9LB6 | pdb_00009lb6

Crystal structure of trehalose 6-phosphate phosphatase Weissella ceti


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.181 (Depositor), 0.181 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Structural Insights into Trehalose-6-Phosphate Phosphorylase and Its Role in Trehalose 6-Phosphate Biosynthesis via a Multienzyme Cascade.

Feng, Y.Wang, N.Cao, Q.Li, S.Xu, Y.Che, X.Zhao, J.Yang, C.Xue, S.

(2025) J Agric Food Chem 73: 19065-19075

  • DOI: https://doi.org/10.1021/acs.jafc.5c05090
  • Primary Citation of Related Structures:  
    9LB6, 9LB7

  • PubMed Abstract: 

    Trehalose 6-phosphate (Tre6P) is a critical metabolic signaling molecule in plants, orchestrating diverse biological processes, including stress resistance and photosynthetic efficiency. Recent advancements highlight its promising role in improving crop yield. However, the efficient synthesis of Tre6P in vitro remains a major challenge. Here, we identified a trehalose-6-phosphate phosphorylase WcTre6PPase from Weissella ceti , the enzyme catalyzes the reversible synthesis of Tre6P from β-glucose 1-phosphate (βGlc1P) and glucose 6-phosphate (Glc6P), with a strong catalytic bias for Tre6P synthesis. The crystal structure of WcTre6PPase resolved in complex with βGlc1P reveals critical molecular determinants for substrate recognition and catalytic efficiency. Binding studies demonstrate a higher affinity of WcTre6PPase for βGlc1P by 1.0 ± 0.2 mM compared to Glc6P by 24.3 ± 7.1 mM. Complementary molecular docking and dynamics simulations provide detailed insights into the catalytic mechanism. Subsequently, by integrating WcTre6PPase into a novel multienzyme cascade, comprising maltose phosphorylase, polyphosphate glucokinase, and AMP/ADP-polyphosphate phosphotransferase, and optimizing reaction conditions, we achieved a remarkable Tre6P yield of 90% from maltose. This study provides molecular insights into the function of WcTre6PPase and establishes a prospective platform for Tre6P production for agricultural applications.


  • Organizational Affiliation
    • MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning 116024, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trehalose-6-phosphate hydrolase777Weissella cetiMutation(s): 0 
Gene Names: WS74_1295
UniProt
Find proteins for A0A075U1V9 (Weissella ceti)
Explore A0A075U1V9 
Go to UniProtKB:  A0A075U1V9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A075U1V9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
B [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.181 (Depositor), 0.181 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.541α = 90
b = 61.695β = 105.82
c = 77.048γ = 90
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateChinaDUT24LAB104

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