segatella copri in th... -

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Basic information

Entry
Database: EMDB / ID: EMD-67418
TitleR583A mutant of glycogen phosphorylase from Segatella copri in the presence of AMP
Map data
Sample
  • Complex: glycogen phosphorylase
    • Protein or peptide: Alpha-glucan family phosphorylase
Keywordsglycogen phosphorylase / TRANSFERASE
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: 2.96 Å
AuthorsTakai M / Fukuda Y
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
DepositionDec 3, 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_67418.png

Downloads & links

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Map

FileDownload / File: emd_67418.map.gz / Format: CCP4 / Size: 512 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 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0586
Minimum - Maximum-0.353711 - 0.57425225
Average (Standard dev.)-0.00003446317 (±0.011154718)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67418_msk_1.map
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Mask #2

Fileemd_67418_msk_2.map
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Mask #3

Fileemd_67418_msk_3.map
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Half map: half B

Fileemd_67418_half_map_1.map
Annotationhalf B
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Half map: half A

Fileemd_67418_half_map_2.map
Annotationhalf A
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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

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Supramolecule #1: glycogen phosphorylase

SupramoleculeName: glycogen phosphorylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: glycogen phosphorylase from Segatella copri
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: 5 / Enantiomer: LEVO
Source (natural)Organism: Segatella copri (bacteria)
Molecular weightTheoretical: 101.014227 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGENLYFQS MKIKADYANA PQWKETTIKS SLPKELKCLD EIAHNMWWAW NYEGRDLFKS LDPDLYEKCN ANPVLLLER LSYDRKEAIV KDKETMAKVK NVYKMFREYM DVKPNAKRPS VAYFCMEYGI NQVVKIYSGG LGMLAGDYLK E ASDSNVDM ...String:
MGSSHHHHHH SSGENLYFQS MKIKADYANA PQWKETTIKS SLPKELKCLD EIAHNMWWAW NYEGRDLFKS LDPDLYEKCN ANPVLLLER LSYDRKEAIV KDKETMAKVK NVYKMFREYM DVKPNAKRPS VAYFCMEYGI NQVVKIYSGG LGMLAGDYLK E ASDSNVDM CAVGFLYRYG YFKQSLSMDG QQIANYDAQN FNSLPIERVY DENGNPLVVD VPYTNYQVHA YVWQMNVGRI KL YLLDTDN DMNSEFDRPI TYSLYGGDWE NRLKQEILLG IGGILTLKKL GIKKEIYHCN EGHAALCNLQ RLCDYIEEDG LNF NQALEL VRASSLYTVH TPVPAGHDYF DEALFGKYMG GYPQRLGISW DEFIGMGREN ADDHNERFCL STFACNTCQE VNGV SKLHG WVSQQMFSNI WKGYFPEENH VGYVTNGVHF PTWTATEWRK LYDTYFDKNF MNDQSNEEIW HAIYKVSDAE IWNTR MTLK KKLVAYIREK FTQTWLKNQG DPARVVSLLE RINPNALMIG FCRRFATYKR AHLLFTDLER LSKIVNDPEH PVLFFF SGK AHPADGAGQG LIKKIFEISQ RPEFLGKIIF LEDYDMTLAA RLVSGVDIWM NTPTRPLEAS GTSGE(LLP)AEMN GVV NLSVLD GWWVEGYREG AGWALPEKRT YQNQGYQDQL DAATIYNLLE NDIIPMYYNK NKEGFSKEWI QVVKNSIATI APHY TMKRQ LDDYYDKFYN KEAARFKKLS ANDNALAKEI ALWKESVAER WDGIHVVSKD DCMLMAAETG QKIKVQYVID EQGLN DAVG LELVVLKEQP EDGKQVYAVY PFKMVGHEGN NFTFEAEIEP INAGSFKTGV RMYPKNDKLP HRQDFCYVKW LN

UniProtKB: Alpha-glucan family 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

Concentration1.30 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
100.0 mMsodium chlorideNaCl
5.0 mMAMP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters droplet, 10 seconds delay before blotting, 3 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) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9l6i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 283158
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9l6i


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-20ys:
R583A mutant of glycogen phosphorylase from Segatella copri in the presence of AMP

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