1UYP | pdb_00001uyp

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 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.5 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 Biological Chem 279: 18903-18910

  • DOI: https://doi.org/10.1074/jbc.M313911200
  • Primary Citation 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." 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.

Macromolecule Content 

  • Total Structure Weight: 301.43 kDa 
  • Atom Count: 22,996 
  • Modeled Residue Count: 2,592 
  • Deposited Residue Count: 2,592 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-FRUCTOSIDASE
A, B, C, D, E
A, B, C, D, E, F
432Thermotoga maritima MSB8Mutation(s): 0 
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / 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
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
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
NA

Query on NA



Download:Ideal Coordinates CCD File
L [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.220 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
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

View Full Validation Report



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
  • Version 1.4: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.5: 2025-10-01
    Changes: Advisory, Derived calculations