beta-fructosidase from Thermotoga maritima in complex with raffinose

Experimental Data Snapshot

  • Resolution: 1.87 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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This is version 2.1 of the entry. See complete history


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: https://doi.org/10.1042/BJ20051936
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
432Thermotoga maritima MSB8Mutation(s): 1 
Find proteins for O33833 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore O33833 
Go to UniProtKB:  O33833
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO33833
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
G, H, I, J, K
G, H, I, J, K, L
Glycosylation Resources
GlyTouCan:  G40178VU
GlyCosmos:  G40178VU
Experimental Data & Validation

Experimental Data

  • Resolution: 1.87 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.5α = 90
b = 114.7β = 98.9
c = 130γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary