1UYP

The three-dimensional structure of beta-fructosidase (invertase) from Thermotoga maritima

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The three-dimensional structure of invertase (beta-fructosidase) from Thermotoga maritima reveals a bimodular arrangement and an evolutionary relationship between retaining and inverting glycosidases.

Alberto, F., Bignon, C., Sulzenbacher, G., Henrissat, B., Czjzek, M.

(2004) J Biol Chem 279: 18903-18910

  • DOI: https://doi.org/10.1074/jbc.M313911200
  • Primary Citation of Related Structures:  
    1UYP

  • PubMed Abstract: 

    • Thermotoga maritima invertase (beta-fructosidase) hydrolyzes sucrose to release fructose and glucose, which are major carbon and energy sources for both prokaryotes and eukaryotes. The name "invertase" was given to this enzyme over a century ago, because the 1:1 mixture of glucose and fructose that it produces was named "invert sugar ...

    Thermotoga maritima invertase (beta-fructosidase) hydrolyzes sucrose to release fructose and glucose, which are major carbon and energy sources for both prokaryotes and eukaryotes. The name "invertase" was given to this enzyme over a century ago, because the 1:1 mixture of glucose and fructose that it produces was named "invert sugar." Despite its name, the enzyme operates with a mechanism leading to the retention of the anomeric configuration at the site of cleavage. The enzyme belongs to family GH32 of the sequence-based classification of glycosidases. The crystal structure, determined at 2-A resolution, reveals two modules, namely a five-bladed beta-propeller with structural similarity to the beta-propeller structures of glycosidase from families GH43 and GH68 connected to a beta-sandwich module. Three carboxylates at the bottom of a deep, negatively charged funnel-shaped depression of the beta-propeller are essential for catalysis and function as nucleophile, general acid, and transition state stabilizer, respectively. The catalytic machinery of invertase is perfectly superimposable to that of the enzymes of families GH43 and GH68. The variation in the position of the furanose ring at the site of cleavage explains the different mechanisms evident in families GH32 and GH68 (retaining) and GH43 (inverting) furanosidases.

    Organizational Affiliation: 

    Architecture et Fonction des Macromolécules Biologiques, CNRS and Université Aix-Marseille I & II, Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, 13402 Marseille cedex 20, France.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-FRUCTOSIDASE
A, B, C, D, E, F
A, B, C, D, E, F
432Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: bfrA, TM_1414
EC: 3.2.1.26
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT
Download Ideal Coordinates CCD File 
J [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth F],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
AA [auth F],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
Q [auth B],
R [auth C],
S [auth C],
T [auth C],
W [auth E],
Y [auth F],
Z [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
BA [auth F],
K [auth A],
P [auth B],
U [auth C],
V [auth D],
BA [auth F],
K [auth A],
P [auth B],
U [auth C],
V [auth D],
X [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
L [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.48α = 90
b = 114.67β = 98.96
c = 130.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RESOLVEphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-22
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-06-13
    Changes: Data collection, Database references, Refinement description