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Structural insights into the molecular mechanisms of pectinolytic enzymes

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Abstract

Pectinolytic enzymes produced by a large variety of organisms are well characterized concerning their physiological and pathological activities during modification or degradation of the complex plant cell wall. The exponential growth in structural information of these enzymes over past decades has rendered insights into functionally relevant residues, active sites and molecular basis of the enzymatic mechanism, which in turn, endorses its usage in industrial applications. This review highlights a comprehensive and up to date summary of structural information and the structure–function correlation of pectinolytic enzymes.

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References

  • Abbott DW, Boraston AB (2007a) A family 2 pectate lyase displays a rare fold and transition metal-assisted β-elimination. J Biol Chem 282:35328–35336

    CAS  PubMed  Google Scholar 

  • Abbott DW, Boraston AB (2007b) The structural basis for exopolygalacturonase activity in a family 28 glycoside hydrolase. J Mol Biol 368:1215–1222

    CAS  PubMed  Google Scholar 

  • Abbott DW, Gilbert HJ, Boraston AB (2010) The active site of oligogalacturonate lyase provides unique insights into cytoplasmic oligogalacturonate β-elimination. J Biol Chem 285:39029–39038

    CAS  PubMed  PubMed Central  Google Scholar 

  • Abbott DW, Thomas D, Pluvinage B, Boraston AB (2013) An ancestral member of the polysaccharide lyase family 2 displays endolytic activity and magnesium dependence. Appl Biochem Biotechnol 171:1911–1923

    CAS  PubMed  Google Scholar 

  • Ahlawat S, Mandhan R, Dhiman SS, Kumar R, Sharma J (2008) Potential application of alkaline pectinase from Bacillus subtilis SS in pulp and paper industry. Appl Biochem Biotechnol 149:287–293

    CAS  PubMed  Google Scholar 

  • Akita M, Suzuki A, Kobayashi T, Ito S, Yamane T (2001) The first structure of pectate lyase belonging to polysaccharide lyase family 3. Acta Crystallogr D Biol Crystallogr 57:1786–1792

    CAS  PubMed  Google Scholar 

  • Alahuhta M, Chandrayan P, Kataeva I, Adams MW, Himmel ME, Lunin VV (2011) A 1.5 Å resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase. Acta Crystallogr F Struct Biol Cryst Commun 67(12):1498–1500

    CAS  Google Scholar 

  • Alahuhta M et al (2015) The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase. Acta Crystallogr D Biol Crystallogr 71:1946–1954

    CAS  PubMed  PubMed Central  Google Scholar 

  • Amin F, Bhatti HN, Bilal M (2019) Recent advances in the production strategies of microbial pectinases—a review. Int J Biol Macromol 122:1017–1026

    CAS  PubMed  Google Scholar 

  • Armand S et al (2000) The active site topology of Aspergillus niger endopolygalacturonase II as studied by site-directed mutagenesis. J Biol Chem 275:691–696

    CAS  PubMed  Google Scholar 

  • Atmodjo MA, Hao Z, Mohnen D (2013) Evolving views of pectin biosynthesis. Annu Rev Plant Biol 64:747–779

    CAS  PubMed  Google Scholar 

  • Azadi P, O’Neill MA, Bergmann C, Darvill AG, Albersheim P (1995) The backbone of the pectic polysaccharide rhamnogalacturonan I is cleaved by an endohydrolase and an endolyase. Glycobiology 5:783–789

    CAS  PubMed  Google Scholar 

  • Bolvig PU, Pauly M, Orfila C, Scheller HV, Schnorr K (2003) Sequence analysis and characterisation of a novel pectin acetyl esterase from Bacillus subtilis. In: Voragen F, Schols H, Visser R (eds) Advances in pectin and pectinase research. Springer, Berlin, pp 315–330

    Google Scholar 

  • Bonivento D et al (2008) Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins. Proteins Struct Funct Bioinform 70:294–299

