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PDBsum entry 1uyp

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1uyp
Jmol
Contents
Protein chains
(+ 0 more) 432 a.a. *
Ligands
SO4 ×14
CIT
GOL ×6
Metals
_NA
Waters ×1756
* Residue conservation analysis
PDB id:
1uyp
Name: Hydrolase
Title: The three-dimensional structure of beta-fructosidase (invertase) from thermotoga maritima
Structure: Beta-fructosidase. Chain: a, b, c, d, e, f. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Expressed in: escherichia coli. Expression_system_taxid: 511693. Other_details: german collection of microorganisms (dsm 3109)
Resolution:
1.90Å     R-factor:   0.179     R-free:   0.220
Authors: F.Alberto,C.Bignon,G.Sulzenbacher,B.Henrissat,M.Czjzek
Key ref:
F.Alberto et al. (2004). The three-dimensional structure of invertase (beta-fructosidase) from Thermotoga maritima reveals a bimodular arrangement and an evolutionary relationship between retaining and inverting glycosidases. J Biol Chem, 279, 18903-18910. PubMed id: 14973124 DOI: 10.1074/jbc.M313911200
Date:
02-Mar-04     Release date:   22-Mar-04    
Supersedes: 1utw
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 3 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     5 terms  

 

 
DOI no: 10.1074/jbc.M313911200 J Biol Chem 279:18903-18910 (2004)
PubMed id: 14973124  
 
 
The three-dimensional structure of invertase (beta-fructosidase) from Thermotoga maritima reveals a bimodular arrangement and an evolutionary relationship between retaining and inverting glycosidases.
F.Alberto, C.Bignon, G.Sulzenbacher, B.Henrissat, M.Czjzek.
 
  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.
 
  Selected figure(s)  
 
Figure 4.
FIG. 4. Structural comparison of families GH32, GH68, and GH43. A, structural superimposition of the three strictly conserved residues in the catalytic sites of T. maritima invertase (magenta), Bacillus subtilis levansucrase (dark blue) and Cellvibrio japonicus -L-arabinanase (yellow). B, stereographic view of the superimposed catalytic active sites of -L-arabinanase (yellow) in complex with arabinotriose (orange; Protein Data Bank identification 1GYE [PDB] ), and invertase (dark purple) in complex with the modeled sucrose molecule (blue). The different binding modes of the two enzymes lead to a different position of the glycosidic bond with respect to the catalytic machinery. The anomeric carbons at the point of cleavage of both substrate molecules are colored red. The loops, including residues Trp-41 and Trp-14, which define the -1 subsite in invertase, are either not present or are displaced in -L-arabinanase. In contrast, the loop containing Phe-114, which encloses the substrate in the binding cleft in -L-arabinanase, is absent in invertase. Single letter amino acid abbreviations are used with position numbers.
Figure 5.
FIG. 5. The C-terminal -sandwich module. A, ribbon representation of residues 306-432 of T. maritima invertase displaying the -sandwich fold with colors ranging from blue at the N-terminal end to red at the C-terminal end. B, comparison of A to the structure of human galectin-3 (Protein Data Bank identification 1A3K [PDB] ) in approximately the same orientation, highlighting the similarity of the two structures.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 18903-18910) copyright 2004.  
  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
  21332624 E.Rebuffet, A.Groisillier, A.Thompson, A.Jeudy, T.Barbeyron, M.Czjzek, and G.Michel (2011).
Discovery and structural characterization of a novel glycosidase family of marine origin.
  Environ Microbiol, 13, 1253-1270.
PDB code: 3p2n
20563857 M.A.Rodríguez, O.F.Sánchez, and C.J.Alméciga-Díaz (2011).
Gene cloning and enzyme structure modeling of the Aspergillus oryzae N74 fructosyltransferase.
  Mol Biol Rep, 38, 1151-1161.  
20972892 M.M.Sari (2011).
Investigation of Yeast Invertase Immobilization onto Cupric Ion-Chelated, Porous, and Biocompatible Poly(Hydroxyethyl Methacrylate-n-Vinyl Imidazole) Microspheres.
  Appl Biochem Biotechnol, 163, 1020-1037.  
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
19505290 A.Alhassid, A.Ben-David, O.Tabachnikov, D.Libster, E.Naveh, G.Zolotnitsky, Y.Shoham, and G.Shoham (2009).
Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate.
  Biochem J, 422, 73-82.
PDB codes: 3cu9 3d5y 3d5z 3d60 3d61
19936386 A.Homann, and J.Seibel (2009).
Chemo-enzymatic synthesis and functional analysis of natural and modified glycostructures.
  Nat Prod Rep, 26, 1555-1571.  
19139238 C.Menéndez, A.Banguela, J.Caballero-Mellado, and L.Hernández (2009).
Transcriptional regulation and signal-peptide-dependent secretion of exolevanase (LsdB) in the endophyte Gluconacetobacter diazotrophicus.
  Appl Environ Microbiol, 75, 1782-1785.  
18821058 D.Altenbach, E.Rudiño-Pinera, C.Olvera, T.Boller, A.Wiemken, and T.Ritsema (2009).
An acceptor-substrate binding site determining glycosyl transfer emerges from mutant analysis of a plant vacuolar invertase and a fructosyltransferase.
  Plant Mol Biol, 69, 47-56.  
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.  
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.  
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
19020964 Gangadhara, P.Ramesh Kumar, and V.Prakash (2008).
Influence of Polyols on the Stability and Kinetic Parameters of Invertase from Candida utilis: Correlation with the Conformational Stability and Activity.
  Protein J, 27, 440-449.  
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
18712537 M.de Los Angeles Calixto-Romo, J.A.Santiago-Hernández, V.Vallejo-Becerra, L.Amaya-Delgado, M.Del Carmen Montes-Horcasitas, and M.E.Hidalgo-Lara (2008).
Expression, purification and immobilization of the intracellular invertase INVA, from Zymomonas mobilis on crystalline cellulose and Nylon-6.
  J Ind Microbiol Biotechnol, 35, 1455-1463.  
17938954 P.N.Bocock, A.M.Morse, C.Dervinis, and J.M.Davis (2008).
Evolution and diversity of invertase genes in Populus trichocarpa.
  Planta, 227, 565-576.  
18848471 T.M.Gloster, J.P.Turkenburg, J.R.Potts, B.Henrissat, and G.J.Davies (2008).
Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora.
  Chem Biol, 15, 1058-1067.
PDB codes: 2jka 2jke 2jkp
17917744 X.L.Yuan, J.A.Roubos, C.A.van den Hondel, and A.F.Ram (2008).
Identification of InuR, a new Zn(II)2Cys6 transcriptional activator involved in the regulation of inulinolytic genes in Aspergillus niger.
  Mol Genet Genomics, 279, 11-26.  
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.  
17888113 K.Le Roy, M.Verhaest, A.Rabijns, S.Clerens, A.Van Laere, and W.Van den Ende (2007).
N-glycosylation affects substrate specificity of chicory fructan 1-exohydrolase: evidence for the presence of an inulin binding cleft.
  New Phytol, 176, 317-324.  
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
16899050 L.K.Ozimek, S.Kralj, T.Kaper, M.J.van der Maarel, and L.Dijkhuizen (2006).
Single amino acid residue changes in subsite -1 of inulosucrase from Lactobacillus reuteri 121 strongly influence the size of products synthesized.
  FEBS J, 273, 4104-4113.  
17139091 M.Verhaest, W.Lammens, K.Le Roy, B.De Coninck, C.J.De Ranter, A.Van Laere, W.Van den Ende, and A.Rabijns (2006).
X-ray diffraction structure of a cell-wall invertase from Arabidopsis thaliana.
  Acta Crystallogr D Biol Crystallogr, 62, 1555-1563.
PDB code: 2ac1
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
17081122 T.Guevara, N.Mallorquí-Fernández, R.García-Castellanos, S.García-Piqué, G.Ebert Petersen, C.Lauritzen, J.Pedersen, J.Arnau, F.X.Gomis-Rüth, and M.Solà (2006).
Papaya glutamine cyclotransferase shows a singular five-fold beta-propeller architecture that suggests a novel reaction mechanism.
  Biol Chem, 387, 1479-1486.
PDB code: 2iwa
17018033 T.Ritsema, L.Hernández, A.Verhaar, D.Altenbach, T.Boller, A.Wiemken, and S.Smeekens (2006).
Developing fructan-synthesizing capability in a plant invertase via mutations in the sucrose-binding box.
  Plant J, 48, 228-237.  
15708971 M.R.Proctor, E.J.Taylor, D.Nurizzo, J.P.Turkenburg, R.M.Lloyd, M.Vardakou, G.J.Davies, and H.J.Gilbert (2005).
Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A.
  Proc Natl Acad Sci U S A, 102, 2697-2702.
PDB code: 1uv4
  16511152 M.Verhaest, K.Le Roy, S.Sansen, B.De Coninck, W.Lammens, C.J.De Ranter, A.Van Laere, W.Van den Ende, and A.Rabijns (2005).
Crystallization and preliminary X-ray diffraction study of a cell-wall invertase from Arabidopsis thaliana.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 766-768.  
15659099 M.Verhaest, W.V.Ende, K.L.Roy, C.J.De Ranter, A.V.Laere, and A.Rabijns (2005).
X-ray diffraction structure of a plant glycosyl hydrolase family 32 protein: fructan 1-exohydrolase IIa of Cichorium intybus.
  Plant J, 41, 400-411.
PDB code: 1st8
16158237 T.Ritsema, A.Verhaar, I.Vijn, and S.Smeekens (2005).
Using natural variation to investigate the function of individual amino acids in the sucrose-binding box of fructan:fructan 6G-fructosyltransferase (6G-FFT) in product formation.
  Plant Mol Biol, 58, 597-607.  
15983871 X.Ji, W.Van den Ende, A.Van Laere, S.Cheng, and J.Bennett (2005).
Structure, evolution, and expression of the two invertase gene families of rice.
  J Mol Evol, 60, 615-634.  
15604656 T.Ritsema, A.Verhaar, I.Vijin, and S.Smeekens (2004).
Fructosyltransferase mutants specify a function for the beta-fructosidase motif of the sucrose-binding box in specifying the fructan type synthesized.
  Plant Mol Biol, 54, 853-863.  
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.