3HJ6 | pdb_00003hj6

Structure of Halothermothrix orenii fructokinase (FRK)

• PDB DOI: https://doi.org/10.2210/pdb3HJ6/pdb

• Classification: TRANSFERASE
• Organism(s): Halothermothrix orenii H 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-21 Released: 2010-06-09 
• Deposition Author(s): Chua, T.K., Seetharaman, J., Kasprzak, J.M., Ng, C., Patel, B.K., Love, C., Bujnicki, J.M., Sivaraman, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.288 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.284 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Literature

Crystal structure of a fructokinase homolog from Halothermothrix orenii

Chua, T.K., Seetharaman, J., Kasprzak, J.M., Ng, C., Patel, B.K., Love, C., Bujnicki, J.M., Sivaraman, J.

(2010) J Struct Biol 171: 397-401

• PubMed: 20493950 
• DOI: https://doi.org/10.1016/j.jsb.2010.05.007
• Primary Citation of Related Structures:  
  3HJ6


• PubMed Abstract: 
  

  Fructokinase (FRK; EC 2.7.1.4) catalyzes the phosphorylation of d-fructose to d-fructose 6-phosphate (F6P). This irreversible and near rate-limiting step is a central and regulatory process in plants and bacteria, which channels fructose into a metabolically active state for glycolysis. Towards understanding the mechanism of FRK, here we report the crystal structure of a FRK homolog from a thermohalophilic bacterium Halothermothrixorenii (Hore_18220 in sequence databases). The structure of the Hore_18220 protein reveals a catalytic domain with a Rossmann-like fold and a beta-sheet "lid" for dimerization. Based on comparison of Hore_18220 to structures of related proteins, we propose its mechanism of action, in which the lid serves to regulate access to the substrate binding sites. Close relationship of Hore_18220 and plant FRK enzymes allows us to propose a model for the structure and function of FRKs.

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Organizational Affiliation: 

Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore 117543, Singapore.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.52 kDa 
• Atom Count: 4,079 
• Modelled Residue Count: 556 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructokinase	A, B	327	Halothermothrix orenii H 168	Mutation(s): 0  EC: 2.7.1.4
UniProt
Find proteins for B8CZ52 (Halothermothrix orenii (strain H 168 / OCM 544 / DSM 9562)) Explore B8CZ52  Go to UniProtKB:  B8CZ52

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.288 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.284 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.446	α = 90
b = 171.941	β = 112.97
c = 46.598	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-09 
Deposition Author(s): Chua, T.K., Seetharaman, J., Kasprzak, J.M., Ng, C., Patel, B.K., Love, C., Bujnicki, J.M., Sivaraman, J.

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-02-12
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary