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- PDB-9s8b: Structure of glycogen phosphorylase - dimeric form - in complex w... -

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Basic information

Entry
Database: PDB / ID: 9s8b
TitleStructure of glycogen phosphorylase - dimeric form - in complex with HPr from Escherichia coli
Components
  • (Phosphocarrier protein HPr) x 2
  • Glycogen phosphorylase
KeywordsTRANSFERASE / Glycogen phosphorylase
Function / homology
Function and homology information


phosphotransferase activity, nitrogenous group as acceptor / antisigma factor binding / regulation of carbon utilization / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / enzyme regulator activity / enzyme inhibitor activity ...phosphotransferase activity, nitrogenous group as acceptor / antisigma factor binding / regulation of carbon utilization / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / enzyme regulator activity / enzyme inhibitor activity / enzyme activator activity / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / PTS HPR domain serine phosphorylation site signature. / Glycogen/starch/alpha-glucan phosphorylase ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / PTS HPR domain serine phosphorylation site signature. / 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
Phosphocarrier protein HPr / Glycogen phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsDi Domenico, V. / Mastrella, L. / Alcaide-Jimenez, A. / Villegas-Ruiz, J.C. / D'Angelo, C. / Cifuente, J.O. / Connell, S.R. / Guerin, M.E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO) Spain
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for phosphorylation and allosteric regulation of bacterial glycogen phosphorylase by histidine phosphocarrier protein.
Authors: Valerio Di Domenico / Jorick Franceus / Leonardo Mastrella / Emma De Beul / Adrià Alcaide-Jiménez / Francisco Paredes-Martínez / Juan Carlos Villegas-Ruiz / Elena Holden / Alejandro ...Authors: Valerio Di Domenico / Jorick Franceus / Leonardo Mastrella / Emma De Beul / Adrià Alcaide-Jiménez / Francisco Paredes-Martínez / Juan Carlos Villegas-Ruiz / Elena Holden / Alejandro Delgado Rey / Cecilia D'Angelo / Javier O Cifuente / Weston B Struwe / Ricardo M Biondi / Alberto Marina / Sean R Connell / Justin L P Benesch / Patricia Casino / Christophe Colleoni / Tom Desmet / Marcelo E Guerin /
Abstract: Protein phosphorylation is a universal regulatory mechanism, controlling virtually all aspects of bacterial physiology and pathogenesis, yet histidine phosphorylation remains among the least ...Protein phosphorylation is a universal regulatory mechanism, controlling virtually all aspects of bacterial physiology and pathogenesis, yet histidine phosphorylation remains among the least understood. The histidine phosphocarrier protein HPr not only drives bacterial glucose transmembrane uptake through the phosphotransferase system (PTS), but also controls key enzymes for central carbon metabolism, including glycogen phosphorylase (GP). Here we report cryoEM structures of multimeric Escherichia coli GP and their complexes with HPr. The EM maps reveal an unanticipated density at H806 of GP, consistent with histidine phosphorylation within a histidine-rich pocket at the N-terminal domain. Enzymatic assays reveal that HPr transfers a phosphoryl group to the N1 position of a histidine residue in GP. Through an integrative structural, mutational and functional approach, we uncover the molecular basis of HPr- GP selectivity and define the allosteric mechanism by which HPr regulates GP. We establish histidine phosphorylation as a mechanism of GP regulation, expanding the traditional paradigm of glycogen metabolism control in bacteria.
History
DepositionAug 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
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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: Phosphocarrier protein HPr
D: Phosphocarrier protein HPr


Theoretical massNumber of molelcules
Total (without water)213,4664
Polymers213,4664
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Glycogen phosphorylase


Mass: 95536.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glgP, glgY, b3428, JW3391 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC86, glycogen phosphorylase
#2: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 11236.499 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ptsH, hpr, b2415, JW2408 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA04
#3: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 11156.519 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ptsH, hpr, b2415, JW2408 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA04
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Recombinantly purified Glycogen phosphorylase in complex with the phosphocarrier protein HPr from E. coli
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.228 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategoryImage processing-ID
1cryoSPARCparticle selection1
13cryoSPARC3D reconstruction1
14cryoSPARCparticle selection2
19cryoSPARC3D reconstruction2
Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
Symmetry
IDImage processing-IDEntry-IDPoint symmetry
119S8BC2 (2 fold cyclic)
219S8BC2 (2 fold cyclic)
329S8BC2 (2 fold cyclic)
429S8BC2 (2 fold cyclic)
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
12.79FSC 0.143 CUT-OFF14431219S8BPOINT
22.79FSC 0.143 CUT-OFF14431219S8BPOINT
32.79FSC 0.143 CUT-OFF14431229S8BPOINT
42.79FSC 0.143 CUT-OFF14431229S8BPOINT
Atomic model buildingProtocol: OTHER
Atomic model buildingPDB-ID: 9S7V

9s7v


Accession code: 9S7V / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.79 Å

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