Introduction

Structural proteins and polysaccharides—predominantly cellulose, hemicellulose, and pectin, contribute to the structural integrity of the plant cell walls (Jacob 2009). The structural analysis of primary and secondary cell walls of plant shows the chemical compositions of these polysaccharides differ significantly between plant species. Based on the pectin and hemicellulose content the primary cell walls are usually divided into type I and type II walls. Type I walls in dicots, non-graminaceous monocots, and gymnosperms contain xyloglucan (20% w/w) as major hemicellulose and 20–30% (w/w) pectin. Type II walls in grasses are rich in xylans (20–30% w/w) and contain 2–10% (w/w) pectin. In both types, the cellulose content is 30–40% (w/w) (Held et al. 2015; O’Neill and York 2003; Rytioja et al. 2014). The pectate network is divided into two regions: ‘smooth’ regions consist of homogalacturonans (HG) and ‘hairy’ regions which mainly consist of highly branched rhamnogalacturonans (RG) and xylogalacturonans (XGA) (Mohnen et al. 2008; Vincken et al. 2003). In HG, d-galacturonic acid (GalA) residues are joined together by α-1,4-glycosidic bonds and partially methylated at O-6 or acetylated at O-2 or O-3 (Atmodjo et al. 2013; Mohnen 2008; Normand et al. 2010). Depending on the pattern of substitution and side-chain composition, RG is further classified as RG-I and RG-II. RG-I is a polymer with a repeating dimer of d-GalA and l-rhamnose, to which l-arabinose and d-galactose are attached at O-4 of l-rhamnose. Some of GalA in RG-I at the O-2 or O-3 may also be acetyl-esterified (Caffall and Mohnen 2009). RG-II has a backbone of short stretches of d-GalA residues with four distinct side chains comprising of 12 different glycosyl residues attached to O-2 or O-3 of the main chain (Rytioja et al. 2014; Yapo 2011). XGA consists of a galacturonic acid backbone with xylose attached to the O-3 through β-1,3-glycosidic bond and can be methyl esterified (Harholt et al. 2010). XGAs from different sources show different linkage pattern; apple and potato comprise 1,4-linked xylose residues (Zandleven et al. 2006), while in soybean, 1,4- and 1,2-linked xylose residues can be observed (Nakamura et al. 2002). XGA from pea pectin contains xylose linked with 1,2- and 1,3-glycosidic bonds (Le Goff et al. 2001; Wong 2008). Although the comprehension of an exact methodology of connection of different pectic polysaccharides is elusive, a schematic model is shown in Fig. 1 (Mohnen 2008).

Fig. 1
figure 1

Schematic representation of pectin showing homogalacturonan (HG), rhamnogalacturonan-I (RG-I), rhamnogalacturonan-II (RG-II) and xylogalacturonan (XGA) linked to each other (Mohnen 2008)

Full size image

Pectinolytic enzymes, pectic enzymes, or pectinases are the umbrella term that encompasses enzymes for modification and degradation of the complex pectate network. Based on the cleavage site, substrate specificity, and degradation mechanism, pectinases belong to three classes: (a) glycoside hydrolases (GHs) consisting of polygalacturonase (PG; endo-PG, EC 3.2.1.15; and exo-PG, EC 3.2.1.67), exo-polygalacturonosidase (EPGD; EC 3.2.1.82), rhamnogalacturonase or RG-hydrolase (RGH; EC 3.2.1.171), RG-galacturonohydrolase (RG-GH; EC 3.2.1.173), RG-rhamnohydrolase (RG-RH; EC 3.2.1.174), endo-xylogalacturonan hydrolase (endo-XGH; EC 3.2.1.-); (b) polysaccharide lyases (PLs) comprising of pectin lyase (PNL; EC 4.2.2.10), pectate lyase (PGL; EC 4.2.2.2), exo-pectate lyase (exo-PGL; EC 4.2.2.9), rhamnogalacturonan lyase (RGL; RG endo-lyase, EC 4.2.2.23; and RG exo-lyase, EC 4.2.2.24), oligogalacturonate lyase (OGL; now also classified as pectate lyase family 22; EC 4.2.2.6); and (c) carbohydrate esterases (CEs) consisting of pectin methylesterase (PME; EC 3.1.1.11), pectin acetylesterase (PAE; EC 3.1.1.6), rhamnogalacturonan acetylesterase (RGAE; EC 3.1.1.86) (Azadi et al. 1995; Gou et al. 2012; Hatanaka and Ozawa 1971; Jensen et al. 2010; Martens-Uzunova et al. 2006; Mutter et al. 1994, 1998; Ochiai et al. 2009) (Table 1).

