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- EMDB-47167: Cryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis -

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Basic information

Entry
Database: EMDB / ID: EMD-47167
TitleCryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis
Map data
Sample
  • Complex: Cryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis
    • Protein or peptide: Phosphoglucomutase/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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsNaz Z / Rathore I / Saleem M / Rahman M / Rashid N / Wlodawer A
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47167.png

Downloads & links

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Map

FileDownload / File: emd_47167.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
0.81 Å/pix.
x 256 pix.
= 207.36 Å		0.81 Å/pix.
x 256 pix.
= 207.36 Å		0.81 Å/pix.
x 256 pix.
= 207.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-15.508989 - 27.597201999999999
Average (Standard dev.)-0.000000000005358 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 207.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47167_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_47167_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis

EntireName: Cryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis
Components
  • Complex: Cryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis
    • Protein or peptide: Phosphoglucomutase/phosphomannomutase

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Supramolecule #1: Cryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis

SupramoleculeName: Cryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermococcus kodakarensis (archaea)

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Macromolecule #1: Phosphoglucomutase/phosphomannomutase

MacromoleculeName: Phosphoglucomutase/phosphomannomutase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 49.922047 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGKLFGTFGV RGIANEEITP EFALKIGMAF GTLLKREGRE RPLVVVGRDT RVSGEMLKDA LISGLLSTGC DVIDVGIAPT PAIQWATNH FNADGGAVIT ASHNPPEYNG IKLLEPNGMG LKKEREAIVE ELFFSEDFHR AKWNEIGELR KEDIIKPYIE A IKNRVDVE ...String:
MGKLFGTFGV RGIANEEITP EFALKIGMAF GTLLKREGRE RPLVVVGRDT RVSGEMLKDA LISGLLSTGC DVIDVGIAPT PAIQWATNH FNADGGAVIT ASHNPPEYNG IKLLEPNGMG LKKEREAIVE ELFFSEDFHR AKWNEIGELR KEDIIKPYIE A IKNRVDVE AIKKRRPFVV VDTSNGAGSL TLPYLLRELG CKVVSVNAHP DGHFPARNPE PNEENLKGFM EIVKALGADF GV AQDGDAD RAVFIDENGR FIQGDKTFAL VADAVLRENG GGLLVTTIAT SNLLDDIAKR NGAKVMRTKV GDLIVARALL ENN GTIGGE ENGGVIFPDF VLGRDGAMTT AKIVEIFAKS GKKFSELIDE LPKYYQFKTK RHVEGDRKAI VAKVAELAEK KGYK IDTTD GTKIIFDDGW VLVRASGTEP IIRIFSEAKS EEKAREYLEL GIKLLEEALK G

UniProtKB: Phosphoglucomutase/phosphomannomutase

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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

Concentration2 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
50.0 mMHEPES
200.0 mMsodium chlorideNaCl

Details: 50 mM HEPES, 200 mM NaCl pH 7.0
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 200 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 56.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 645208
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
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
Output model

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

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