2PWE | pdb_00002pwe

Crystal structure of the MutB E254Q mutant in complex with the substrate sucrose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.235 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.194 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2PWE

This is version 2.2 of the entry. See complete history

Literature

Trehalulose synthase native and carbohydrate complexed structures provide insights into sucrose isomerization.

Ravaud, S.Robert, X.Watzlawick, H.Haser, R.Mattes, R.Aghajari, N.

(2007) J Biological Chem 282: 28126-28136

  • DOI: https://doi.org/10.1074/jbc.M704515200
  • Primary Citation Related Structures: 
    1ZJA, 2PWD, 2PWE, 2PWF, 2PWG, 2PWH

  • PubMed Abstract: 

    Various diseases related to the overconsumption of sugar make a growing need for sugar substitutes. Because sucrose is an inexpensive and readily available d-glucose donor, the industrial potential for enzymatic synthesis of the sucrose isomers trehalulose and/or isomaltulose from sucrose is large. The product specificity of sucrose isomerases that catalyze this reaction depends essentially on the possibility for tautomerization of sucrose, which is required for trehalulose formation. For optimal use of the enzyme, targeting controlled synthesis of these functional isomers, it is necessary to minimize the side reactions. This requires an extensive analysis of substrate binding modes and of the specificity-determining sites in the structure. The 1.6-2.2-A resolution three-dimensional structures of native and mutant complexes of a trehalulose synthase from Pseudomonas mesoacidophila MX-45 mimic successive states of the enzyme reaction. Combined with mutagenesis studies they give for the first time thorough insights into substrate recognition and processing and reaction specificities of these enzymes. Among the important outcomes of this study is the revelation of an aromatic clamp defined by Phe(256) and Phe(280) playing an essential role in substrate recognition and in controlling the reaction specificity, which is further supported by mutagenesis studies. Furthermore, this study highlights essential residues for binding the glucosyl and fructosyl moieties. The introduction of subtle changes informed by comparative three-dimensional structural data observed within our study can lead to fundamental modifications in the mode of action of sucrose isomerases and hence provide a template for industrial catalysts.


  • Organizational Affiliation
    • Laboratoire de BioCristallographie, Institut de Biologie et Chimie des Protéines, CNRS et Université de Lyon, UMR 5086, IFR 128 BioSciences Gerland-Lyon Sud, F-69367 Lyon Cedex 07, France.

Macromolecule Content 

  • Total Structure Weight: 128.38 kDa 
  • Atom Count: 10,566 
  • Modeled Residue Count: 1,112 
  • Deposited Residue Count: 1,112 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sucrose isomerase
A, B
556Burkholderia ubonensis subsp. mesacidophilaMutation(s): 1 
Gene Names: mutB
EC: 5.4.99.11
UniProt
Find proteins for Q2PS28 (Burkholderia ubonensis subsp. mesacidophila)
Explore Q2PS28 
Go to UniProtKB:  Q2PS28
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2PS28
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan: G05551OP
GlyCosmos: G05551OP

Small Molecules

Biologically Interesting Molecules (External Reference) 

1 Unique
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
C, D
sucroseOligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.235 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.194 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.31α = 66.18
b = 73.73β = 74.51
c = 82.75γ = 72.55
Software Package:
Software NamePurpose
MAR345data collection
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Structure summary
  • Version 2.2: 2024-02-21
    Changes: Data collection