1
|
Cimini S, Di Paola L, Giuliani A, Ridolfi A, De Gara L. GH32 family activity: a topological approach through protein contact networks. PLANT MOLECULAR BIOLOGY 2016; 92:401-410. [PMID: 27503472 DOI: 10.1007/s11103-016-0515-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/14/2016] [Indexed: 05/24/2023]
Abstract
The application of Protein Contact Networks methodology allowed to highlight a novel response of border region between the two domains to substrate binding. Glycoside hydrolases (GH) are enzymes that mainly hydrolyze the glycosidic bond between two carbohydrates or a carbohydrate and a non-carbohydrate moiety. These enzymes are involved in many fundamental and diverse biological processes in plants. We have focused on the GH32 family, including enzymes very similar in both sequence and structure, each having however clear specificities of substrate preferences and kinetic properties. Structural and topological differences among proteins of the GH32 family have been here identified by means of an emerging approach (Protein Contact network, PCN) based on the formalization of 3D structures as contact networks among amino-acid residues. The PCN approach proved successful in both reconstructing the already known functional domains and in identifying the structural counterpart of the properties of GH32 enzymes, which remain uncertain, like their allosteric character. The main outcome of the study was the discovery of the activation upon binding of the border (cleft) region between the two domains. This reveals the allosteric nature of the enzymatic activity for all the analyzed forms in the GH32 family, a character yet to be highlighted in biochemical studies. Furthermore, we have been able to recognize a topological signature (graph energy) of the different affinity of the enzymes towards small and large substrates.
Collapse
Affiliation(s)
- Sara Cimini
- Unit of Food Science and Nutrition, Department of Medicine, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy
| | - Luisa Di Paola
- Unit of Chemical-physics Fundamentals in Chemical Engineering, Department of Engineering, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy.
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Alessandra Ridolfi
- Unit of Chemical-physics Fundamentals in Chemical Engineering, Department of Engineering, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy
| | - Laura De Gara
- Unit of Food Science and Nutrition, Department of Medicine, Università Campus Bio-Medico di Roma, via Álvaro del Portillo 21, 00128, Rome, Italy
| |
Collapse
|
2
|
Mazola Y, Guirola O, Palomares S, Chinea G, Menéndez C, Hernández L, Musacchio A. A comparative molecular dynamics study of thermophilic and mesophilic β-fructosidase enzymes. J Mol Model 2015; 21:228. [PMID: 26267297 DOI: 10.1007/s00894-015-2772-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/20/2015] [Indexed: 02/02/2023]
Abstract
Arabidopsis thaliana cell wall invertase 1 (AtcwINV1) and Thermotoga maritima β-fructosidase (BfrA) are among the best structurally studied members of the glycoside hydrolase family 32. Both enzymes hydrolyze sucrose as the main substrate but differ strongly in their thermal stability. Mesophilic AtcwINV1 and thermophilic BfrA have divergent sequence similarities in the N-terminal five bladed β-propeller catalytic domain (31 %) and the C-terminal β-sandwich domain (15 %) of unknown function. The two enzymes were subjected to 200 ns molecular dynamics simulations at 300 K (27 °C) and 353 K (80 °C). Regular secondary structure regions, but not loops, in AtcwINV1 and BfrA showed no significant fluctuation differences at both temperatures. BfrA was more rigid than AtcwINV1 at 300 K. The simulation at 353 K did not alter the structural stability of BfrA, but did increase the overall flexibility of AtcwINV1 exhibiting the most fluctuating regions in the β-propeller domain. The simulated heat treatment also increased the gyration radius and hydrophobic solvent accessible surface area of the plant enzyme, consistent with the initial steps of an unfolding process. The preservation of the conformational rigidity of BfrA at 353 K is linked to the shorter size of the protein loops. Shortening of BfrA loops appears to be a key mechanism for thermostability.
