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Shen L, Viljoen A, Villaume S, Joe M, Halloum I, Chêne L, Méry A, Fabre E, Takegawa K, Lowary TL, Vincent SP, Kremer L, Guérardel Y, Mariller C. The endogenous galactofuranosidase GlfH1 hydrolyzes mycobacterial arabinogalactan. J Biol Chem 2020; 295:5110-5123. [PMID: 32107309 DOI: 10.1074/jbc.ra119.011817] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 02/11/2020] [Indexed: 12/14/2022] Open
Abstract
Despite impressive progress made over the past 20 years in our understanding of mycolylarabinogalactan-peptidoglycan (mAGP) biogenesis, the mechanisms by which the tubercle bacillus Mycobacterium tuberculosis adapts its cell wall structure and composition to various environmental conditions, especially during infection, remain poorly understood. Being the central portion of the mAGP complex, arabinogalactan (AG) is believed to be the constituent of the mycobacterial cell envelope that undergoes the least structural changes, but no reports exist supporting this assumption. Herein, using recombinantly expressed mycobacterial protein, bioinformatics analyses, and kinetic and biochemical assays, we demonstrate that the AG can be remodeled by a mycobacterial endogenous enzyme. In particular, we found that the mycobacterial GlfH1 (Rv3096) protein exhibits exo-β-d-galactofuranose hydrolase activity and is capable of hydrolyzing the galactan chain of AG by recurrent cleavage of the terminal β-(1,5) and β-(1,6)-Galf linkages. The characterization of this galactosidase represents a first step toward understanding the remodeling of mycobacterial AG.
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Affiliation(s)
- Lin Shen
- Univ. Lille, CNRS, UMR8576 - UGSF - Unit[c33c]zpi;● de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Albertus Viljoen
- Institut de Recherche en Infectiologie de Montpellier (IRIM), UMR9004 - CNRS/UM, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Sydney Villaume
- Laboratoire de Chimie Bio-Organic (CBO), Université de Namur, rue de Bruxelles 61, 5000 Namur, Belgium
| | - Maju Joe
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton AB T6G 2G2, Canada
| | - Iman Halloum
- Institut de Recherche en Infectiologie de Montpellier (IRIM), UMR9004 - CNRS/UM, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Loïc Chêne
- Laboratoire de Chimie Bio-Organic (CBO), Université de Namur, rue de Bruxelles 61, 5000 Namur, Belgium
| | - Alexandre Méry
- Univ. Lille, CNRS, UMR8576 - UGSF - Unit[c33c]zpi;● de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Emeline Fabre
- Univ. Lille, CNRS, UMR8576 - UGSF - Unit[c33c]zpi;● de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Todd L Lowary
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton AB T6G 2G2, Canada
| | - Stéphane P Vincent
- Laboratoire de Chimie Bio-Organic (CBO), Université de Namur, rue de Bruxelles 61, 5000 Namur, Belgium
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), UMR9004 - CNRS/UM, 1919 route de Mende, 34293 Montpellier cedex 5, France.,INSERM, Institut de Recherche en Infectiologie de Montpellier, 34293 Montpellier, France
| | - Yann Guérardel
- Univ. Lille, CNRS, UMR8576 - UGSF - Unit[c33c]zpi;● de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Christophe Mariller
- Univ. Lille, CNRS, UMR8576 - UGSF - Unit[c33c]zpi;● de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
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2
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González-Garcinuño Á, Tabernero A, Domínguez Á, Galán MA, Martin del Valle EM. Levan and levansucrases: Polymer, enzyme, micro-organisms and biomedical applications. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1314467] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Antonio Tabernero
- Department of Chemical Engineering, University of Salamanca, Salamanca, Spain
| | - Ángel Domínguez
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Miguel A. Galán
- Department of Chemical Engineering, University of Salamanca, Salamanca, Spain
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3
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Holyavka M, Artyukhov V, Kovaleva T. Structural and functional properties of inulinases: A review. BIOCATAL BIOTRANSFOR 2016. [DOI: 10.1080/10242422.2016.1196486] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Artyukhov VG, Holyavka MG, Kovaleva TA. Structural and functional properties of inulinases. Ways to regulate their activity. Biophysics (Nagoya-shi) 2013. [DOI: 10.1134/s0006350913040039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Naumoff DG. GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily. BMC Genomics 2005; 6:112. [PMID: 16131397 PMCID: PMC1249566 DOI: 10.1186/1471-2164-6-112] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Accepted: 08/30/2005] [Indexed: 11/29/2022] Open
Abstract
Background As a rule, about 1% of genes in a given genome encode glycoside hydrolases and their homologues. On the basis of sequence similarity they have been grouped into more than ninety GH families during the last 15 years. The GH97 family has been established very recently and initially included only 18 bacterial proteins. However, the evolutionary relationship of the genes encoding proteins of this family remains unclear, as well as their distribution among main groups of the living organisms. Results The extensive search of the current databases allowed us to double the number of GH97 family proteins. Five subfamilies were distinguished on the basis of pairwise sequence comparison and phylogenetic analysis. Iterative sequence analysis revealed the relationship of the GH97 family with the GH27, GH31, and GH36 families of glycosidases, which belong to the α-galactosidase superfamily, as well as a more distant relationship with some other glycosidase families (GH13 and GH20). Conclusion The results of this study show an unexpected sequence similarity of GH97 family proteins with glycoside hydrolases from several other families, that have (β/α)8-barrel fold of the catalytic domain and a retaining mechanism of the glycoside bond hydrolysis. These data suggest a common evolutionary origin of glycosidases representing different families and clans.
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Affiliation(s)
- Daniil G Naumoff
- State Institute for Genetics and Selection of Industrial Microorganisms, I-Dorozhny proezd, 1, Moscow 117545, Russia.
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Shallom D, Leon M, Bravman T, Ben-David A, Zaide G, Belakhov V, Shoham G, Schomburg D, Baasov T, Shoham Y. Biochemical Characterization and Identification of the Catalytic Residues of a Family 43 β-d-Xylosidase from Geobacillus stearothermophilus T-6. Biochemistry 2004; 44:387-97. [PMID: 15628881 DOI: 10.1021/bi048059w] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Beta-D-xylosidases are hemilcellulases that hydrolyze short xylooligosaccharides into xylose units. Here, we describe the characterization and kinetic analysis of a family 43 beta-xylosidase from Geobacillus stearothermophilus T-6 (XynB3). Enzymes in this family use an inverting single-displacement mechanism with two conserved carboxylic acids, a general acid, and a general base. XynB3 was most active at 65 degrees C and pH 6.5, with clear preference to xylose-based substrates. Products analysis indicated that XynB3 is an exoglycosidase that cleaves single xylose units from the nonreducing end of xylooligomers. On the basis of sequence homology, amino acids Asp15 and Glu187 were suggested to act as the general-base and general-acid catalytic residues, respectively. Kinetic analysis with substrates bearing different leaving groups showed that, for the wild-type enzyme, the k(cat) and k(cat)/K(m) values were only marginally affected by the leaving-group reactivity, whereas for the E187G mutant, both values exhibited significantly greater dependency on the pK(a) of the leaving group. The pH-dependence activity profile of the putative general-acid mutant (E187G) revealed that the protonated catalytic residue was removed. Addition of the exogenous nucleophile azide did not affect the activities of the wild type or the E187G mutant but rescued the activity of the D15G mutant. On the basis of thin-layer chromatography and (1)H NMR analyses, xylose and not xylose azide was the only product of the accelerated reaction, suggesting that the azide ion does not attack the anomeric carbon directly but presumably activates a water molecule. Together, these results confirm the suggested catalytic role of Glu187 and Asp15 in XynB3 and provide the first unequivocal evidence regarding the exact roles of the catalytic residues in an inverting GH43 glycosidase.
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Affiliation(s)
- Dalia Shallom
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
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Nagem RAP, Rojas AL, Golubev AM, Korneeva OS, Eneyskaya EV, Kulminskaya AA, Neustroev KN, Polikarpov I. Crystal Structure of Exo-inulinase from Aspergillus awamori: The Enzyme Fold and Structural Determinants of Substrate Recognition. J Mol Biol 2004; 344:471-80. [PMID: 15522299 DOI: 10.1016/j.jmb.2004.09.024] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 08/26/2004] [Accepted: 09/14/2004] [Indexed: 10/26/2022]
Abstract
Exo-inulinases hydrolyze terminal, non-reducing 2,1-linked and 2,6-linked beta-d-fructofuranose residues in inulin, levan and sucrose releasing beta-d-fructose. We present the X-ray structure at 1.55A resolution of exo-inulinase from Aspergillus awamori, a member of glycoside hydrolase family 32, solved by single isomorphous replacement with the anomalous scattering method using the heavy-atom sites derived from a quick cryo-soaking technique. The tertiary structure of this enzyme folds into two domains: the N-terminal catalytic domain of an unusual five-bladed beta-propeller fold and the C-terminal domain folded into a beta-sandwich-like structure. Its structural architecture is very similar to that of another member of glycoside hydrolase family 32, invertase (beta-fructosidase) from Thermotoga maritima, determined recently by X-ray crystallography The exo-inulinase is a glycoprotein containing five N-linked oligosaccharides. Two crystal forms obtained under similar crystallization conditions differ by the degree of protein glycosylation. The X-ray structure of the enzyme:fructose complex, at a resolution of 1.87A, reveals two catalytically important residues: Asp41 and Glu241, a nucleophile and a catalytic acid/base, respectively. The distance between the side-chains of these residues is consistent with a double displacement mechanism of reaction. Asp189, which is part of the Arg-Asp-Pro motif, provides hydrogen bonds important for substrate recognition.
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Affiliation(s)
- R A P Nagem
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, CEP 13560-970, São Carlos, SP, Brazil
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Pons T, Naumoff DG, Martínez-Fleites C, Hernández L. Three acidic residues are at the active site of a beta-propeller architecture in glycoside hydrolase families 32, 43, 62, and 68. Proteins 2004; 54:424-32. [PMID: 14747991 DOI: 10.1002/prot.10604] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Multiple-sequence alignment of glycoside hydrolase (GH) families 32, 43, 62, and 68 revealed three conserved blocks, each containing an acidic residue at an equivalent position in all the enzymes. A detailed analysis of the site-directed mutations so far performed on invertases (GH32), arabinanases (GH43), and bacterial fructosyltransferases (GH68) indicated a direct implication of the conserved residues Asp/Glu (block I), Asp (block II), and Glu (block III) in substrate binding and hydrolysis. These residues are close in space in the 5-bladed beta-propeller fold determined for Cellvibrio japonicus alpha-L-arabinanase Arb43A [Nurizzo et al., Nat Struct Biol 2002;9:665-668] and Bacillus subtilis endo-1,5-alpha-L-arabinanase. A sequence-structure compatibility search using 3D-PSSM, mGenTHREADER, INBGU, and SAM-T02 programs predicted indistinctly the 5-bladed beta-propeller fold of Arb43A and the 6-bladed beta-propeller fold of sialidase/neuraminidase (GH33, GH34, and GH83) as the most reliable topologies for GH families 32, 62, and 68. We conclude that the identified acidic residues are located at the active site of a beta-propeller architecture in GH32, GH43, GH62, and GH68, operating with a canonical reaction mechanism of either inversion (GH43 and likely GH62) or retention (GH32 and GH68) of the anomeric configuration. Also, we propose that the beta-propeller architecture accommodates distinct binding sites for the acceptor saccharide in glycosyl transfer reaction.
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Affiliation(s)
- Tirso Pons
- Centro de Ingeniería Genética y Biotecnología, Habana, Cuba.
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Park BS, Vladimir A, Kim CH, Rhee SK, Kang HA. Secretory production of Zymomonas mobilis levansucrase by the methylotrophic yeast Hansenula polymorpha. Enzyme Microb Technol 2004. [DOI: 10.1016/j.enzmictec.2003.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Meng G, Fütterer K. Structural framework of fructosyl transfer in Bacillus subtilis levansucrase. Nat Struct Mol Biol 2003; 10:935-41. [PMID: 14517548 DOI: 10.1038/nsb974] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2003] [Accepted: 07/31/2003] [Indexed: 11/09/2022]
Abstract
Many bacteria and about 40,000 plant species form primary carbohydrate reserves based on fructan; these polymers of beta-D-fructofuranose are thought to confer tolerance to drought and frost in plants. Microbial fructan, the beta(2,6)-linked levan, is synthesized directly from sucrose by levansucrase, which is able to catalyze both sucrose hydrolysis and levan polymerization. The crystal structure of Bacillus subtilis levansucrase, determined to a resolution of 1.5 A, shows a rare five-fold beta-propeller topology with a deep, negatively charged central pocket. Arg360, a residue essential for polymerase activity, lies in a solvent-exposed site adjacent to the central pocket. Mutagenesis data and the sucrose-bound structure of inactive levansucrase E342A, at a resolution of 2.1 A, strongly suggest that three conserved acidic side chains in the central pocket are critical for catalysis, and presumably function as nucleophile (Asp86) and general acid (Glu342), or stabilize the transition state (Asp247).
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Affiliation(s)
- Guoyu Meng
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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Rigden DJ, Franco OL. Beta-helical catalytic domains in glycoside hydrolase families 49, 55 and 87: domain architecture, modelling and assignment of catalytic residues. FEBS Lett 2002; 530:225-32. [PMID: 12387897 DOI: 10.1016/s0014-5793(02)03490-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
X-ray crystallography and bioinformatics studies reveal a tendency for the right-handed beta-helix domain architecture to be associated with carbohydrate binding proteins. Here we demonstrate the presence of catalytic beta-helix domains in glycoside hydrolase (GH) families 49, 55 and 87 and provide evidence for their sharing a common evolutionary ancestor with two structurally characterized GH families, numbers 28 and 82. This domain assignment helps assign catalytic residues to each family. Further analysis of domain architecture reveals the association of carbohydrate binding modules with catalytic GH beta-helices, as well as an unexpected pair of beta-helix domains in GH family 55.
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Affiliation(s)
- Daniel J Rigden
- Embrapa Genetic Resources and Biotechnology, Cenargen/Embrapa, S.A.I.N. Parque Rural, Final W5, Asa Norte, 70770-900 Brasília DF, Brazil.
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Rigden DJ. Iterative database searches demonstrate that glycoside hydrolase families 27, 31, 36 and 66 share a common evolutionary origin with family 13. FEBS Lett 2002; 523:17-22. [PMID: 12123797 DOI: 10.1016/s0014-5793(02)02879-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Classification of glycoside hydrolases (GHs) into families, along with the structure-based grouping together of families into clans, improve our understanding of the evolution of the large natural variety of these enzymes, help rationalise experimental data and guide further studies. Here we identify triose phosphate isomerase (TIM) barrels in GH families 27, 31, 36 and 66. We further show that iterated sequence database searches provide evidence for their sharing a common evolutionary origin with GH family 13. The catalytic, nucleophilic residue common to all these families is thereby determined and candidate catalytic proton donors identified within each family.
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Affiliation(s)
- Daniel J Rigden
- Embrapa Genetic Resources and Biotechnology, Cenargen/Embrapa, S.A.I.N. Parque Rural, Final W5, Asa Norte, 70770-900, Brasília, Brazil.
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Abstract
Comparison of the amino acid sequences of four families of glycosyl hydrolases reveals that they are homologous and have several common conserved regions. Two of these families contain beta-fructosidases (glycosyl hydrolase families GH32 and GH68) and the other two include alpha-L-arabinases and beta-xylosidases (families GH43 and GH62). The latter two families are proposed to be grouped together with the former two into the beta-fructosidase (furanosidase) superfamily. Several ORFs can be considered as a fifth family of the superfamily on the basis of sequence similarity. It is shown for the first time that a glycosyl hydrolase superfamily can include enzymes with both inversion and retention mechanism of action. Composition of the active center for enzymes of the superfamily is discussed.
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Affiliation(s)
- D G Naumoff
- State Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia.
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