6UPD

Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium in complex with trehalose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural Analysis of Binding Determinants ofSalmonella typhimuriumTrehalose-6-phosphate Phosphatase Using Ground-State Complexes.

Harvey, C.M.O'Toole, K.H.Liu, C.Mariano, P.Dunaway-Mariano, D.Allen, K.N.

(2020) Biochemistry 59: 3247-3257

  • DOI: https://doi.org/10.1021/acs.biochem.0c00317
  • Primary Citation of Related Structures:  
    6UPB, 6UPC, 6UPD, 6UPE

  • PubMed Abstract: 

    Trehalose-6-phosphate phosphatase (T6PP) catalyzes the dephosphorylation of trehalose 6-phosphate (T6P) to the disaccharide trehalose. The enzyme is not present in mammals but is essential to the viability of multiple lower organisms as trehalose is a critical metabolite, and T6P accumulation is toxic. Hence, T6PP is a target for therapeutics of human pathologies caused by bacteria, fungi, and parasitic nematodes. Here, we report the X-ray crystal structures of Salmonella typhimurium T6PP ( St T6PP) in its apo form and in complex with the cofactor Mg 2+ and the substrate analogue trehalose 6-sulfate (T6S), the product trehalose, or the competitive inhibitor 4- n -octylphenyl α-d-glucopyranoside 6-sulfate (OGS). OGS replaces the substrate phosphoryl group with a sulfate group and the glucosyl ring distal to the sulfate group with an octylphenyl moiety. The structures of these substrate-analogue and product complexes with T6PP show that specificity is conferred via hydrogen bonds to the glucosyl group proximal to the phosphoryl moiety through Glu123, Lys125, and Glu167, conserved in T6PPs from multiple species. The structure of the first-generation inhibitor OGS shows that it retains the substrate-binding interactions observed for the sulfate group and the proximal glucosyl ring. The OGS octylphenyl moiety binds in a unique manner, indicating that this subsite can tolerate various chemotypes. Together, these findings show that these conserved interactions at the proximal glucosyl ring binding site could provide the basis for the development of broad-spectrum therapeutics, whereas variable interactions at the divergent distal subsite could present an opportunity for the design of potent organism-specific therapeutics.


  • Organizational Affiliation

    Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trehalose-phosphate phosphatase
A, B
267Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344Mutation(s): 0 
Gene Names: otsBSL1344_1863
EC: 3.1.3.12
UniProt
Find proteins for E1WGG9 (Salmonella typhimurium (strain SL1344))
Explore E1WGG9 
Go to UniProtKB:  E1WGG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1WGG9
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan:  G92130SN
GlyCosmos:  G92130SN
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.767α = 90
b = 52.955β = 100.61
c = 108.762γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI127623

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description