Table 1 Classification of pectinases based on the mode of action
Full size table

So far, the Carbohydrate-Active enZYme database (CAZy) (Lombard et al. 2014) lists 156, 29 and 16 families of GHs, PLs, and CEs, respectively. Based on the sequence homologies, all pectin degrading hydrolases including PGs, EPGD, RGH, RG-GH, RG-RH, and XGH are classified into family GH28. Pectin and pectate lyases are categorized into PL1, PL2, PL3, PL9, PL10, and PL22, whereas RGLs belong to three families, PL4, PL11, and PL26. PAEs belong to CE12 and CE13 of the carbohydrate esterase family. Similarly, PMEs and RGAEs are categorized as members of family CE8 and CE12, respectively.

These enzymes are widely reported in plants, fungi, bacteria, and many yeasts (Garg et al. 2016). Pectinase from phytopathogenic fungi and bacteria contributes to pathogenicity or virulence (Herron et al. 2000; Lionetti et al. 2012; Liu et al. 2017; Wu et al. 2018). During fruit ripening/softening, it changes cell wall organization and reduces firmness (Brummell and Harpster 2001; Paniagua et al. 2017; Wang et al. 2000, 2018). PME involvement has been reported in cell elongation (Derbyshire et al. 2007; Pelletier et al. 2010), pollen grain germination in Arabidopsis (Leroux et al. 2015) and pollen tube growth (Bosch et al. 2005; Tian et al. 2006; Yue et al. 2018). The industrial applications of these enzymes are also substantially explored (Ahlawat et al. 2008; Amin et al. 2019; Kashyap et al. 2001; Khan et al. 2013; Lee et al. 2006; Murthy and Naidu 2011; Najafian et al. 2009; Sandri et al. 2011; Singh et al. 2019). The main emphasis of this review is on analysis of structural and mechanistic features of these enzymes relating to their catalytic mechanism.

Mode of action of pectinase

Pectinases degrade the complex pectic network through depolymerization (hydrolysis/β-elimination) and de-esterification reactions. Depolymerizing enzymes from the GH28 family hydrolyze glycosidic bonds through an inverting mechanism (Zandleven et al. 2005). HG-degrading enzymes (endo-PGs, exo-PGs, and EPGDs) cleave the α-1,4-glycosidic bond between two d-GalA units (Bonnin et al. 2014), whereas RG-degrading enzymes target specifically on the RG-I backbone (Silva et al. 2016). RGHs, attack randomly in an endo-fashion on α-1,2-glycosidic bonds between d-GalA and l-rhamnose (van den Brink and de Vries 2011). Contrary to that, RG-GHs and RG-RHs (exo-acting enzymes) act at the non-reducing end of the RG-I backbone (Silva et al. 2016). XGHs are endo-acting enzymes which degrade glycosidic bond between two β-xylose-substituted GalA-backbone (Zandleven et al. 2005). The other group of depolymerases, PNLs, PGLs, and RGLs, degrade the network via the β-elimination mechanism. Pectate and pectin lyases cleave α-1,4-glycosidic linkage resulting in the formation of 4,5-unsaturated oligogalacturonates (Yip and Withers 2006). PGLs prefer non-methylated or low-esterified substrates and require Ca2+ for catalysis, except those from PL2 family which preferentially utilize Mn2+ ions (Abbott et al. 2013). In contrast, PNLs prefer methyl esterified substrate and do not require Ca2+ ions (Rytioja et al. 2014). RGLs degrade the backbone of RG-I by breaking down the α-1,4-glycosidic bond resulting in the formation of oligomers with unsaturated d-galactopyranosyluronic acid at the non-reducing end (Silva et al. 2016). Pectin esterases (PMEs, PAEs, and RGAEs) remove methyl and acetyl groups from the pectin backbone. PMEs hydrolyze methyl ester bond at C-6 through a double-displacement mechanism of methyl esterified GalA releasing methanol and protons (Jolie et al. 2010; Pelloux et al. 2007). PAEs and RGAEs catalyze the removal of O-2 and/or O-3 acetyl group from HG or RG-I. Deacetylation in RG-I provides access to other RG-I modifying enzymes (lyases and hydrolases) for further degradation of the complex network (Silva et al. 2016). The overall catalytic mechanism is illustrated in Fig. 2.

