9LL3 | pdb_00009ll3

X-ray structure of Enterobacter cloaca transaldolase in complex with D-fructose-6-phosphate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.201 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Synthetic Study of 8- and 9-Carbon Sugars by Transaldolase.

Yoshihara, A.Miyoshi, E.Tomino, S.Hanaki, Y.Mochizuki, S.Yoshida, H.Izumori, K.Kamitori, S.

(2025) J Agric Food Chem 73: 18914-18922

  • DOI: https://doi.org/10.1021/acs.jafc.5c05539
  • Primary Citation of Related Structures:  
    9LKP, 9LL3, 9UI2

  • PubMed Abstract: 

    In nature, higher carbon sugars composed of 7 or more carbons exist in limited quantities. Since some higher carbon sugars have attracted attention due to their biological activities, it is necessary to develop a strategy to synthesize them. Transaldolase catalyzes the transfer of three-carbon units from d-fructose-6-phosphate (donor) to d-erythrulose-4-phosphate (acceptor) to produce d-sedoheptulose-7-phosphate. If transaldolase can recognize nonphosphorylated monosaccharides as substrates, it can synthesize 8-carbon octuloses and 9-carbon nonuloses using nonphosphorylated pentoses and hexoses as acceptors, respectively. We performed biochemical and structural characterization of thermophilic Thermus thermophilus HB8 transaldolase and successfully synthesized octuloses and nonuloses using nonphosphorylated aldoses as acceptors: d-ribose (conversion rate of 74%), d-xylose (55%), l-arabinose (49%), l-lyxose (84%), d-allose (13%), d-galactose (56%), and l-altrose (71%). Products were identified by LC/MS and NMR spectroscopic analyses. X-ray structure of the enzyme showed that the wide and hydrophilic catalytic site facilitates the binding of nonphosphorylated aldoses as acceptors.


  • Organizational Affiliation
    • International Institute of Rare Sugar Research and Education, Kagawa University, Takamatsu, Kagawa 760-8521, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fructose-6-phosphate aldolase
A, B, C, D, E
241Enterobacter cloacaeMutation(s): 0 
Gene Names: fsaDP202_18755
EC: 4.1.2
UniProt
Find proteins for A0A6G4MPG4 (Enterobacter hormaechei)
Explore A0A6G4MPG4 
Go to UniProtKB:  A0A6G4MPG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6G4MPG4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.201 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.56α = 90
b = 179.96β = 90
c = 133.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-07-30 
  • Deposition Author(s): Kamitori, S.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references