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2013 | 60 | 4 | 553-564
Article title

A computational approach to structural properties of glycoside hydrolase family 4 from bacteria

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Structural bioinformatics approaches applied to the alpha- and beta-glycosidases from the GH4 enzyme family reveal that, despite low sequence identity, these enzymes possess quite similar global structural characteristics reflecting a common reaction mechanism. Locally, there are a few distinctive structural characteristics of GH4 alpha- and beta-glycosidases, namely, surface cavities with different geometric characteristics and two regions with highly dissimilar structural organizations and distinct physicochemical properties in the alpha- and beta-glucosidases from Thermotoga maritima. We suggest that these structurally dissimilar regions may be involved in specific protein-protein interactions and this hypothesis is sustained by the predicted distinct functional partners of the investigated proteins. Also, we predict that alpha- and beta-glycosidases from the GH4 enzyme family interact with difenoconazole, a fungicide, but there are different features of these interactions especially concerning the identified structurally distinct regions of the investigated proteins.
Physical description
  • West University of Timisoara, Teacher Training Department, Timisoara, Romania
  • West University of Timisoara, Department of Biology and Chemistry, Timisoara, Romania
  • West University of Timisoara, Department of Biology and Chemistry, Timisoara, Romania
  • West University of Timisoara, Department of Biology and Chemistry, Timisoara, Romania
  • West University of Timisoara, Department of Biology and Chemistry, Timisoara, Romania
  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
  • Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37: D233-D238.
  • Carugo O, Eisenhaber F (1997) Probabilistic evaluation of similarity between pairs of three-dimensional protein structures utilizing temperature factors. J Appl Crystallogr 30: 547-549.
  • Chhabra SR, Shockley KR, Ward DE, Kelly RM (2002) Regulation of endo-acting glycosyl hydrolases in the hyperthermophilic bacterium Thermotoga maritima grown on glucan- and mannan-based polysaccharides. Appl Environ Microbiol 68: 545-554.
  • Conners SB, Mongodin EF, Johnson MR, Montero CI, Nelson KE, Kelly RM (2006) Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species. FEMS Microbiol Rev 30: 872-905.
  • Del Pozo MV, Fernández-Arrojo L, Gil-Martínez J, Montesinos A, Chernikova TN, Nechitaylo TY, Waliszek A, Tortajada M, Rojas A, Huws SA, Golyshina O, Newbold CJ, Polaina J, Ferrer M, Golyshin PN (2012) Microbial β-glucosidases from cow rumen metagenome enhance the saccharification of lignocellulose in combination with commercial cellulase cocktail. Biotechnol Biofuels 5: 73.
  • DeLano WL (2002) The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos.
  • Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 34: W116-W118.
  • European Food Safety Authority (2011) Conclusion on the peer review of the pesticide risk assessment of the active substance difenoconazole. EFSA J 9: 1967. [71 pp.]. doi:10.2903/j.efsa.2011.1967.
  • Franczkiewicz R, Braun W (1998) A new efficient algorithm for calculating solvent accessible surface areas of macromolecules. J Comput Chem 19: 319-326.
  • Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In The proteomics protocols handbook. Walker JM, ed, pp 571-607. Humana Press, Totowa, New Jersey.
  • Grosdidier A, Zoete V, Michielin O (2011) SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res 39: W270-W277.
  • Ikai A (1980) Thermostability and aliphatic index of globular proteins. J Biochem 88: 1895-1898.
  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2. Bioinformatics 23: 2947-2948.
  • Leinonen R, Nardone F, Zhu W, Apweiler R (2006) UniSave: the UniProtKB Sequence/Annotation Version database. Bioinformatics 22: 1284-1285.
  • Leisch H, Shi R, Grosse S, Morley K, Bergeron H, Cygler M, Iwaki H, Hasegawa Y, Lau PC (2012) Cloning, Baeyer-Villiger biooxidations, and structures of the camphor pathway 2-oxo-Δ(3)-4,5,5-trimethylcyclopentenylacetyl-coenzyme A monooxygenase of Pseudomonas putida ATCC 17453. Appl Environ Microbiol 78: 2200-2212.
  • Leite TB, Gomes D, Miteva MA, Chomilier J, Villoutreix BO, Tufféry P (2007) Frog: a FRee Online druG 3D conformation generator. Nucleic Acids Res 35: W568-W5672.
  • Lewis M, Rees DC (1985) Fractal surfaces of proteins. Science 230: 1163-1165.
  • Li B, Turuvekere S, Agrawal M, La D, Ramani K, Kihara D (2008) Characterization of local geometry of protein surfaces with the Visibility Criterion. Proteins 71: 670-683.
  • Lodge JA, Maier T, Liebl W, Hoffmann V, Sträter N (2003) Crystal structure of Thermotoga maritima alpha-glucosidase AglA defines a new clan of NAD+-dependent glycosidases. J Biol Chem 278: 19151-19158.
  • McCarter JD, Withers SG (1994) Mechanisms of enzymatic glycoside hydrolysis. Curr Opin Struct Biol 4: 885-892.
  • Pei J, Pang Q, Zhao L, Fan S, Shi H (2012) Thermoanaerobacterium thermosaccharolyticum β-glucosidase: a glucose-tolerant enzyme with high specific activity for cellobiose. Biotechnol Biofuels 5: 31.
  • Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera - A visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612.
  • Rajan SS, Yang X, Collart F, Yip VY, Withers SG, Varrot A, Thompson J, Davies GJ, Anderson WF (2004) Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+-dependent phospho-alpha-glucosidase from Bacillus subtilis. Structure 12: 1619-1629.
  • Snel B, Lehmann G, Bork P, Huynen MA (2000) STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res 28: 3442-3444.
  • Thom E, Ottow JC, Benckiser G (1997) Degradation of the fungicide difenoconazole in a silt loam soil as affected by pretreatment and organic amendment, Environ Pollut 96: 409-414.
  • Ugwuanyi JO (2008) Yield and protein quality of thermophilic Bacillus spp. biomass related to thermophilic aerobic digestion of agricultural wastes for animal feed supplementation. Bioresour Technol 99: 3279-3290.
  • Varrot A, Yip VLY, Li Y, Rajan SS, Yang X, Anderson W, Thompson J, Withers SG, Davies GJ (2005) NAD+ and metal-ion dependent hydrolysis by family 4 glycosidases: Structural insight into specificity for phospho-beta-D-glucosides. J Mol Biol 346: 423-435.
  • Weininger D (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Model 28: 31-36.
  • Yang B, Dai Z, Ding S-Y, Wyman CE (2011) Enzymatic hydrolysis of cellulosic biomass. Biofuels 2: 421-450.
  • Yip VL, Varrot A, Davies GJ, Rajan SS, Yang X, Thompson J, Anderson WF, Withers SG (2004) An unusual mechanism of glycoside hydrolysis involving redox and elimination steps by a family 4 beta-glycosidase from Thermotoga maritima. J Am Chem Soc 126: 8354-8355.
  • Yip VL, Withers SG (2006) Mechanistic analysis of the unusual redox-elimination sequence employed by Thermotoga maritima BglT: a 6-phospho-beta-glucosidase from glycoside hydrolase family 4. Biochemistry 45: 571-580.
  • Yip VL, Thompson J, Withers SG (2007) Mechanism of GlvA from Bacillus subtilis: a detailed kinetic analysis of a 6-phospho-alpha-glucosidase from glycoside hydrolase family 4. Biochemistry 46: 9840-9852.
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