Fig. 2
figure 2

Overview of reaction mechanism a homogalacturonan (HG) with methyl and acetyl esterification and xylogalacturonan (XGA), enzymes that cleave HG and XGA are polygalacturonase (PG), pectin/pectate lyase (PNL/PGL), pectin methylesterase (PME), pectin acetylesterase (PAE), xylogalacturonan hydrolase (XGH), b rhamnogalacturonan (RG) and modifying enzymes are RG-hydrolase (RGH), RG-lyase (RGL), and RG-acetylesterase (RGAE). Site of action is indicated by arrows

Full size image

Structural features and enzymatic mechanism

Three-dimensional structures enable understanding of the functional significance and interaction properties at the molecular level. Yoder et al. (1993a) reported the first crystallographic structure of pectinase, Erwinia chrysanthemi pectate lyase C (PelC) and since then, many structures from plant pathogens and other sources have been resolved (Table 2; references cited therein). The X-ray analysis reveals that most of the members of pectinase family share a right-handed β-helix topology. Others like PGLs in PL2 and PL10, RGLs in PL4 and PL11 and RGAE, adopt (α,α)7-barrel, (α,α)3-barrel, β-sandwich + β-sheets, β-propeller and α/β/α-sandwich structures, respectively (Lombard et al. 2010; Mølgaard et al. 2000). Recently identified exo-RGL of PL26 family shows β-Sandwich + (α/α)n barrel fold (Kunishige et al. 2018). The major differences in topology are seen in the number of turns, the conformation of loops, and the terminal regions. On the basis of their shared topological structure, members of the pectinase family can be classified into six classes, namely (a) right-handed β-helix, (b) (α/α)n-barrel, (c) β-sandwich + β-sheets, (d) β-sandwich + (α/α)n-barrel, (e) β-propeller, and (f) α/β/α-sandwich (Table 3, Fig. 3).

Table 2 Crystallographic structures of pectinase released by Protein Data Bank (PDB)
Full size table
Table 3 Structural fold and pectinolytic enzyme families
Full size table
Fig. 3
figure 3

Representative fold structures of each pectinase family. GH28 (exo-PG, PDB ID: 3JUR; endo-PG, PDB ID: 2IQ7; RGH, PDB ID: 1RMG; endo-XGH, PDB ID: 4C2L), PL1 (PDB ID: 2QXZ), PL3 (PDB ID: 1EE6), PL9 (PDB ID:1RU4), CE8 (PDB ID: 1QJV), PL10 (PDB ID: 1GXM), PL2 (PDB ID: 2V8I), PL4 (PDB ID: 1NKG), PL26 (PDB ID: 5XQ3), PL11 (PDB ID: 2ZUX), PL22 (PDB ID: 3PE7), CE12 (PDB ID: 1DEO)

Full size image

Right-handed β-helix class

Enzymes of the GH28 family, three families of pectin and pectate lyases (PL1, PL3, PL9), and PMEs from the CE8 family share the right-handed β-helix fold. Pectate lyase C (PelC) from Erwinia chrysanthemi was the first structure to describe the right-handed β-helix fold (Yoder et al. 1993a). Subsequently, similar structural fold has been reported in structures of, PelC (Herron et al. 2003; Yoder and Jurnak 1995a, b), PelC complex with plant cell wall (Scavetta et al. 1999), pectate lyase E (PelE) (Lietzke et al. 1994, 1996; Yoder et al. 1993b), pectate lyase A (PelA) (Dehdashti et al. 2003; Thomas et al. 2002), pectate lyase L (Pel9A) (Jenkins et al. 2004), pectate lyase (PelI) in complex with substrate (Creze et al. 2008) from Erwinia chrysanthemi; pectate lyase complex with Ca2+ from Bacillus subtilis (BsPel) (Pickersgill et al. 1994), pectate lyase (Pel-15) and Bsp165PelA from Bacillus sp. strain KSM-P15 and strain N16-5, respectively (Akita et al. 2001; Zheng et al. 2012), pectate lyase from Acidovorax citrulli (AcPel) (Tang et al. 2013); Aspergillus niger pectin lyase A (PL1A) (Mayans et al. 1997) and pectin lyase B (PL1B) (Vitali et al. 1998); Erwinia carotovora endo-PG (PehA) (Pickersgill et al. 1998), endo-PG II (van Santen et al. 1999) and endo-PG I (van Pouderoyen et al. 2003) from Aspergillus niger, Aspergillus aculeatus PG (Cho et al. 2001), Fusarium moniliforme PG (FmPG) (Federici et al. 2001), Stereum purpureum endo-PG I (Shimizu et al. 2002), Yersinia enterocolitica exo-PG (YeGH28) (Abbott and Boraston 2007b), PG from Colletotrichum lupini (CluPG1) (Bonivento et al. 2008); exo-PG from Thermotoga maritime (Pijning et al. 2009); RGHA from Aspergillus aculeatus (Petersen et al. 1997); endo-XGH from Aspergillus tubingensis (XghA) (Rozeboom et al. 2013); PME from Erwinia chrysanthemi (Fries et al. 2007; Jenkins et al. 2001), Daucus carota (Johansson et al. 2002), Solanum lycopersicum (Di Matteo et al. 2005), Yersinia enterocolitica (Boraston and Abbott 2012), Sitophilus oryzae (rice weevils; first animal PME) (Teller et al. 2014) and Aspergillus niger (Kent et al. 2016).