Collapse
Affiliation(s)
- Yuliet Mazola
- Department of Bioinformatics, Center for Genetic Engineering and Biotechnology (CIGB), Ave. 31 e/ 158 and 190, Playa, P.O. Box 6162, Havana, 10600, Cuba,
| | | | | | | | | | | | | |
Collapse
|
3
|
Chlubnova I, Legentil L, Dureau R, Pennec A, Almendros M, Daniellou R, Nugier-Chauvin C, Ferrières V. Specific and non-specific enzymes for furanosyl-containing conjugates: biosynthesis, metabolism, and chemo-enzymatic synthesis. Carbohydr Res 2012; 356:44-61. [PMID: 22554502 DOI: 10.1016/j.carres.2012.04.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/02/2012] [Accepted: 04/03/2012] [Indexed: 11/27/2022]
Abstract
There is no doubt now that the synthesis of compounds of varying complexity such as saccharides and derivatives thereof continuously grows with enzymatic methods. This review focuses on recent basic knowledge on enzymes specifically involved in the biosynthesis and degradation of furanosyl-containing polysaccharides and conjugates. Moreover, and when possible, biocatalyzed approaches, alternative to standard synthesis, will be detailed in order to strengthen the high potential of these biocatalysts to go further with the preparation of rare furanosides. Interesting results will be also proposed with chemo-enzymatic processes based on nonfuranosyl-specific enzymes.
Collapse
Affiliation(s)
- Ilona Chlubnova
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7, France
| | | | | | | | | | | | | | | |
Collapse
|
4
|
Bujacz A, Jedrzejczak-Krzepkowska M, Bielecki S, Redzynia I, Bujacz G. Crystal structures of the apo form of β-fructofuranosidase from Bifidobacterium longum and its complex with fructose. FEBS J 2011; 278:1728-44. [DOI: 10.1111/j.1742-4658.2011.08098.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
5
|
Lammens W, Le Roy K, Schroeven L, Van Laere A, Rabijns A, Van den Ende W. Structural insights into glycoside hydrolase family 32 and 68 enzymes: functional implications. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:727-40. [PMID: 19129163 DOI: 10.1093/jxb/ern333] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Glycoside hydrolases (GH) have been shown to play unique roles in various biological processes like the biosynthesis of glycans, cell wall metabolism, plant defence, signalling, and the mobilization of storage reserves. To date, GH are divided into more than 100 families based upon their overall structure. GH32 and GH68 are combined in clan GH-J, not only harbouring typical hydrolases but also non-Leloir type transferases (fructosyltransferases), involved in fructan biosynthesis. This review summarizes the recent structure-function research progress on plant GH32 enzymes, and highlights the similarities and differences compared with the microbial GH32 and GH68 enzymes. A profound analysis of ligand-bound structures and site-directed mutagenesis experiments identified key residues in substrate (or inhibitor) binding and recognition. In particular, sucrose can bind as inhibitor in Cichorium intybus 1-FEH IIa, whereas it binds as substrate in Bacillus subtilis levansucrase and Arabidopsis thaliana cell wall invertase (AtcwINV1). In plant GH32, a single residue, the equivalent of Asp239 in AtcwINV1, appears to be important for sucrose stabilization in the active site and essential in determining sucrose donor specificity.
Collapse
Affiliation(s)
- Willem Lammens
- Laboratorium voor Moleculaire Plantenfysiologie, Faculteit Wetenschappen, Departement Biologie, K. U. Leuven, Kasteelpark Arenberg 31, bus 2434, B-3001 Heverlee, Belgium
| | | | | | | | | | | |
Collapse
|
6
|
Schroeven L, Lammens W, Kawakami A, Yoshida M, Van Laere A, Van den Ende W. Creating S-type characteristics in the F-type enzyme fructan:fructan 1-fructosyltransferase of Triticum aestivum L. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:3687-96. [PMID: 19726634 DOI: 10.1093/jxb/erp208] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Invertases cleave sucrose in glucose and fructose, using water as an acceptor. Fructosyltransferases catalyse the transfer of a fructosyl residue between sucrose and/or fructan molecules. Plant fructosyltransferases (FTs) evolved from vacuolar invertases by small mutational changes, leading to differences in substrate specificity. The S-type of enzymes (invertases, sucrose:sucrose 1-fructosyltransferases or 1-SSTs, and sucrose:fructan 6-fructosyltransferases or 6-SFTs) prefer sucrose as the donor substrate while F-type enzymes (fructan:fructan 1-fructosyltransferases or 1-FFTs and fructan:fructan 6(G)-fructosyltransferases or 6(G)-FFTs) preferentially use fructan as the donor substrate. Recently, a functional Asp/Arg or Asp/Lys couple in the Hypervariable Loop (HVL) was suggested to be essential to keep Asp in a favourable orientation for binding sucrose as the donor substrate in S-type enzymes. However, the F-type enzyme 1-FFT of Triticum aestivum (Ta1-FFT) also contains the Asp/Arg couple in the HVL, although it prefers fructan as the donor substrate. In this paper, mutagenesis studies on Ta1-FFT are presented. In Ta1-SST, Tyr282 (the Asp281 homologue) seems to be essential in creating a tight H-bond Network (HBN) in which the Arg-residue of the Asp/Arg couple is held in a fixed position. This tight HBN is disrupted in Ta1-FFT, leading to a more flexible Arg-residue and a dysfunctional Asp/Arg couple. A single D281Y mutation in Ta1-FFT restored the tight HBN and introduced typical S-type characteristics. Conclusively, in wheat FTs Asp281 (and its homologues) is involved in donor substrate specificity.
Collapse
Affiliation(s)
- Lindsey Schroeven
- Faculteit Wetenschappen, Departement Biologie, KU Leuven, Heverlee, Belgium
| | | | | | | | | | | |
Collapse
|
7
|
Altenbach D, Rudiño-Pinera E, Olvera C, Boller T, Wiemken A, Ritsema T. An acceptor-substrate binding site determining glycosyl transfer emerges from mutant analysis of a plant vacuolar invertase and a fructosyltransferase. PLANT MOLECULAR BIOLOGY 2009; 69:47-56. [PMID: 18821058 PMCID: PMC2709226 DOI: 10.1007/s11103-008-9404-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 09/11/2008] [Indexed: 05/04/2023]
Abstract
Glycoside hydrolase family 32 (GH32) harbors hydrolyzing and transglycosylating enzymes that are highly homologous in their primary structure. Eight amino acids dispersed along the sequence correlated with either hydrolase or glycosyltransferase activity. These were mutated in onion vacuolar invertase (acINV) according to the residue in festuca sucrose:sucrose 1-fructosyltransferase (saSST) and vice versa. acINV(W440Y) doubles transferase capacity. Reciprocally, saSST(C223N) and saSST(F362Y) double hydrolysis. SaSST(N425S) shows a hydrolyzing activity three to four times its transferase activity. Interestingly, modeling acINV and saSST according to the 3D structure of crystallized GH32 enzymes indicates that mutations saSST(N425S), acINV(W440Y), and the previously reported acINV(W161Y) reside very close together at the surface in the entrance of the active-site pocket. Residues in- and outside the sucrose-binding box determine hydrolase and transferase capabilities of GH32 enzymes. Modeling suggests that residues dispersed along the sequence identify a location for acceptor-substrate binding in the 3D structure of fructosyltransferases.