    CAS  Google Scholar 

  • Bonnin E, Garnier C, Ralet M-C (2014) Pectin-modifying enzymes and pectin-derived materials: applications and impacts. Appl Microbiol Biotechnol 98:519–532

    CAS  PubMed  Google Scholar 

  • Boraston AB, Abbott D (2012) Structure of a pectin methylesterase from Yersinia enterocolitica. Acta Crystallogr F Struct Biol Cryst Commun 68:129–133

    CAS  Google Scholar 

  • Bosch M, Cheung AY, Hepler PK (2005) Pectin methylesterase, a regulator of pollen tube growth. Plant Physiol 138:1334–1346

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brummell DA, Harpster MH (2001) Cell wall metabolism in fruit softening and quality and its manipulation in transgenic plants. In: Carpita NC, Campbell M, Tierney M (eds) Plant cell walls. Springer, Berlin, pp 311–340

    Google Scholar 

  • Caffall KH, Mohnen D (2009) The structure, function, and biosynthesis of plant cell wall pectic polysaccharides. Carbohydr Res 344:1879–1900

    CAS  PubMed  Google Scholar 

  • Charnock SJ, Brown IE, Turkenburg JP, Black GW, Davies GJ (2002) Convergent evolution sheds light on the anti-β-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proc Natl Acad Sci 99:12067–12072

    CAS  PubMed  Google Scholar 

  • Cho SW, Lee S, Shin W (2001) The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex. J Mol Biol 311:863–878

    CAS  PubMed  Google Scholar 

  • Choi D-H, Kim Y-D, Chung I-S, Lee S-H, Kang S-M, Kwon T-J, Han K-S (2000) Gene cloning and expression of cephalosporin-C deacetylase from Bacillus sp. KCCM10143. J Microbiol Biotechnol 10:221–226

    CAS  Google Scholar 

  • Creze C, Castang S, Derivery E, Haser R, Hugouvieux-Cotte-Pattat N, Shevchik VE, Gouet P (2008) The crystal structure of pectate lyase peli from soft rot pathogen Erwinia chrysanthemi in complex with its substrate. J Biol Chem 283:18260–18268

    CAS  PubMed  Google Scholar 

  • Dehdashti SJ, Doan CN, Chao KL, Yoder MD (2003) Effect of mutations in the T1. 5 loop of pectate lyase A from Erwinia chrysanthemi EC16. Acta Crystallogr D Biol Crystallogr 59:1339–1342

    PubMed  Google Scholar 

  • Derbyshire P, McCann MC, Roberts K (2007) Restricted cell elongation in Arabidopsis hypocotyls is associated with a reduced average pectin esterification level. BMC Plant Biol 7:31

    PubMed  PubMed Central  Google Scholar 

  • Di Matteo A et al (2005) Structural basis for the interaction between pectin methylesterase and a specific inhibitor protein. Plant Cell 17:849–858

    PubMed  PubMed Central  Google Scholar 

  • Federici L et al (2001) Structural requirements of endopolygalacturonase for the interaction with PGIP (polygalacturonase-inhibiting protein). Proc Natl Acad Sci 98:13425–13430

    CAS  PubMed  Google Scholar 

  • Fries M, Ihrig J, Brocklehurst K, Shevchik VE, Pickersgill RW (2007) Molecular basis of the activity of the phytopathogen pectin methylesterase. EMBO J 26:3879–3887

    CAS  PubMed  PubMed Central  Google Scholar 

  • Garg G, Singh A, Kaur A, Singh R, Kaur J, Mahajan R (2016) Microbial pectinases: an ecofriendly tool of nature for industries. 3 Biotech 6:47

    CAS  PubMed  PubMed Central  Google Scholar 

  • Garron M-L, Cygler M (2010) Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology 20:1547–1573

    CAS  PubMed  Google Scholar 

  • Gou J-Y, Miller LM, Hou G, Yu X-H, Chen X-Y, Liu C-J (2012) Acetylesterase-mediated deacetylation of pectin impairs cell elongation, pollen germination, and plant reproduction. Plant Cell 24:50–65

