Structure of periplasmic trehalase from Diamondback moth gut bacteria complexed with validoxylamine

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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This is version 1.3 of the entry. See complete history


Mechanistic insights into enzymatic catalysis by trehalase from the insect gut endosymbiont Enterobacter cloacae.

Adhav, A.Harne, S.Bhide, A.Giri, A.Gayathri, P.Joshi, R.

(2019) FEBS J 286: 1700-1716

  • DOI: https://doi.org/10.1111/febs.14760
  • Primary Citation of Related Structures:  
    5Z66, 5Z6H

  • PubMed Abstract: 

    Energy metabolism in the diamondback moth Plutella xylostella is facilitated by trehalase, an enzyme which assists in trehalose hydrolysis, from the predominant gut bacterium Enterobacter cloacae. We report the biochemical and structural characterization of recombinant trehalase from E. cloacae (Px_EclTre). Px_EclTre showed K M of 1.47 (±0.05) mm, k cat of 6254.72 min -1 and V max 0.2 (±0.002) mm·min -1 at 55 °C and acidic pH. Crystal structures of Px_EclTre were determined in the ligand-free form and bound to the inhibitor Validoxylamine A. The crystal structure of the ligand-free form, unavailable until now for any other bacterial trehalases, enabled us to delineate the conformational changes accompanying ligand binding in trehalases. Multiple salt bridges were identified that potentially facilitated closure of a hood over the substrate-binding site. A cluster of five tryptophans lined the -1 substrate-binding subsite, interacted with crucial active site residues and contributed to both trehalase activity and stability. The importance of these residues in enzyme activity was further validated by mutagenesis studies. Many of these identified residues form part of signature motifs and other conserved sequences in trehalases. The structure analysis thus led to the assignment of the functional role to these conserved residues. This information can be further explored for the design of effective inhibitors against trehalases.

  • Organizational Affiliation

    Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic trehalase563Enterobacter cloacaeMutation(s): 3 
Gene Names: treASAMEA2273171_02252
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VDM (Subject of Investigation/LOI)
Query on VDM

Download Ideal Coordinates CCD File 
C14 H25 N O8
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.03α = 90
b = 51.45β = 106.95
c = 96.4γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Science and Technology, SERB, Government of IndiaIndiaECR/2015/000502

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description