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Hydrolase PDB id
2qqv
Jmol
Contents
Protein chain
537 a.a. *
Ligands
SUC
NAG-NAG-MAN-MAN-
MAN
NAG-NAG
NAG
Metals
_ZN ×4
_NA ×2
Waters ×14
* Residue conservation analysis
PDB id:
2qqv
Name: Hydrolase
Title: Crystal structure of a cell-wall invertase (e203a) from arab thaliana in complex with sucrose
Structure: Beta-fructofuranosidase. Chain: a. Synonym: putative beta-fructofuranosidase 1. Engineered: yes. Mutation: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: atbfruct1. Expressed in: pichia pastoris. Expression_system_taxid: 4922
Resolution:
3.01Å     R-factor:   0.201     R-free:   0.237
Authors: W.Lammens,K.Le Roy,A.Van Laere,A.Rabijns,W.Van Den Ende
Key ref:
W.Lammens et al. (2008). Crystal structures of Arabidopsis thaliana cell-wall invertase mutants in complex with sucrose. J Mol Biol, 377, 378-385. PubMed id: 18258263 DOI: 10.1016/j.jmb.2007.12.074
Date:
27-Jul-07     Release date:   22-Apr-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q43866  (INV1_ARATH) -  Beta-fructofuranosidase, insoluble isoenzyme CWINV1
Seq:
Struc: 		 
Seq:
Struc: 		584 a.a.
537 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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!
  Cellular component     extracellular region   3 terms 
  Biological process     metabolic process   5 terms 
  Biochemical function     hydrolase activity     6 terms  

 

 
DOI no: 10.1016/j.jmb.2007.12.074 J Mol Biol 377:378-385 (2008)
PubMed id: 18258263  
 
 
Crystal structures of Arabidopsis thaliana cell-wall invertase mutants in complex with sucrose.
W.Lammens, K.Le Roy, A.Van Laere, A.Rabijns, W.Van den Ende.
 
  ABSTRACT  
 
In plants, cell-wall invertases fulfil important roles in carbohydrate partitioning, growth, development and crop yield. In this study, we report on different X-ray crystal structures of Arabidopsis thaliana cell-wall invertase 1 (AtcwINV1) mutants with sucrose. These structures reveal a detailed view of sucrose binding in the active site of the wild-type AtcwINV1. Compared to related enzyme-sucrose complexes, important differences in the orientation of the glucose subunit could be observed. The structure of the E203Q AtcwINV1 mutant showed a complete new binding modus, whereas the D23A, E203A and D239A structures most likely represent the productive binding modus. Together with a hydrophobic zone formed by the conserved W20, W47 and W82, the residues N22, D23, R148, E203, D149 and D239 are necessary to create the ideal sucrose-binding pocket. D239 can interact directly with the glucose moiety of sucrose, whereas K242 has an indirect role in substrate stabilization. Most probably, K242 keeps D239 in a favourable position upon substrate binding. Unravelling the exact position of sucrose in plant cell-wall invertases is a necessary step towards the rational design of superior invertases to further increase crop yield and biomass production.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Reaction scheme for AtcwINV1. D23 and E203 are identified as the nucleophile and the acid/base catalyst, respectively. 		Figure 3.
Fig. 3. An overview of the different sucrose complexes available within clan J of glycoside hydrolases. Sucrose molecules are depicted in orange. Distances are measured in angstroms. (a) The E203A AtcwINV1/sucrose structure, (b) the D239A AtcwINV1/sucrose structure, (c) the D23A AtcwINV1/sucrose structure, (d) the E203Q AtcwINV1/sucrose structure, (e) the 1-fructan exohydrolase IIa/sucrose structure from Cichorium intybus and (f) the E342A-levansucrase/sucrose structure from B. subtilis.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 377, 378-385) copyright 2008.  
  Figures were selected by the author.  

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
20416079 E.Wang, X.Xu, L.Zhang, H.Zhang, L.Lin, Q.Wang, Q.Li, S.Ge, B.R.Lu, W.Wang, and Z.He (2010).
Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication.
  BMC Evol Biol, 10, 108.  
20858733 M.Hothorn, W.Van den Ende, W.Lammens, V.Rybin, and K.Scheffzek (2010).
Structural insights into the pH-controlled targeting of plant cell-wall invertase by a specific inhibitor protein.
  Proc Natl Acad Sci U S A, 107, 17427-17432.
PDB code: 2xqr
19603465 C.Mauve, J.Bleton, C.Bathellier, C.Lelarge-Trouverie, F.Guérard, J.Ghashghaie, A.Tchapla, and G.Tcherkez (2009).
Kinetic 12C/13C isotope fractionation by invertase: evidence for a small in vitro isotope effect and comparison of two techniques for the isotopic analysis of carbohydrates.
  Rapid Commun Mass Spectrom, 23, 2499-2506.  
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.  
19037899 U.Kusch, K.Harms, T.Rausch, and S.Greiner (2009).
Inhibitors of plant invertases do not affect the structurally related enzymes of fructan metabolism.
  New Phytol, 181, 601-612.  
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.  
19765078 W.Van den Ende, W.Lammens, A.Van Laere, L.Schroeven, and K.Le Roy (2009).
Donor and acceptor substrate selectivity among plant glycoside hydrolase family 32 enzymes.
  FEBS J, 276, 5788-5798.  
18704491 T.Canam, F.Unda, and S.D.Mansfield (2008).
Heterologous expression and functional characterization of two hybrid poplar cell-wall invertases.
  Planta, 228, 1011-1019.  
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.