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gough J, Karplus K, Hughey R, Chothia C (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 313:903–919

    CAS  PubMed  Google Scholar 

  • Harholt J, Suttangkakul A, Scheller HV (2010) Biosynthesis of pectin. Plant Physiol 153:384–395

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hatanaka C, Ozawa I (1971) Enzymic degradation of pectic acid XIII. A new exopolygalacturonase producing digalacturonic acid from pectic acid. Berichte des Ohara Instituts für landwirtschaftliche Biologie, Okayama Universität 15:47–60

    Google Scholar 

  • Held MA, Jiang N, Basu D, Showalter AM, Faik A (2015) Plant cell wall polysaccharides: structure and biosynthesis. In: Ramawat KG, Mérillon JM (eds) Polysaccharides. Springer, Switzerland, pp 3–54

    Google Scholar 

  • Herron SR, Benen JA, Scavetta RD, Visser J, Jurnak F (2000) Structure and function of pectic enzymes: virulence factors of plant pathogens. Proc Natl Acad Sci 97:8762–8769

    CAS  PubMed  Google Scholar 

  • Herron SR, Scavetta RD, Garrett M, Legner M, Jurnak F (2003) Characterization and implications of Ca2+ binding to pectate lyase C. J Biol Chem 278:12271–12277

    CAS  PubMed  Google Scholar 

  • Ho YS et al (1997) Brain acetylhydrolase that inactivates platelet-activating factor is a G-protein-like trimer. Nature 385:89–93

    CAS  PubMed  Google Scholar 

  • Jacob N (2009) Pectinolytic enzymes. In: Singh nee’ Nigam P, Pandey A (eds) Biotechnology for agro-industrial residues utilisation. Springer, Berlin, pp 383–396

    Google Scholar 

  • Jenkins J, Mayans O, Smith D, Worboys K, Pickersgill RW (2001) Three-dimensional structure of Erwinia chrysanthemi pectin methylesterase reveals a novel esterase active site. J Mol Biol 305:951–960

    CAS  PubMed  Google Scholar 

  • Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, Pickersgill RW (2004) The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi. J Biol Chem 279:9139–9145

    CAS  PubMed  Google Scholar 

  • Jensen MH, Otten H, Christensen U, Borchert TV, Christensen LL, Larsen S, Leggio LL (2010) Structural and biochemical studies elucidate the mechanism of rhamnogalacturonan lyase from Aspergillus aculeatus. J Mol Biol 404:100–111

    CAS  PubMed  Google Scholar 

  • Johansson K, El-Ahmad M, Friemann R, Jörnvall H, Markovič O, Eklund H (2002) Crystal structure of plant pectin methylesterase. FEBS Lett 514:243–249

    CAS  PubMed  Google Scholar 

  • Jolie RP, Duvetter T, Van Loey AM, Hendrickx ME (2010) Pectin methylesterase and its proteinaceous inhibitor: a review. Carbohydr Res 345:2583–2595

    CAS  PubMed  Google Scholar 

  • Kashyap D, Vohra P, Chopra S, Tewari R (2001) Applications of pectinases in the commercial sector: a review. Bioresour Technol 77:215–227

    CAS  PubMed  Google Scholar 

  • Kent LM, Loo TS, Melton LD, Mercadante D, Williams MA, Jameson GB (2016) Structure and properties of a non-processive, salt-requiring, and acidophilic pectin methylesterase from Aspergillus niger provide insights into the key determinants of processivity control. J Biol Chem 291:1289–1306

    CAS  PubMed  Google Scholar 

  • Kester H, Someren MA, Müller Y, Visser J (1996) Primary structure and characterization of an exopolygalacturonase from Aspergillus tubingensis. Eur J Biochem 240:738–746

    CAS  PubMed  Google Scholar 

  • Khan M, Nakkeeran E, Umesh-Kumar S (2013) Potential application of pectinase in developing functional foods. Annu Rev Food Sci Technol 4:21–34

