1W2T

beta-fructosidase from Thermotoga maritima in complex with raffinose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Inactivated Thermotoga Maritima Invertase in Complex with the Trisaccharide Substrate Raffinose.

Alberto, F.Jordi, E.Henrissat, B.Czjzek, M.

(2006) Biochem.J. 395: 457

  • DOI: 10.1042/BJ20051936

  • PubMed Abstract: 
  • Thermotoga maritima invertase (beta-fructosidase), a member of the glycoside hydrolase family GH-32, readily releases beta-D-fructose from sucrose, raffinose and fructan polymers such as inulin. These carbohydrates represent major carbon and energy s ...

    Thermotoga maritima invertase (beta-fructosidase), a member of the glycoside hydrolase family GH-32, readily releases beta-D-fructose from sucrose, raffinose and fructan polymers such as inulin. These carbohydrates represent major carbon and energy sources for prokaryotes and eukaryotes. The invertase cleaves beta-fructopyranosidic linkages by a double-displacement mechanism, which involves a nucleophilic aspartate and a catalytic glutamic acid acting as a general acid/base. The three-dimensional structure of invertase shows a bimodular enzyme with a five bladed beta-propeller catalytic domain linked to a beta-sandwich of unknown function. In the present study we report the crystal structure of the inactivated invertase in interaction with the natural substrate molecule alpha-D-galactopyranosyl-(1,6)-alpha-D-glucopyranosyl-beta-D-fructofuranoside (raffinose) at 1.87 A (1 A=0.1 nm) resolution. The structural analysis of the complex reveals the presence of three binding-subsites, which explains why T. maritima invertase exhibits a higher affinity for raffinose than sucrose, but a lower catalytic efficiency with raffinose as substrate than with sucrose.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA FRUCTOSIDASE
A, B, C, D, E, F
432Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 1 
Gene Names: bfrA
EC: 3.2.1.26
Find proteins for O33833 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  O33833
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GLA
Query on GLA

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 94.500α = 90.00
b = 114.700β = 98.90
c = 130.000γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-05-08
    Type: Data collection, Derived calculations, Experimental preparation, Other