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Hydrolase PDB id
1w2t
Jmol
Contents
Protein chains
(+ 0 more) 432 a.a. *
Ligands
CIT
SUC-GLA ×6
SO4 ×4
Waters ×1888
* Residue conservation analysis
PDB id:
1w2t
Name: Hydrolase
Title: Beta-fructosidase from thermotoga maritima in complex with raffinose
Structure: Beta fructosidase. Chain: a, b, c, d, e, f. Synonym: sucrase, invertase. Engineered: yes. Mutation: yes
Source: Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: strain msb8 (dsm 3109) kindly provided by dr. W. Liebl
Resolution:
1.87Å     R-factor:   0.199     R-free:   0.229
Authors: F.Alberto,B.Henrissat,M.Czjzek
Key ref: F.Alberto et al. (2006). Crystal structure of inactivated Thermotoga maritima invertase in complex with the trisaccharide substrate raffinose. Biochem J, 395, 457-462. PubMed id: 16411890 DOI: 10.1042/BJ20051936
Date:
08-Jul-04     Release date:   26-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O33833  (BFRA_THEMA) -  Beta-fructosidase
Seq:
Struc: 		432 a.a.
432 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.26  - Beta-fructofuranosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1042/BJ20051936 Biochem J 395:457-462 (2006)
PubMed id: 16411890  
 
 
Crystal structure of inactivated Thermotoga maritima invertase in complex with the trisaccharide substrate raffinose.
F.Alberto, E.Jordi, B.Henrissat, M.Czjzek.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21418142 A.Bujacz, M.Jedrzejczak-Krzepkowska, S.Bielecki, I.Redzynia, and G.Bujacz (2011).
Crystal structures of the apo form of β-fructofuranosidase from Bifidobacterium longum and its complex with fructose.
  FEBS J, 278, 1728-1744.
PDB codes: 3pig 3pij
19936386 A.Homann, and J.Seibel (2009).
Chemo-enzymatic synthesis and functional analysis of natural and modified glycostructures.
  Nat Prod Rep, 26, 1555-1571.  
18953653 A.Kumar, N.K.Singhal, B.Ramanujam, A.Mitra, N.R.Rameshwaram, S.K.Nadimpalli, and C.P.Rao (2009).
C(1)-/C(2)-aromatic-imino-glyco-conjugates: experimental and computational studies of binding, inhibition and docking aspects towards glycosidases isolated from soybean and jack bean.
  Glycoconj J, 26, 495-510.  
19088319 D.Linde, I.Macias, L.Fernández-Arrojo, F.J.Plou, A.Jiménez, and M.Fernández-Lobato (2009).
Molecular and biochemical characterization of a beta-fructofuranosidase from Xanthophyllomyces dendrorhous.
  Appl Environ Microbiol, 75, 1065-1073.  
19125220 L.Dipasquale, A.Gambacorta, R.A.Siciliano, M.F.Mazzeo, and L.Lama (2009).
Purification and biochemical characterization of a native invertase from the hydrogen-producing Thermotoga neapolitana (DSM 4359).
  Extremophiles, 13, 345-354.  
19726634 L.Schroeven, W.Lammens, A.Kawakami, M.Yoshida, A.Van Laere, and W.Van den Ende (2009).
Creating S-type characteristics in the F-type enzyme fructan:fructan 1-fructosyltransferase of Triticum aestivum L.
  J Exp Bot, 60, 3687-3696.  
19129163 W.Lammens, K.Le Roy, L.Schroeven, A.Van Laere, A.Rabijns, and W.Van den Ende (2009).
Structural insights into glycoside hydrolase family 32 and 68 enzymes: functional implications.
  J Exp Bot, 60, 727-740.  
18366639 G.Meng, and K.Fütterer (2008).
Donor substrate recognition in the raffinose-bound E342A mutant of fructosyltransferase Bacillus subtilis levansucrase.
  BMC Struct Biol, 8, 16.
PDB codes: 3byj 3byk 3byl 3byn
17963237 J.Mátrai, W.Lammens, A.Jonckheer, K.Le Roy, A.Rabijns, W.Van den Ende, and M.De Maeyer (2008).
An alternate sucrose binding mode in the E203Q Arabidopsis invertase mutant: an X-ray crystallography and docking study.
  Proteins, 71, 552-564.
PDB code: 2oxb
17293485 C.Goosen, X.L.Yuan, J.M.van Munster, A.F.Ram, M.J.van der Maarel, and L.Dijkhuizen (2007).
Molecular and biochemical characterization of a novel intracellular invertase from Aspergillus niger with transfructosylating activity.
  Eukaryot Cell, 6, 674-681.  
17335500 M.Verhaest, W.Lammens, K.Le Roy, C.J.De Ranter, A.Van Laere, A.Rabijns, and W.Van den Ende (2007).
Insights into the fine architecture of the active site of chicory fructan 1-exohydrolase: 1-kestose as substrate vs sucrose as inhibitor.
  New Phytol, 174, 90.
PDB codes: 2add 2ade 2aey 2aez
17192265 W.S.Jung, C.K.Hong, S.Lee, C.S.Kim, S.J.Kim, S.I.Kim, and S.Rhee (2007).
Structural and functional insights into intramolecular fructosyl transfer by inulin fructotransferase.
  J Biol Chem, 282, 8414-8423.
PDB codes: 2inu 2inv
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.