In general, the central core region consists of 7–13 complete β-helical turns. The sequential arrangement of β-strands results in the formation of three parallel β-sheets (PB1, PB2, and PB3) connected by loops. An antiparallel β-sandwich arrangement can be seen between PB1 and PB2, and PB3 lies almost perpendicular to PB2 (Sharma et al. 2013). Contrary to the structural fold observed in lyase, few members of GH28 enzymes have additional β-sheets as seen in Aspergillus niger endo-PG II, Aspergillus aculeatus RGHA, and Aspergillus tubingensis endo-XGH. Despite similar right-handed β-helix topology, the reaction mechanisms within this enzyme class are completely different. PGs and RGHs cleave the substrate by acid/base-catalyzed hydrolysis (single displacement), PMEs use double displacement mechanism, whereas lyases (PNLs, PGLs) cleave by β-elimination.

Kester et al. (1996) suggested four blocks of residues (NxD, G/QDD, HG, and RxK) conserved in all endo- and exo-PGs and which are clustered at subsites − 1 and + 1. These conserved patches on the surface of the PB1 and nearby loops form the catalytic site (Pickersgill et al. 1998). Site-directed mutagenesis studies in endo-PG II from Aspergillus niger have revealed the involvement of aspartate residues in the catalytic function (Armand et al. 2000; Pagès et al. 2000). All enzymes from GH28 family act via an inverting mechanism (Abbott and Boraston 2007b). In inverting enzymes, the reaction proceeds through a single displacement mechanism. Two acidic amino acid residues acting as general acid and base, respectively, are involved in the reaction process (Shallom et al. 2005). Comparative sequence alignment of known structures of PGs, RGH, and XGH shows seven conserved amino acid residues (Supplementary Figure, S1). Among them, three catalytic aspartates are functionally conserved (D202, D223, and D224; sequence numbering according to endo-PG from Erwinia carotovora (PehA), PDB ID: 1BHE) (Fig. 4a) except in RGH from Aspergillus aculeatus where D224 (198 in RGH) is substituted by glutamate (E). One out of the three conserved aspartates protonates the scissile glycosidic oxygen, while the other two activate the nucleophilic water molecule. In Aspergillus niger endo-PG II (PDB ID: 1CZF), van Santen et al. (1999)suggested that D180 and D202 activate the water molecule and D201 acts as a proton donor. A generalized reaction mechanism based on endo-PG II is shown in Fig. 4b. In Aspergillus tubingensis endo-XGH (XghA) (PDB ID: 4C2L), the active site contains catalytic residues D207, D228, and D229 (Rozeboom et al. 2013). Other conserved residues N205 and Y322 are required for substrate binding. The substrate binding cleft is wider (~ 15.3 Å) in XghA as compared to other GH28 endo-PGs (ranges from 6.4 to 11.0 Å) (Rozeboom et al. 2013). Similar arrangements have also been observed in the other GH28 enzymes (Table 3). The structural firmness of the β-helix is stabilized by disulfide bridges. In fungal endo-PGs and RGH, four disulfide bridges are found to be conserved. N- and C-terminal disulfide bonds ensure the capping of β-helix, while other two disulfides located in the middle of the β-helix confirm correct local folding around the active site. On the other hand, bacterial endo-PG (PehA from Erwinia carotovora) has only two disulfides (C41-C62, C115-C125; numbering in PehA) (Pickersgill et al. 1998) and endo-XGH from Aspergillus tubingensis (XghA) has shown six disulfide bridges: C37-C60, C85-C88, C230-C247, C321-C329, C32-C369 and C389-C400 (numbering in XghA) (Rozeboom et al. 2013).

