7WRT

X-ray structure ofThermus thermophilus HB8 transketorase demonstrate in complex with TPP and D-erythrose-4-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.202 

Starting Model: experimental
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Literature

Structural and biochemical characterizations of Thermus thermophilus HB8 transketolase producing a heptulose.

Yoshihara, A.Takamatsu, Y.Mochizuki, S.Yoshida, H.Masui, R.Izumori, K.Kamitori, S.

(2023) Appl Microbiol Biotechnol 107: 233-245

  • DOI: https://doi.org/10.1007/s00253-022-12297-z
  • Primary Citation of Related Structures:  
    7WRR, 7WRT

  • PubMed Abstract: 

    Transketolase is a key enzyme in the pentose phosphate pathway in all organisms, recognizing sugar phosphates as substrates. Transketolase with a cofactor of thiamine pyrophosphate catalyzes the transfer of a 2-carbon unit from D-xylulose-5-phosphate to D-ribose-5-phosphate (5-carbon aldose), giving D-sedoheptulose-7-phosphate (7-carbon ketose). Transketolases can also recognize non-phosphorylated monosaccharides as substrates, and catalyze the formation of non-phosphorylated 7-carbon ketose (heptulose), which has attracted pharmaceutical attention as an inhibitor of sugar metabolism. Here, we report the structural and biochemical characterizations of transketolase from Thermus thermophilus HB8 (TtTK), a well-characterized thermophilic Gram-negative bacterium. TtTK showed marked thermostability with maximum enzyme activity at 85 °C, and efficiently catalyzed the formation of heptuloses from lithium hydroxypyruvate and four aldopentoses: D-ribose, L-lyxose, L-arabinose, and D-xylose. The X-ray structure showed that TtTK tightly forms a homodimer with more interactions between subunits compared with transketolase from other organisms, contributing to its thermal stability. A modeling study based on X-ray structures suggested that D-ribose and L-lyxose could bind to the catalytic site of TtTK to form favorable hydrogen bonds with the enzyme, explaining the high conversion rates of 41% (D-ribose) and 43% (L-lyxose) to heptulose. These results demonstrate the potential of TtTK as an enzyme producing a rare sugar of heptulose. KEY POINTS: • Transketolase catalyzes the formation of a 7-carbon sugar phosphate • Structural and biochemical characterizations of thermophilic transketolase were done • The enzyme could produce non-phosphorylated 7-carbon ketoses from sugars.


  • Organizational Affiliation

    International Institute of Rare Sugar Research and Education, Kagawa University, Takamatsu, Kagawa, 760-8521, Japan. yoshihara.akihide@kagawa-u.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transketolase
A, B, C, D
672Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA0108
EC: 2.2.1.1
UniProt
Find proteins for Q5SM35 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SM35 
Go to UniProtKB:  Q5SM35
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SM35
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
K [auth C],
O [auth D]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
E4P
Query on E4P

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
M [auth C],
N [auth D]
ERYTHOSE-4-PHOSPHATE
C4 H9 O7 P
NGHMDNPXVRFFGS-IUYQGCFVSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
L [auth C],
P [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.68α = 72.308
b = 88.86β = 88.696
c = 117.37γ = 73.459
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2022-12-28
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description