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- PDB-9du5: Cryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis -

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Basic information

Entry
Database: PDB / ID: 9du5
TitleCryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis
ComponentsPhosphoglucomutase/phosphomannomutase
KeywordsISOMERASE / phosphotransferase activity / glycogen metabolism / Thermococcus kodakarensis
Function / homology
Function and homology information


phosphoglucosamine mutase activity / phosphomannomutase / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphomannomutase activity / phosphoglucomutase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Phosphoglucosamine mutase, archaeal type / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III ...Phosphoglucosamine mutase, archaeal type / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
Similarity search - Domain/homology
Phosphoglucomutase/phosphomannomutase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsNaz, Z. / Rathore, I. / Saleem, M. / Rahman, M. / Rashid, N. / Wlodawer, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Biomolecules / Year: 2025
Title: A Bifunctional Phosphoglucomutase/Phosphomannomutase from : Biophysical Analysis and Cryo-EM Structure.
Authors: Zahra Naz / Ishan Rathore / Muhammad Saleem / Moazur Rahman / Alexander Wlodawer / Naeem Rashid /
Abstract: Phosphoglucomutase (EC 5.4.2.2., PGM), a key enzyme of glycogenolysis and glycogenesis, catalyzes the interconversion of glucose 1-phosphate and glucose 6-phosphate, whereas phosphomannomutase (EC 5. ...Phosphoglucomutase (EC 5.4.2.2., PGM), a key enzyme of glycogenolysis and glycogenesis, catalyzes the interconversion of glucose 1-phosphate and glucose 6-phosphate, whereas phosphomannomutase (EC 5.4.2.8., PMM) transfers the phosphate group from the 1' to the 6', or from the 6' to the 1' position in mannose phosphate. However, in the hyperthermophilic archaeon , a single gene, , encodes a protein with both PGM and PMM activities. Here, we report biophysical analysis and the 2.45 Å resolution cryo-EM structure of this novel enzyme. Our results demonstrate a specific arrangement of the four subunits in the quaternary structure, displaying a distinct catalytic cleft required for the bifunctional activity at extremely high temperatures. To the best of our knowledge, this is the first biophysical characterization and cryo-EM structure elucidation of a thermostable, bifunctional PGM/PMM.
History
DepositionOct 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglucomutase/phosphomannomutase
B: Phosphoglucomutase/phosphomannomutase
C: Phosphoglucomutase/phosphomannomutase
D: Phosphoglucomutase/phosphomannomutase


Theoretical massNumber of molelcules
Total (without water)199,6884
Polymers199,6884
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Phosphoglucomutase/phosphomannomutase / PGM/PMM


Mass: 49922.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK1108, Tko1621 / Production host: Escherichia coli (E. coli)
References: UniProt: Q68BJ6, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent), phosphomannomutase
Has protein modificationN

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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: Cryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7 / Details: 50 mM HEPES, 200 mM NaCl pH 7.0
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES1
2200 mMsodium chlorideNaCl1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 56.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4cryoSPARCCTF correction
9PHENIX1.21.1_5286model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 645208 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 109.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002414218
ELECTRON MICROSCOPYf_angle_d0.457619173
ELECTRON MICROSCOPYf_chiral_restr0.04192155
ELECTRON MICROSCOPYf_plane_restr0.00372513
ELECTRON MICROSCOPYf_dihedral_angle_d4.11451962

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