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Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger.

van Pouderoyen G, Snijder HJ, Benen JA, Dijkstra BW
FEBS Lett 554 462-6 (2003)
Cited: 43 times
EuropePMC logo PMID: 14623112

Abstract

Endopolygalacturonase I is a processive enzyme, while the 60% sequence identical endopolygalacturonase II is not. The 1.70 A resolution crystal structure of endopolygalacturonase I reveals a narrowed substrate binding cleft. In addition, Arg96, a residue in this cleft previously shown to be critical for processivity, interacts with the substrate mimics glycerol and sulfate in several well-defined conformations in the six molecules in the asymmetric unit. From this we conclude that both Arg96 and the narrowed substrate binding cleft contribute to retaining the substrate while it moves through the active site after a cleavage event has occurred.

Articles - 1nhc mentioned but not cited (7)

  1. Pi-Pi contacts are an overlooked protein feature relevant to phase separation. Vernon RM, Chong PA, Tsang B, Kim TH, Bah A, Farber P, Lin H, Forman-Kay JD. Elife 7 e31486 (2018)
  2. New Insights into the Role of T3 Loop in Determining Catalytic Efficiency of GH28 Endo-Polygalacturonases. Tu T, Meng K, Luo H, Turunen O, Zhang L, Cheng Y, Su X, Ma R, Shi P, Wang Y, Yang P, Yao B. PLoS One 10 e0135413 (2015)
  3. Nanotechnology enabled enhancement of enzyme activity and thermostability: study on impaired pectate lyase from attenuated Macrophomina phaseolina in presence of hydroxyapatite nanoparticle. Dutta N, Mukhopadhyay A, Dasgupta AK, Chakrabarti K. PLoS One 8 e63567 (2013)
  4. Study of the mode of action of a polygalacturonase from the phytopathogen Burkholderia cepacia. Massa C, Clausen MH, Stojan J, Lamba D, Campa C. Biochem J 407 207-217 (2007)
  5. Crystallization, X-ray diffraction analysis and preliminary structure determination of the polygalacturonase PehA from Agrobacterium vitis. Vordtriede PB, Yoder MD. Acta Crystallogr Sect F Struct Biol Cryst Commun 64 645-647 (2008)
  6. Functional Classification and Characterization of the Fungal Glycoside Hydrolase 28 Protein Family. Villarreal F, Stocchi N, Ten Have A. J Fungi (Basel) 8 217 (2022)
  7. The Synthesis, Fungicidal Activity, and in Silico Study of Alkoxy Analogues of Natural Precocenes I, II, and III. Ramadan KMA, El-Beltagi HS, Iqbal Z, Bendary ESA. Molecules 27 7177 (2022)


Reviews citing this publication (4)

  1. Fungal enzyme sets for plant polysaccharide degradation. van den Brink J, de Vries RP. Appl Microbiol Biotechnol 91 1477-1492 (2011)
  2. Homogalacturonan-modifying enzymes: structure, expression, and roles in plants. Sénéchal F, Wattier C, Rustérucci C, Pelloux J. J Exp Bot 65 5125-5160 (2014)
  3. Pectins, Endopolygalacturonases, and Bioenergy. Latarullo MB, Tavares EQ, Maldonado GP, Leite DC, Buckeridge MS. Front Plant Sci 7 1401 (2016)
  4. Cold active pectinases: advancing the food industry to the next generation. Adapa V, Ramya LN, Pulicherla KK, Rao KR. Appl Biochem Biotechnol 172 2324-2337 (2014)

Articles citing this publication (32)

  1. Polygalacturonase inhibiting proteins: players in plant innate immunity? Federici L, Di Matteo A, Fernandez-Recio J, Tsernoglou D, Cervone F. Trends Plant Sci 11 65-70 (2006)
  2. Structural biology of pectin degradation by Enterobacteriaceae. Abbott DW, Boraston AB. Microbiol Mol Biol Rev 72 301-16, table of contents (2008)
  3. The polygalacturonase-inhibiting protein PGIP2 of Phaseolus vulgaris has evolved a mixed mode of inhibition of endopolygalacturonase PG1 of Botrytis cinerea. Sicilia F, Fernandez-Recio J, Caprari C, De Lorenzo G, Tsernoglou D, Cervone F, Federici L. Plant Physiol 139 1380-1388 (2005)
  4. The structural basis for exopolygalacturonase activity in a family 28 glycoside hydrolase. Abbott DW, Boraston AB. J Mol Biol 368 1215-1222 (2007)
  5. A new group of exo-acting family 28 glycoside hydrolases of Aspergillus niger that are involved in pectin degradation. Martens-Uzunova ES, Zandleven JS, Benen JA, Awad H, Kools HJ, Beldman G, Voragen AG, Van den Berg JA, Schaap PJ. Biochem J 400 43-52 (2006)
  6. Evolutionary analysis of glycosyl hydrolase family 28 (GH28) suggests lineage-specific expansions in necrotrophic fungal pathogens. Sprockett DD, Piontkivska H, Blackwood CB. Gene 479 29-36 (2011)
  7. Structural and mutational characterization of the catalytic A-module of the mannuronan C-5-epimerase AlgE4 from Azotobacter vinelandii. Rozeboom HJ, Bjerkan TM, Kalk KH, Ertesvåg H, Holtan S, Aachmann FL, Valla S, Dijkstra BW. J Biol Chem 283 23819-23828 (2008)
  8. Mapping the polysaccharide degradation potential of Aspergillus niger. Andersen MR, Giese M, de Vries RP, Nielsen J. BMC Genomics 13 313 (2012)
  9. Functional analysis of Pcipg2 from the straminopilous plant pathogen Phytophthora capsici. Sun WX, Jia YJ, Feng BZ, O'Neill NR, Zhu XP, Xie BY, Zhang XG. Genesis 47 535-544 (2009)
  10. Control of root cap maturation and cell detachment by BEARSKIN transcription factors in Arabidopsis. Kamiya M, Higashio SY, Isomoto A, Kim JM, Seki M, Miyashima S, Nakajima K. Development 143 4063-4072 (2016)
  11. Biochemical characterization of three distinct polygalacturonases from Neosartorya fischeri P1. Pan X, Li K, Ma R, Shi P, Huang H, Yang P, Meng K, Yao B. Food Chem 188 569-575 (2015)
  12. Substrate dynamics in enzyme action: rotations of monosaccharide subunits in the binding groove are essential for pectin methylesterase processivity. Mercadante D, Melton LD, Jameson GB, Williams MA, De Simone A. Biophys J 104 1731-1739 (2013)
  13. Cloning, expression and characterization of a metagenome derived thermoactive/thermostable pectinase. Singh R, Dhawan S, Singh K, Kaur J. Mol Biol Rep 39 8353-8361 (2012)
  14. Annotation of proteins of unknown function: initial enzyme results. McKay T, Hart K, Horn A, Kessler H, Dodge G, Bardhi K, Bardhi K, Mills JL, Bernstein HJ, Craig PA. J Struct Funct Genomics 16 43-54 (2015)
  15. Identification, biochemical characterization, and evolution of the Rhizopus oryzae 99-880 polygalacturonase gene family. Mertens JA, Burdick RC, Rooney AP. Fungal Genet Biol 45 1616-1624 (2008)
  16. Pectinase secreted by psychrotolerant fungi: identification, molecular characterization and heterologous expression of a cold-active polygalacturonase from Tetracladium sp. Carrasco M, Rozas JM, Alcaíno J, Cifuentes V, Baeza M. Microb Cell Fact 18 45 (2019)
  17. Crystal Structure of 4,6-α-Glucanotransferase Supports Diet-Driven Evolution of GH70 Enzymes from α-Amylases in Oral Bacteria. Bai Y, Gangoiti J, Dijkstra BW, Dijkhuizen L, Pijning T. Structure 25 231-242 (2017)
  18. Crystal structure of Aspergillus niger isopullulanase, a member of glycoside hydrolase family 49. Mizuno M, Koide A, Yamamura A, Akeboshi H, Yoshida H, Kamitori S, Sakano Y, Nishikawa A, Tonozuka T. J Mol Biol 376 210-220 (2008)
  19. Effects of ultrasound on the enzymatic degradation of pectin. Larsen LR, van der Weem J, Caspers-Weiffenbach R, Schieber A, Weber F. Ultrason Sonochem 72 105465 (2021)
  20. The crystal structure of a hyperthermoactive exopolygalacturonase from Thermotoga maritima reveals a unique tetramer. Pijning T, van Pouderoyen G, Kluskens L, van der Oost J, Dijkstra BW. FEBS Lett 583 3665-3670 (2009)
  21. Production of polygalacturonase from Coriolus versicolor grown on tomato pomace and its chromatographic behaviour on immobilized metal chelates. do Rosário Freixo M, Karmali A, Arteiro JM. J Ind Microbiol Biotechnol 35 475-484 (2008)
  22. Genomic organization of a polygalacturonase gene from a hyperpectinolytic mutant strain of Penicillium occitanis. Trigui-Lahiani H, Ayadi M, Hadj-Taïeb N, Ali MB, Gargouri A. FEMS Microbiol Lett 281 23-29 (2008)
  23. Glycan analysis of recombinant Aspergillus niger endo-polygalacturonase A. Woosley BD, Kim YH, Kumar Kolli VS, Wells L, King D, Poe R, Orlando R, Bergmann C. Carbohydr Res 341 2370-2378 (2006)
  24. Analysis of a polygalacturonase gene of Ustilago maydis and characterization of the encoded enzyme. Castruita-Domínguez JP, González-Hernández SE, Polaina J, Flores-Villavicencio LL, Alvarez-Vargas A, Flores-Martínez A, Ponce-Noyola P, Leal-Morales CA. J Basic Microbiol 54 340-349 (2014)
  25. Effects of power ultrasound on the activity and structure of β-D-glucosidase with potentially aroma-enhancing capability. Sun Y, Zeng L, Xue Y, Yang T, Cheng Z, Sun P. Food Sci Nutr 7 2043-2049 (2019)
  26. Isolation, heterologous expression and characterization of an endo-polygalacturonase produced by the phytopathogen Burkholderia cepacia. Massa C, Degrassi G, Devescovi G, Venturi V, Lamba D. Protein Expr Purif 54 300-308 (2007)
  27. Crystal structure of endo-xylogalacturonan hydrolase from Aspergillus tubingensis. Rozeboom HJ, Beldman G, Schols HA, Dijkstra BW. FEBS J 280 6061-6069 (2013)
  28. Molecular and biochemical characterization of recombinant cel12B, cel8C, and peh28 overexpressed in Escherichia coli and their potential in biofuel production. Ibrahim E, Jones KD, Taylor KE, Hosseney EN, Mills PL, Escudero JM. Biotechnol Biofuels 10 52 (2017)
  29. Polygalacturonases from Moniliophthora perniciosa are regulated by fermentable carbon sources and possible post-translational modifications. Argôlo Santos Carvalho H, de Andrade Silva EM, Carvalho Santos S, Micheli F. Fungal Genet Biol 60 110-121 (2013)
  30. Insight into the structure of an endopolygalacturonase from the phytopathogen Burkholderia cepacia: a biochemical and computational study. Massa C, Guarnaccia C, Lamba D, Anselmi C. Biochimie 92 1445-1453 (2010)
  31. High-level secretive expression of a novel achieved Talaromyces cellulolyticus endo-polygalacturonase in Pichia pastoris by improving gene dosage for hydrolysis of natural pectin. Peng XB, Chen GJ, Han ZG, Yang JK. World J Microbiol Biotechnol 35 84 (2019)
  32. Conserved cysteine variants of metagenomic derived polygalacturonase concurrently shift its optima at acidic pH and enhanced thermostability: structural and functional analysis. Singh R, Kumar A, Chopra N, Mahajan R, Kaur J. J Biomol Struct Dyn 37 265-273 (2019)


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