Fig. 4
figure 4

Right-handed β-helix fold a overall structural fold of Erwinia carotovora endo-PG with catalytic residues (D202, D223, and D224) (PDB ID: 1BHE); b generalized reaction mechanism for inverting family 28 GHs (based on endo-PG II). D201 acts as proton donor, while D180 and D202 activate the hydrolytic water molecule (van Santen et al. 1999)

Full size image

Structural comparison of PMEs in CE8 family shows similarities in folding topology and reaction mechanisms. Sequence analysis of known structures reveals five functionally important conserved sequence motifs with few replacements: GxYxE, QAVAL, QDTL, DFIFG, and LGRPW (Markovič and Janeček 2004; Zega and D’Ovidio 2016) (Supplementary Figure, S2). PMEs catalyze reactions through a double displacement mechanism which includes the formation of glycosyl-enzyme intermediate and subsequent hydrolysis. The process requires two aspartates as nucleophile and acid/base catalyst. A catalytic triad, glutamine-aspartate-aspartate, is strictly conserved in all PME active site. In Erwinia chrysanthemi PME (PDB ID: 2NSP), the reaction mechanism requires Q177, D178, and D199. As proposed by Fries et al., D199 performs a nucleophilic attack on carboxymethyl carbonyl carbon supposedly forming a tetrahedral intermediate. The negative charge on the carbonyl oxygen of the intermediate is stabilized by Q177 and D178. D178 acts as a proton donor and assists the release of methanol. Later, D178 acts as a base and accepts proton from water molecule restoring the active site (Fries et al. 2007) (Fig. 5). Similar reaction mechanisms have also been observed in plant PMEs, carrot PME (PDB ID: 1GQ8) (Johansson et al. 2002) and tomato PME (PDB ID: 1XG2) (Di Matteo et al. 2005). Polarized by the presence of R225 (R221 in tomato PME), D157 (D153 in tomato PME) acts as the nucleophile and attacks the carboxymethyl group forming an intermediate. The negative charge of the intermediate is stabilized by Q113 and Q135 (Q109 and Q131 in tomato PME). D136 (D132 in tomato PME), first acts as an acid result in the release of methanol and subsequently as a base to draw proton from the water molecule. Apart of the catalytic residues, many aromatic residues (F80, Y135, F156, Y218, W223, W248 in tomato PME; F84, Y139, F160, Y222, W227, F250, W252 in carrot PME) are assumed to be involved in substrate binding (Di Matteo et al. 2005; Johansson et al. 2002). When plant PMEs compared with bacterial PME, the overall folding topologies found to be very similar, except longer loops in the bacterial PME and an additional helix in C-termini of plant PME. Structural analysis of Sitophilus oryzae (rice weevils) PME (RwPME; PDB ID: 4PMH) also suggests the similar arrangement of catalytic residues (Q199, D200, and D226) and enzymatic mechanism (Teller et al. 2014).

Fig. 5
figure 5

The right-handed β-helix fold a overall structural fold of Erwinia chrysanthemi PME with hexasaccharide (PDB ID: 2NSP) and Daucus carota PME (PDB ID: 1GQ8); b reaction mechanism of PME (as proposed by Fries et al. 2007)

Full size image

Unlike PGs and PMEs, lyases (PNLs, PGLs) degrade pectin by a β-elimination which involves neutralization of carboxyl group at C-5, proton abstraction at C-5, and removal of glycosidic linkage (Garron and Cygler 2010). Members of family PL1 (only PGLs), PL3, and PL9 shows Ca2+-assisted β-elimination. Ca2+ ion is essential for catalysis as it helps to neutralize the acidic substrate. PGL structures have two kinds of Ca2+ ion: (a) primary Ca2+ ion, in the absence of substrate it binds to the enzyme, as seen in many PGLs structures: BsPel from Bacillus subtilis (PDB ID: 1BN8), Erwinia chrysanthemi PelC (PDB ID: 1O88), Pel-15 from Bacillus sp. KSM-P15 (PDB ID: 1EE6), Bsp165PelA (PDB ID: 3VMV), and Bsp47Pel (PDB ID: 1VBL; to be published); and (b) additional Ca2+ ions (two or three), which coordinate the enzyme and substrate (Tang et al. 2013). The active site of PGL from family PL1 shows the involvement of a group of conserved acidic residues in Ca2+ coordination (D184, D223, and D227; BsPel numbering) (Fig. 6a). Within the extracellular PGLs family, D184 and D227 are conserved, whereas D223 is conservatively substituted with glutamate (E). Usually, arginine or lysine and water molecule act as a catalytic base and acid, respectively (Fig. 6e). The available structural data suggest that arginine is strictly conserved among the PL1 family, whereas the catalytic base in family PL3 and PL9 is lysine.

Fig. 6
figure 6

The right-handed β-helix fold in lyases (PGLs and PNLs) a overall structural fold of Bacillus subtilis PGL (PDB ID: 1BN8) with calcium-binding site (D184, D223, D227). The catalytic base is R279; b structural fold of Erwinia chrysanthemi PGL (PDB ID: 1RU4) with calcium-binding site (D209, D233, D234, D237). The putative catalytic base is K273; c structural fold of Aspergillus niger PNLs (PDB ID: 1IDK and PDB ID: 1QCX) with catalytic residues; d structural fold of Bacillus sp. KSM-P15 PGL (PDB ID: 1EE6) with calcium-binding site (D63, E83, D84). The putative catalytic base is K107; e general reaction mechanism of PGL (calcium assisted β-elimination) where arginine or lysine acts as a catalytic base (in representation, calcium ions are shown as red balls)

Full size image

Analysis of Caldicellulosiruptor bescii PGL (PDB ID: 4Z06) of PL3 family exhibits an antiperiplanar trans-elimination reaction mechanism. K108 abstracts a proton from the C5 atom and a water molecule protonates the O4 atom of the substrate completing the elimination process (Alahuhta et al. 2015). Acidic residue E84, E39, and D107 are involved in calcium coordination, whereas Q111 and R133 play a role in substrate binding (Alahuhta et al. 2015). Similarly, in Bacillus sp. KSM-P15 PGL (PDB ID: 1EE6) the calcium-binding site is formed by D63, E83, D84, and the putative catalytic base is K107 (Fig. 6d). In PL9 family, PGL from Erwinia chrysanthemi (PDB ID: 1RU4), four aspartate residues (D209, D233, D234, and D237) coordinate calcium-binding site (Jenkins et al. 2004) (Fig. 6b). However, not all enzymes of the PL1 family require Ca2+ ion for the catalytic mechanism. PNLs from Aspergillus niger (PNLA, PDB ID: 1IDK and PNLB, PDB ID: 1QCX) eliminate the need of Ca2+ ion. In contrast to PGLs, aromatic residues (D154, R176, and R236) dominate the binding site of PL1A and PL1B. The catalytic arginine residue (R236) plays a key role in catalysis, while D176 in a similar position to catalytic Ca2+ ion in PGLs stabilizes the negative charge of the substrate and aids proper orientation of R236 (Mayans et al. 1997; Vitali et al. 1998).

(α/α)n barrel class

PGLs from PL2 and PL10 family display (α/α)n barrel topology. The formation of such structural domain is due to the repetition of a pair of antiparallel α-helices (Garron and Cygler 2010). PGLs of PL2 and PL10 family have seven repeats, (α/α)7 and three repeats, (α/α)3, respectively (Fig. 7a). The crystal structure of PL2 family PGLs from Yersinia enterocolitica (YePL2A) (PDB ID: 2V8I) (Abbott and Boraston 2007a), and Vibrio vulnificus (VvPL2) (PDB ID: 5A29) (McLean et al. 2015) showed that Mn2+ is the preferred transition metal for catalysis over Ca2+. The metal-binding site is coordinated by two histidine and one glutamate (H109, H172, E130 in YePL2A, and H129, H192, E150 in VvPL2). In YePL2A, R171 at subsite + 1 assumed to play the role of the catalytic base while water molecule acts as the proton donor and R272 is involved in substrate recognition. Similarly, in VvPL2, R191 and R304 acts as the catalytic base and stabilizing residue, respectively (McLean et al. 2015).