    CAS  PubMed  Google Scholar 

  • Kunishige Y, Iwai M, Nakazawa M, Ueda M, Tada T, Nishimura S, Sakamoto T (2018) Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26. FEBS Lett 592:1378–1388

    CAS  PubMed  Google Scholar 

  • Langkilde A, Kristensen SM, Lo Leggio L, Mølgaard A, Jensen JH, Houk AR, Navarro Poulsen J-C, Kauppinen S, Larsen S (2008) Short strong hydrogenbonds in proteins: a case study of rhamnogalacturonan acetylesterase. Acta Crystallogr D Biol Crystallogr 64:851–863

    CAS  PubMed Central  Google Scholar 

  • Le Goff A, Renard C, Bonnin E, Thibault J-F (2001) Extraction, purification and chemical characterisation of xylogalacturonans from pea hulls. Carbohydr Polym 45:325–334

    Google Scholar 

  • Lee W, Yusof S, Hamid NSA, Baharin BS (2006) Optimizing conditions for enzymatic clarification of banana juice using response surface methodology (RSM). J Food Eng 73:55–63

    CAS  Google Scholar 

  • Leroux C et al (2015) Pectin methylesterase 48 is involved in Arabidopsis pollen grain germination. Plant Physiol 167:367–380

    CAS  PubMed  Google Scholar 

  • Lietzke SE, Yoder MD, Keen NT, Jurnak F (1994) The three-dimensional structure of pectate lyase E, a plant virulence factor from Erwinia chrysanthemi. Plant Physiol 106:849–862

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lietzke SE, Scavetta RD, Yoder MD, Jurnak F (1996) The refined three-dimensional structure of pectate lyase E from Erwinia chrysanthemi at 2.2 A resolution. Plant Physiol 111:73–92

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lionetti V, Cervone F, Bellincampi D (2012) Methyl esterification of pectin plays a role during plant–pathogen interactions and affects plant resistance to diseases. J Plant Physiol 169:1623–1630

    CAS  PubMed  Google Scholar 

  • Liu C-Q et al (2017) Polygalacturonase gene pgxB in Aspergillus niger is a virulence factor in apple fruit. PLoS ONE 12:e0173277

    PubMed  PubMed Central  Google Scholar 

  • Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho PM, Henrissat B (2010) A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem J 432:437–444

    CAS  PubMed  Google Scholar 

  • Lombard V, Ramulu HG, Drula E, Coutinho PM, Henrissat B (2014) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495

    CAS  PubMed  Google Scholar 

  • Markovič O, Janeček Š (2004) Pectin methylesterases: sequence-structural features and phylogenetic relationships. Carbohydr Res 339:2281–2295

    PubMed  Google Scholar 

  • Martens-Uzunova ES et al (2006) A new group of exo-acting family 28 glycoside hydrolases of Aspergillus niger that are involved in pectin degradation. Biochem J 400:43–52

    CAS  PubMed  PubMed Central  Google Scholar 

  • Martínez-Martínez I, Navarro-Fernández J, Daniel Lozada-Ramírez J, García-Carmona F, Sánchez-Ferrer Á (2008) YesT: a new rhamnogalacturonan acetyl esterase from Bacillus subtilis. Proteins Struct Funct Bioinform 71:379–388

    Google Scholar 

  • Mayans O et al (1997) Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure 5:677–689

    CAS  PubMed  Google Scholar 

  • McDonough MA, Kadirvelraj R, Harris P, Poulsen J-CN, Larsen S (2004) Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4. FEBS Lett 565:188–194

    CAS  PubMed  Google Scholar 

  • McLean R, Hobbs JK, Suits MD, Tuomivaara ST, Jones DR, Boraston AB, Abbott DW (2015) Functional analyses of resurrected and contemporary enzymes illuminate an evolutionary path for the emergence of exolysis in polysaccharide lyase family 2. J Biol Chem 290:21231–21243

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mohnen D (2008) Pectin structure and biosynthesis. Curr Opin Plant Biol 11:266–277

    CAS  PubMed  Google Scholar 

  • Mohnen D, Bar-Peled M, Somerville C (2008) Cell wall polysaccharide synthesis. In: Himmel M (ed) Biomass recalcitrance: deconstructing the plant cell wall bioenergy. Blackwell Publishing, Oxford, pp 94–187

    Google Scholar 

  • Mølgaard A, Larsen S (2002) A branched N-linked glycan at atomic resolution in the 1.12 Å structure of rhamnogalacturonan acetylesterase. Acta Crystallogr D Biol Crystallogr 58:111–119

    PubMed  Google Scholar 

  • Mølgaard A, Kauppinen S, Larsen S (2000) Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. Structure 8:373–383

    PubMed  Google Scholar 

  • Munoz-Munoz J, Cartmell A, Terrapon N, Baslé A, Henrissat B, Gilbert HJ (2017) An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins. J Biol Chem M117:794578

    Google Scholar 

  • Murthy PS, Naidu MM (2011) Improvement of robusta coffee fermentation with microbial enzymes. Eur J Appl Sci 3:130–139

    Google Scholar 

  • Mutter M, Beldman G, Schols HA, Voragen AGJ (1994) Rhamnogalacturonan α-l-rhamnopyranohydrolase (A novel enzyme specific for the terminal nonreducing rhamnosyl unit in rhamnogalacturonan regions of pectin). Plant Physiol 106:241–250

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mutter M, Beldman G, Pitson SM, Schols HA, Voragen AG (1998) Rhamnogalacturonan α-d-galactopyranosyluronohydrolase: an enzyme that specifically removes the terminal nonreducing galacturonosyl residue in rhamnogalacturonan regions of pectin. Plant Physiol 117:153–163

    CAS  PubMed  PubMed Central  Google Scholar 

  • Najafian L, Ghodsvali A, Khodaparast MH, Diosady L (2009) Aqueous extraction of virgin olive oil using industrial enzymes. Food Res Int 42:171–175

    CAS  Google Scholar 

  • Nakamura A, Furuta H, Maeda H, Takao T, Nagamatsu Y (2002) Analysis of the molecular construction of xylogalacturonan isolated from soluble soybean polysaccharides. Biosci Biotechnol Biochem 66:1155–1158

    CAS  PubMed  Google Scholar 

  • Navarro-Fernández J, Martínez-Martínez I, Montoro-García S, García-Carmona F, Takami H, Sánchez-Ferrer Á (2008) Characterization of a new rhamnogalacturonan acetyl esterase from Bacillus halodurans C-125 with a new putative carbohydrate binding domain. J Bacteriol 190:1375–1382

    PubMed  Google Scholar 

  • Normand J, Ralet M-C, Thibault J-F, Rogniaux H, Delavault P, Bonnin E (2010) Purification, characterization, and mode of action of a rhamnogalacturonan hydrolase from Irpex lacteus, tolerant to an acetylated substrate. Appl Microbiol Biotechnol 86:577–588

    CAS  PubMed  Google Scholar 

  • Novoa de Armas H, Verboven C, De Ranter C, Desair J, Vande Broek A, Vanderleyden J, Rabijns A (2004) Azospirillum irakense pectate lyase displays a toroidal fold. Acta Crystallogr D Biol Crystallogr 60:999–1007

    PubMed  Google Scholar 

  • O’Neill MA, York WS (2003) The composition and structure of plant primary cell walls. In: Rose JKC (ed) The plant cell wall. Blackwell Publishing, Oxford, pp 1–54

    Google Scholar 

  • Ochiai A, Itoh T, Maruyama Y, Kawamata A, Mikami B, Hashimoto W, Murata K (2007) A novel structural fold in polysaccharide lyases Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed β-propeller. J Biol Chem 282:37134–37145

    CAS  PubMed  Google Scholar 

  • Ochiai A, Itoh T, Mikami B, Hashimoto W, Murata K (2009) Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases. J Biol Chem 284:10181–10189

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pagès S, Heijne WH, Kester HC, Visser J, Benen JA (2000) Subsite Mapping of Aspergillus niger endopolygalacturonase II by site-directed mutagenesis. J Biol Chem 275:29348–29353

    PubMed  Google Scholar 

  • Paniagua C et al (2017) Structural changes in cell wall pectins during strawberry fruit development. Plant Physio Biochem 118:55–63

    CAS  Google Scholar 

  • Pelletier S et al (2010) A role for pectin de-methylesterification in a developmentally regulated growth acceleration in dark-grown Arabidopsis hypocotyls. New Phytol 188:726–739

    CAS  PubMed  Google Scholar 

  • Pelloux J, Rusterucci C, Mellerowicz EJ (2007) New insights into pectin methylesterase structure and function. Trends Plant Sci 12:267–277

    CAS  PubMed  Google Scholar 

  • Petersen TN, Kauppinen S, Larsen S (1997) The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel β helix. Structure 5:533–544

    CAS  PubMed  Google Scholar 

  • Pickersgill R, Jenkins J, Harris G, Nasser W, Robert-Baudouy J (1994) The structure of Bacillus subtilis pectate lyase in complex with calcium. Nat Struct Mol Biol 1:717–723

    CAS  Google Scholar 

  • Pickersgill R, Smith D, Worboys K, Jenkins J (1998) Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora. J Biol Chem 273:24660–24664

    CAS  PubMed  Google Scholar 

  • Pijning T, van Pouderoyen G, Kluskens L, van der Oost J, Dijkstra BW (2009) The crystal structure of a hyperthermoactive exopolygalacturonase from Thermotoga maritima reveals a unique tetramer. FEBS Lett 583:3665–3670

    CAS  PubMed  Google Scholar 

  • Rosenthal PB et al (1998) Structure of the haemagglutinin-esterase-fusion glycoprotein of influenza C virus. Nature 396:92

    CAS  PubMed  Google Scholar 

  • Rozeboom HJ, Beldman G, Schols HA, Dijkstra BW (2013) Crystal structure of endo-xylogalacturonan hydrolase from Aspergillus tubingensis. FEBS J 280:6061–6069

    CAS  PubMed  Google Scholar 

  • Rytioja J, Hildén K, Yuzon J, Hatakka A, de Vries RP, Mäkelä MR (2014) Plant-polysaccharide-degrading enzymes from basidiomycetes. Microbiol Mol Biol Rev 78:614–649

    PubMed  PubMed Central  Google Scholar 

  • Sandri IG, Fontana RC, Barfknecht DM, da Silveira MM (2011) Clarification of fruit juices by fungal pectinases. LWT Food Sci Technol 44:2217–2222

    CAS  Google Scholar 

  • Scavetta RD et al (1999) Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell 11:1081–1092

    CAS  PubMed  PubMed Central  Google Scholar 

  • Seyedarabi A, To TT, Ali S, Hussain S, Fries M, Madsen R, Clausen MH, Teixteira S, Brocklehurst K, Pickersgill RW (2009) Structural insights intosubstrate specificity and the anti β-elimination mechanism of pectate lyase. Biochemistry 49:539–546

    Google Scholar 

  • Shallom D et al (2005) Biochemical characterization and identification of the catalytic residues of a family 43 β-d-xylosidase from Geobacillus stearothermophilus T-6. Biochemistry 44:387–397

    CAS  PubMed  Google Scholar 

  • Sharma N, Rathore M, Sharma M (2013) Microbial pectinase: sources, characterization and applications. Rev Environ Sci Biotechnol 12:45–60

    CAS  Google Scholar 

  • Shimizu T, Nakatsu T, Miyairi K, Okuno T, Kato H (2002) Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution. Biochemistry 41:6651–6659

    CAS  PubMed  Google Scholar 

  • Silva IR et al (2014) Design of thermostable rhamnogalacturonan lyase mutants from Bacillus licheniformis by combination of targeted single point mutations. Appl Microbiol Biotechnol 98:4521–4531

    CAS  PubMed  Google Scholar 

  • Silva IR, Jers C, Meyer AS, Mikkelsen JD (2016) Rhamnogalacturonan I modifying enzymes: an update. New Biotechnol 33:41–54

    CAS  Google Scholar 

  • Singh J, Kundu D, Das M, Banerjee R (2019) Enzymatic processing of juice from fruits/vegetables: an emerging trend and cutting edge research in food biotechnology. In: Kuddus M (ed) Enzymes in food biotechnology. Academic Press, Cambridge, pp 419–432

    Google Scholar 

  • Tang Q, Liu YP, Ren ZG, Yan XX, Zhang LQ (2013) 1.37 Å crystal structure of pathogenic factor pectate lyase from Acidovorax citrulli. Proteins Struct Funct Bioinform 81:1485–1490

    CAS  Google Scholar 

  • Teller DC, Behnke CA, Pappan K, Shen Z, Reese JC, Reeck GR, Stenkamp RE (2014) The structure of rice weevil pectin methylesterase. Acta Crystallogr F Struct Biol Cryst Commun 70:1480–1484

    CAS  Google Scholar 

  • Thomas LM, Doan CN, Oliver RL, Yoder MD (2002) Structure of pectate lyase A: comparison to other isoforms. Acta Crystallogr D Biol Crystallogr 58:1008–1015

    PubMed  Google Scholar 

  • Tian G-W, Chen M-H, Zaltsman A, Citovsky V (2006) Pollen-specific pectin methylesterase involved in pollen tube growth. Dev Biol 294:83–91

    CAS  PubMed  Google Scholar 

  • van den Brink J, de Vries RP (2011) Fungal enzyme sets for plant polysaccharide degradation. Appl Microbiol Biotechnol 91:1477

    CAS  PubMed  PubMed Central  Google Scholar 

  • van Pouderoyen G, Snijder HJ, Benen JA, Dijkstra BW (2003) Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger. FEBS Lett 554:462–466

    PubMed  Google Scholar 

  • van Santen Y, Benen JA, Schröter K-H, Kalk KH, Armand S, Visser J, Dijkstra BW (1999) 1.68-Å crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis. J Biol Chem 274:30474–30480

    PubMed  Google Scholar 

  • Vincken J-P, Schols HA, Oomen RJ, Beldman G, Visser RG, Voragen AG (2003) Pectin—the hairy thing. In: Voragen F, Schols H, Visser R (eds) Advances in pectin and pectinase research. Springer, Berlin, pp 47–59

    Google Scholar 

  • Vitali J, Schick B, Kester HC, Visser J, Jurnak F (1998) The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-Å resolution. Plant Physiol 116:69–80

    CAS  PubMed  PubMed Central  Google Scholar 

  • Walker SG, Ryan ME (2003) Cloning and expression of a pectate lyase from the oral spirochete Treponema pectinovorum ATCC 33768. FEMS Microbiol Lett 226:385–390

    CAS  PubMed  Google Scholar 

  • Wang Z-Y, MacRae EA, Wright MA, Bolitho KM, Ross GS, Atkinson RG (2000) Polygalacturonase gene expression in kiwifruit: relationship to fruit softening and ethylene production. Plant Mol Biol 42:317–328

    CAS  PubMed  Google Scholar 

  • Wang D, Yeats TH, Uluisik S, Rose JK, Seymour GB (2018) Fruit softening: revisiting the role of pectin. Trends Plant Sci 23:302–310

    CAS  PubMed  Google Scholar 

  • Wei Y, Schottel JL, Derewenda U, Swenson L, Patkar S, Derewenda ZS (1995) A novel variant of the catalytic triad in the Streptomyces scabies esterase. Nat Struct Mol Biol 2:218–223

    CAS  Google Scholar 

  • Wong D (2008) Enzymatic deconstruction of backbone structures of the ramified regions in pectins. Protein J 27:30–42

    CAS  PubMed  Google Scholar 

  • Wu Y, Yin Z, Xu L, Feng H, Huang L (2018) VmPacC is required for acidification and virulence in Valsa mali. Front Microbiol 9:1981

    PubMed  PubMed Central  Google Scholar 

  • Xiao Z, Bergeron H, Grosse S, Beauchemin M, Garron M-L, Shaya D, Sulea T, Cygler M, Lau PC (2008) Improvement of the thermostability and activityof a pectate lyase by single amino acid substitutions, using a strategy based on melting-temperature-guided sequence alignment. Appl Environ Microbiol 74:1183–1189

    CAS  PubMed  Google Scholar 

  • Yapo BM (2011) Pectic substances: from simple pectic polysaccharides to complex pectins—a new hypothetical model. Carbohydr Polym 86:373–385

    CAS  Google Scholar 

  • Yip VL, Withers SG (2006) Breakdown of oligosaccharides by the process of elimination. Curr Opin Chem Biol 10:147–155

    CAS  PubMed  Google Scholar 

  • Yoder M, Jurnak F (1995a) Protein motifs. 3. The parallel beta helix and other coiled folds. FASEB J 9:335–342

    CAS  PubMed  Google Scholar 

  • Yoder MD, Jurnak F (1995b) The refined three-dimensional structure of pectate lyase C from Erwinia chrysanthemi at 2.2 angstrom resolution (implications for an enzymatic mechanism). Plant Physiol 107:349–364

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yoder MD, Keen NT, Jurnak F (1993a) New domain motif: the structure of pectate lyase C, a secreted plant virulence factor. Science 260:1503–1507

    CAS  PubMed  Google Scholar 

  • Yoder MD, Lietzke SE, Jurnak F (1993b) Unusual structural features in the parallel β-helix in pectate lyases. Structure 1:241–251

    CAS  PubMed  Google Scholar 

  • Yue X, Lin S, Yu Y, Huang L, Cao J (2018) The putative pectin methylesterase gene, BcMF23a, is required for microspore development and pollen tube growth in Brassica campestris. Plant Cell Rep 37:1003–1009

    CAS  PubMed  Google Scholar 

  • Zandleven J, Beldman G, Bosveld M, Benen J, Voragen A (2005) Mode of action of xylogalacturonan hydrolase towards xylogalacturonan and xylogalacturonan oligosaccharides. Biochem J 387:719–725

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zandleven J, Beldman G, Bosveld M, Schols H, Voragen A (2006) Enzymatic degradation studies of xylogalacturonans from apple and potato, using xylogalacturonan hydrolase. Carbohydr Polym 65:495–503

    CAS  Google Scholar 

  • Zega A, D’Ovidio R (2016) Genome-wide characterization of pectin methyl esterase genes reveals members differentially expressed in tolerant and susceptible wheats in response to Fusarium graminearum. Plant Physiol Biochem 08:1–11

    Google Scholar 

  • Zheng Y et al (2012) Crystal structure and substrate-binding mode of a novel pectate lyase from alkaliphilic Bacillus sp. N16-5. Biochem Biophys Res Commun 420:269–274

    CAS  PubMed  Google Scholar 

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Acknowledgements

The author would like to thank Dr. Bamaprasad Bag at Institute of Minerals and Materials Technology, Bhubaneswar and Dr. Hirak Chakraborty, Department of Chemistry, Sambalpur University for critical reading of the manuscript and fruitful suggestions.

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  1. Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti Vihar, Sambalpur, 768019, India

    Anuradha Kanungo & Bhawani Prasad Bag

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  1. Anuradha Kanungo
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  2. Bhawani Prasad Bag
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Correspondence to Bhawani Prasad Bag.

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Kanungo, A., Bag, B.P. Structural insights into the molecular mechanisms of pectinolytic enzymes. J Proteins Proteom 10, 325–344 (2019). https://doi.org/10.1007/s42485-019-00027-5

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