Collapse
Affiliation(s)
- Denise Altenbach
- Zürich-Basel Plant Science Center, Botanisches Institut der Universität Basel, Hebelstrasse 1, 4056 Basel, Switzerland
- Bioreba AG, Chr. Merian-Ring 7, 4153 Reinach, Switzerland
| | - Enrique Rudiño-Pinera
- Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, MO 62250 Mexico
| | - Clarita Olvera
- Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, MO 62250 Mexico
| | - Thomas Boller
- Zürich-Basel Plant Science Center, Botanisches Institut der Universität Basel, Hebelstrasse 1, 4056 Basel, Switzerland
| | - Andres Wiemken
- Zürich-Basel Plant Science Center, Botanisches Institut der Universität Basel, Hebelstrasse 1, 4056 Basel, Switzerland
| | - Tita Ritsema
- Zürich-Basel Plant Science Center, Botanisches Institut der Universität Basel, Hebelstrasse 1, 4056 Basel, Switzerland
- Plant–Microbe Interactions, Institute of Environmental Biology, University Utrecht, Kruijtgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
8
|
Lammens W, Le Roy K, Van Laere A, Rabijns A, Van den Ende W. Crystal Structures of Arabidopsis thaliana Cell-Wall Invertase Mutants in Complex with Sucrose. J Mol Biol 2008; 377:378-85. [DOI: 10.1016/j.jmb.2007.12.074] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 12/07/2007] [Accepted: 12/19/2007] [Indexed: 11/26/2022]
|
9
|
Mátrai J, Lammens W, Jonckheer A, Le Roy K, Rabijns A, Van den Ende W, De Maeyer M. An alternate sucrose binding mode in the E203QArabidopsis invertase mutant: An X-ray crystallography and docking study. Proteins 2008; 71:552-64. [DOI: 10.1002/prot.21700] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
10
|
Le Roy K, Lammens W, Verhaest M, De Coninck B, Rabijns A, Van Laere A, Van den Ende W. Unraveling the difference between invertases and fructan exohydrolases: a single amino acid (Asp-239) substitution transforms Arabidopsis cell wall invertase1 into a fructan 1-exohydrolase. PLANT PHYSIOLOGY 2007; 145:616-25. [PMID: 17873089 PMCID: PMC2048769 DOI: 10.1104/pp.107.105049] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plant cell wall invertases and fructan exohydrolases (FEHs) are very closely related enzymes at the molecular and structural level (family 32 of glycoside hydrolases), but they are functionally different and are believed to fulfill distinct roles in plants. Invertases preferentially hydrolyze the glucose (Glc)-fructose (Fru) linkage in sucrose (Suc), whereas plant FEHs have no invertase activity and only split terminal Fru-Fru linkages in fructans. Recently, the three-dimensional structures of Arabidopsis (Arabidopsis thaliana) cell wall Invertase1 (AtcwINV1) and chicory (Cichorium intybus) 1-FEH IIa were resolved. Until now, it remained unknown which amino acid residues determine whether Suc or fructan is used as a donor substrate in the hydrolysis reaction of the glycosidic bond. In this article, we present site-directed mutagenesis-based data on AtcwINV1 showing that the aspartate (Asp)-239 residue fulfills an important role in both binding and hydrolysis of Suc. Moreover, it was found that the presence of a hydrophobic zone at the rim of the active site is important for optimal and stable binding of Suc. Surprisingly, a D239A mutant acted as a 1-FEH, preferentially degrading 1-kestose, indicating that plant FEHs lacking invertase activity could have evolved from a cell wall invertase-type ancestor by a few mutational changes. In general, family 32 and 68 enzymes containing an Asp-239 functional homolog have Suc as a preferential substrate, whereas enzymes lacking this homolog use fructans as a donor substrate. The presence or absence of such an Asp-239 homolog is proposed as a reliable determinant to discriminate between real invertases and defective invertases/FEHs.