Fig. 7
figure 7

The (α/α)n fold a structural arrangement of PGL from Yersinia enterocolitica (PDB ID: 2V8I) and Azospirillum irakense (PDB ID: 1R76); b Ca2+ assisted reaction mechanism of PL10 enzymes where catalytic residue R307 abstracts proton (Novoa de Armas et al. 2004)

Full size image

In PL10 family, PGL from Cellvibrio japonicus (Pel10Acm) (PDB ID: 1GXM) (Charnock et al. 2002) and Azospirillum irakense (PelA) (PDB ID: 1R76) (Novoa de Armas et al. 2004) shows the same structural topology with three repeats; (α/α)3. Both Pel10Acm and PelA comprise of two domains and a deep pocket between them hosts substrate binding and catalytic site (Novoa de Armas et al. 2004). In Pel10Acm, analysis of the catalytic center reveals the presence of residues D389, N390, D451, R524, Y526, E527, E535, R596, R610, R625, G628, and S630 (Novoa de Armas et al. 2004; Walker and Ryan 2003). Similarly, in PelA, residue D171, N172, D236, R307, F309, E310, E318, R378, R392, R407, G410, and A412 are present in the active site (Novoa de Armas et al. 2004). In Pel10Acm, the carboxylate group of the substrate at − 1 subsite forms an ionic bond with R596 and a coordinate bond with the Ca2+ ion. Simultaneously, the Ca2+ ion makes coordinate interaction with carboxylate oxygen of D451 as well as + 1 subsite sugar carboxylate (Novoa de Armas et al. 2004). Substitution of D451 leads to loss of enzymatic activity (Charnock et al. 2002). Arginine as a potential catalytic base is located at the + 1 subsite (R524 in Pel10Acm and R307 in PelA) (Fig. 7b) (Novoa de Armas et al. 2004). Although the core topology between PL10 and PL1 is different, superposition of enzymes of both families shows structurally conserved active center. These conserved identical catalytic residues in the active site indicate the convergent evolution of catalytic mechanism (Charnock et al. 2002). In both cases, a conserved acidic residue is essential for stabilization of Ca2+ ion (D451in Pel10Acm and E166 in PelC).

β-Sandwich + β-sheet class

RGLs from Aspergillus aculeatus in the PL4 family (PDB ID: 1NKG) display β-sandwich fold with three structural domains (Fig. 8a). Two antiparallel β-sheets, each comprising eight β-strands form domain I, with two disulfide bonds C30-C73 and C164-C173. Domain II displays topology similar to the fibronectin type III and domain III adopts β-sandwich fold like carbohydrate-binding modules (McDonough et al. 2004). Domain I hosts catalytic (K150, H210) as well as substrate binding residues (R107, R111), whereas R451 and R455 in domain III support the formation of the substrate-binding groove. The correct orientation of domains I and III is mediated by domain II. Mutational studies of RGL with bound substrate (PDB ID: 2XHN) also reveals the involvement of K150 and H210 in catalysis (Jensen et al. 2010). The carboxyl group of the substrate is protonated at the + 1 subsite by D139. K150 plays the role of proton abstractor, while H210 acts as a proton donor (Fig. 8b, c). Unlike PGLs from several PL families, in which the reaction proceeds through the metal-assisted manner, RGLs in PL4 family differ in the mechanism by eliminating the requirement of the Ca2+ ion.

Fig. 8
figure 8

The β-sandwich + β-sheet fold a domain arrangement of Aspergillus aculeatus RGL (PDB ID: 2XHN); b catalytic residues on domain I; c reaction mechanism of RGL where K150 acts as proton abstractor and H210 acts as proton donor (Jensen et al. 2010)

Full size image

β-Sandwich + (α/α)n barrel class

Recently, the three-dimensional structure of Penicillium chrysogenum exo-RGL (PcRGLX) (PDB ID: 5XQ3) of PL26 family shows a unique structural arrangement (Fig. 9a). Domain I and II display β-sandwich fold similar as PL4 endo-RGL of Aspergillus aculeatus and domain III exhibits an (α/α)6-barrel structure like PL2 PGL. Domain I consists of two three-stranded antiparallel β-sheets stabilized by a disulfide bond C24-C113 and domain II possesses β-sandwich fold comprising two antiparallel β-sheets having eighteen β-strands surrounded by five α-helices. A serine-rich loop can be seen at the interface between domains I and II. Domain III has an antiparallel arrangement of six lateral and six inner helices and hosts a Ca2+-binding site enclosed by D562, N585, H616, D621, and H639 (Fig. 9b). An l-shaped cleft active site provides a compact framework for substrate binding specifically galactosyl side chains. Mutagenesis studies suggest the involvement of residues Y458, D460, R634, H635, Q646, R648, and H782 in the catalytic mechanism (Kunishige et al. 2018). At the + 1 subsite, the hydrogen bond between R634 and the carboxyl group of GalA advocates the role of R634 as a neutralizer. The catalytic mechanism proceeds through β-elimination but differs significantly from PL11 Bacillus subtilis RGL (YesX) by eliminating the requirement of divalent cations. PcRGLX shares similar structural folds to l-rhamnose-α-1,4-d-glucuronate lyase of PL27 (Munoz–Munoz et al. 2017), although they show 7% sequence identity.

