6JBW

Structure of Tps1/UDP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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Literature

Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1.

Wang, S.Zhao, Y.Yi, L.Shen, M.Wang, C.Zhang, X.Yang, J.Peng, Y.L.Wang, D.Liu, J.

(2019) Biochem J 476: 3227-3240

  • DOI: https://doi.org/10.1042/BCJ20190289
  • Primary Citation of Related Structures:  
    6JAK, 6JBI, 6JBR, 6JBW

  • PubMed Abstract: 

    Trehalose-6-phosphate (T6P) synthase (Tps1) catalyzes the formation of T6P from UDP-glucose (UDPG) (or GDPG, etc.) and glucose-6-phosphate (G6P), and structural basis of this process has not been well studied. MoTps1 (Magnaporthe oryzae Tps1) plays a critical role in carbon and nitrogen metabolism, but its structural information is unknown. Here we present the crystal structures of MoTps1 apo, binary (with UDPG) and ternary (with UDPG/G6P or UDP/T6P) complexes. MoTps1 consists of two modified Rossmann-fold domains and a catalytic center in-between. Unlike Escherichia coli OtsA (EcOtsA, the Tps1 of E. coli), MoTps1 exists as a mixture of monomer, dimer, and oligomer in solution. Inter-chain salt bridges, which are not fully conserved in EcOtsA, play primary roles in MoTps1 oligomerization. Binding of UDPG by MoTps1 C-terminal domain modifies the substrate pocket of MoTps1. In the MoTps1 ternary complex structure, UDP and T6P, the products of UDPG and G6P, are detected, and substantial conformational rearrangements of N-terminal domain, including structural reshuffling (β3-β4 loop to α0 helix) and movement of a 'shift region' towards the catalytic centre, are observed. These conformational changes render MoTps1 to a 'closed' state compared with its 'open' state in apo or UDPG complex structures. By solving the EcOtsA apo structure, we confirmed that similar ligand binding induced conformational changes also exist in EcOtsA, although no structural reshuffling involved. Based on our research and previous studies, we present a model for the catalytic process of Tps1. Our research provides novel information on MoTps1, Tps1 family, and structure-based antifungal drug design.


  • Organizational Affiliation

    MOA Key Laboratory of Plant Pathology, Joint International Research Laboratory of Crop Molecular Breeding, College of Plant Protection, China Agricultural University, Beijing 100193, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trehalose-6-phosphate synthase
A, B
465Pyricularia oryzae 70-15Mutation(s): 0 
Gene Names: MGG_03860
EC: 2.4.1.15
UniProt
Find proteins for G4NHF4 (Pyricularia oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958))
Explore G4NHF4 
Go to UniProtKB:  G4NHF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG4NHF4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.751α = 90
b = 99.295β = 90
c = 121.708γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description