9DU5 | pdb_00009du5

Cryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis

• PDB DOI: https://doi.org/10.2210/pdb9DU5/pdb
• EM Map EMD-47167: EMDB EMDataResource

• Classification: ISOMERASE
• Organism(s): Thermococcus kodakarensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-02 Released: 2025-04-16 
• Deposition Author(s): Naz, Z., Rathore, I., Saleem, M., Rahman, M., Rashid, N., Wlodawer, A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

A Bifunctional Phosphoglucomutase/Phosphomannomutase from Thermococcus kodakarensis : Biophysical Analysis and Cryo-EM Structure.

Naz, Z., Rathore, I., Saleem, M., Rahman, M., Wlodawer, A., Rashid, N.

(2025) Biomolecules 15

• PubMed: 40149855 
• DOI: https://doi.org/10.3390/biom15030319
• Primary Citation of Related Structures:  
  9DU5


• PubMed 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 5.4.2.8., 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 Thermococcus kodakarensis , a single gene, Tk1108 , 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.

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Organizational Affiliation: 
• School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan.
Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering, gel filtration

Macromolecule Content 

• Total Structure Weight: 199.69 kDa 
• Atom Count: 13,983 
• Modeled Residue Count: 1,806 
• Deposited Residue Count: 1,824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglucomutase/phosphomannomutase	A, B, C, D	456	Thermococcus kodakarensis	Mutation(s): 0  Gene Names: TK1108, Tko1621 EC: 5.4.2.2 (PDB Primary Data), 5.4.2.8 (PDB Primary Data)
UniProt
Find proteins for Q68BJ6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q68BJ6  Go to UniProtKB:  Q68BJ6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Naz, Z., Rathore, I., Saleem, M., Rahman, M., Rashid, N., Wlodawer, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release