Collapse
Affiliation(s)
- Katrien Le Roy
- Laboratory of Molecular Plant Physiology, Institute of Botany and Microbiology , Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | | | | | | | | | | | | |
Collapse
|
11
|
Rademacher C, Shoemaker GK, Kim HS, Zheng RB, Taha H, Liu C, Nacario RC, Schriemer DC, Klassen JS, Peters T, Lowary TL. Ligand specificity of CS-35, a monoclonal antibody that recognizes mycobacterial lipoarabinomannan: a model system for oligofuranoside-protein recognition. J Am Chem Soc 2007; 129:10489-502. [PMID: 17672460 DOI: 10.1021/ja0723380] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose residues, in particular polysaccharides present in the mycobacterial cell wall. A detailed understanding of the combining site of this antibody and the measurement of its binding to different ligands is of interest as this knowledge will have implications in the characterization of arabinofuranose-containing glycoconjugates that are increasingly recognized as important biological molecules. Of even greater significance is that an in-depth study of this carbohydrate-protein interaction will provide insights into the mechanisms by which oligosaccharides containing furanose rings are bound by proteins, an area that has, to date, received little attention. This system has been refractory to X-ray crystallography, and thus we report here a study of the interaction of CS-35 with its ligands using a combination of chemical synthesis, mass spectrometry, titration microcalorimetry, and NMR spectroscopy. Through these investigations we have established that the binding pocket recognizes, as a minimum epitope, a linear tetrasaccharide motif and that the residues at the reducing and non-reducing end of the oligosaccharide are essential for tight binding. The residue at the non-reducing end appears to be bound in an aliphatic pocket, whereas the rest of the tetrasaccharide interacts more strongly with aromatic amino acids.
Collapse
Affiliation(s)
- Christoph Rademacher
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Le Roy K, Verhaest M, Rabijns A, Clerens S, Van Laere A, Van den Ende W. N-glycosylation affects substrate specificity of chicory fructan 1-exohydrolase: evidence for the presence of an inulin binding cleft. THE NEW PHYTOLOGIST 2007; 176:317-324. [PMID: 17888113 DOI: 10.1111/j.1469-8137.2007.02174.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Recently, the three-dimensional structure of chicory (Cichorium intybus) fructan 1-exohydrolase (1-FEH IIa) in complex with its preferential substrate, 1-kestose, was determined. Unfortunately, no such data could be generated with high degree of polymerization (DP) inulin, despite several soaking and cocrystallization attempts. Here, site-directed mutagenesis data are presented, supporting the presence of an inulin-binding cleft between the N- and C-terminal domains of 1-FEH IIa. In general, enzymes that are unable to degrade high DP inulins contain an N-glycosylation site probably blocking the cleft. By contrast, inulin-degrading enzymes have an open cleft configuration. An 1-FEH IIa P294N mutant, introducing an N-glycosylation site near the cleft, showed highly decreased activity against higher DP inulin. The introduction of a glycosyl chain most probably blocks the cleft and prevents inulin binding and degradation. Besides cell wall invertases, fructan 6-exohydrolases (6-FEHs) also contain a glycosyl chain most probably blocking the cleft. Removal of this glycosyl chain by site-directed mutagenesis in Arabidopsis thaliana cell wall invertase 1 and Beta vulgaris 6-FEH resulted in a strong decrease of enzymatic activities of the mutant proteins. By analogy, glycosylation of 1-FEH IIa affected overall enzyme activity. These data strongly suggest that the presence or absence of a glycosyl chain in the cleft is important for the enzyme's stability and optimal conformation.
Collapse
Affiliation(s)
- Katrien Le Roy
- K. U. Leuven, Laboratory of Molecular Plant Physiology, Institute of Botany and Microbiology, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Maureen Verhaest
- K. U. Leuven, Laboratory of Biocrystallography, Herestraat 49, O & N II box 822, B-3000 Leuven, Belgium
| | - Anja Rabijns
- K. U. Leuven, Laboratory of Biocrystallography, Herestraat 49, O & N II box 822, B-3000 Leuven, Belgium
| | - Stefan Clerens
- K. U. Leuven, Laboratory of Neuroplasticity and Neuroproteomics, Naamsestraat 59, B-3000 Leuven, Belgium
| | - André Van Laere
- K. U. Leuven, Laboratory of Molecular Plant Physiology, Institute of Botany and Microbiology, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Wim Van den Ende
- K. U. Leuven, Laboratory of Molecular Plant Physiology, Institute of Botany and Microbiology, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| |
Collapse
|