9UI2 | pdb_00009ui2

Crystal structure of Thermus thermophilus HB8 transaldolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.211 (Depositor) 
  • R-Value Work: 
    0.189 (Depositor) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9UI2

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 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.

Macromolecule Content 

  • Total Structure Weight: 265.73 kDa 
  • Atom Count: 18,735 
  • Modeled Residue Count: 2,250 
  • Deposited Residue Count: 2,430 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable transaldolase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
243Thermus thermophilus HB8Mutation(s): 0 
Gene Names: talTTHA1066
EC: 2.2.1.2
UniProt
Find proteins for Q5SJE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJE8 
Go to UniProtKB:  Q5SJE8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJE8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
BB [auth J]
DA [auth D]
HA [auth E]
IA [auth E]
JA [auth E]
BB [auth J],
DA [auth D],
HA [auth E],
IA [auth E],
JA [auth E],
K [auth A],
OA [auth F],
P [auth B],
Q [auth B],
QA [auth G],
R [auth B],
TA [auth H],
UA [auth H],
W [auth C],
X [auth C],
XA [auth I],
Y [auth C],
YA [auth I],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth I]
BA [auth C]
CA [auth C]
CB [auth J]
AA [auth C],
AB [auth I],
BA [auth C],
CA [auth C],
CB [auth J],
DB [auth J],
EA [auth D],
FA [auth D],
GA [auth D],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
MA [auth E],
N [auth A],
NA [auth E],
O [auth A],
PA [auth F],
RA [auth G],
S [auth B],
SA [auth G],
T [auth B],
U [auth B],
V [auth B],
VA [auth H],
WA [auth H],
ZA [auth I]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.211 (Depositor) 
  • R-Value Work:  0.189 (Depositor) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.38α = 90
b = 173.38β = 90
c = 422.58γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan22K04843

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