Fig. 9
figure 9

The β-Sandwich + (α/α)n barrel fold a structural arrangement of exo-RGL from Penicillium chrysogenum (PDB ID: 5XQ3), the red box shows serine-rich loop (S117-I130) located between domains I and II; b Ca2+ ion (shown as red ball) is coordinated by D562, N585, H616, D621, H639 and located in domain III

Full size image

β-Propeller class

RGLs from PL11 and OGL from PL22 family adopt β-propeller fold. So far, the crystal structures of PL11 family RGLs (endo-acting YesW and exo-acting YesX) from Bacillus subtilis (PDB ID: 2Z8S and 2ZUX) (Ochiai et al. 2007, 2009), and RGI lyase WT from Bacillus licheniformis (PDB ID: 4CAG) (Silva et al. 2014) have been determined. Both YesW and YesX share sequence identity of 67.8% and exhibits similar structure comprising N-terminal β-sheet domain and eight-bladed β-propeller domain (A-H blades) (Fig. 10a) (Ochiai et al. 2007, 2009). Except for blades A, G in YesW and blade A in YesX, each blade contains four antiparallel β-strands. Besides, all blades except for D in YesW and D, G in YesX contain one or two Ca2+ ions. Substrate binding site in both YesW and YesX is located within the pocket of β-propeller. Catalytic residues such as R452, T534, K535, and Y595 in YesW (R419, T518, K519, and Y579 in YesX) are responsible for substrate recognition. During the catalysis, the negative charge of the carboxyl group is neutralized by positively charged R452 and K535 (R419 and K519 in YesX) and Y595 (Y579 in YesX) is important for stacking interaction. Also, residues such as D153, N596 (in site 1) and H363, H399, D401, and E422 (in site 2) are involved in calcium binding within the active site. One Ca2+ ion is assumed to be involved in substrate binding, while the other nine Ca2+ ions help in stabilizing the β-propeller fold (Ochiai et al. 2007). Despite the same structural fold, an extended loop of nine residues (PPGNDGMSY) in YesX determines the difference in substrate specificity and mode of action between YesX and YesW (Ochiai et al. 2009).

Fig. 10
figure 10

The β-propeller fold a overall structural fold of Bacillus subtilis RGL constituting eight blades (A–H) stabilized by Ca2+ ions (PDB ID: 2ZUX); b structural fold of Bacillus subtilis RGL showing seven blades (A–G) (PDB ID: 3PE7); in both representation, calcium ions are shown as red balls and manganese ion as purple ball

Full size image

OGL from Yersinia enterocolitica (YeOGL) (PDB ID: 3PE7) and Vibrio parahaemolyticus (VpOGL) (PDB ID: 3C5 M, unpublished data) in PL22 family adopts a seven-bladed β-propeller fold. Each propeller consists of a repeating four-stranded antiparallel β-strands. In the structure of YeOGL, Mn2+ ion is located in the active site, which is stabilized by H287, H353, H355, and Q350 (Fig. 10b). Residue H242 acts as the Brønsted base, which is highly conserved across OGL family, and residues such as H211 and R217 are involved in substrate stabilization (Abbott et al. 2010).

(α/β/α)-Sandwich class

RGAE from CE12 family exhibits α/β/α sandwich fold. The structure of Aspergillus aculeatus RGAE (AaRGAE) (PDB ID: 1DEO) displays an arrangement of five parallel β-strands surrounded by α-helices (Mølgaard et al. 2000). The 3-layered structural fold is stabilized by two disulfide bonds C88-C96 and C214-C232. At the active site, residue S9 forms a hydrogen bond with the adjacent H195 and D192 establishing a catalytic triad S9-D192-H195 (Fig. 11). The stability of β-turn is maintained by aspartate residue (D8) which forms a hydrogen bond between its side-chain O atom and the Nu + 1 amide group (Mølgaard et al. 2000; Mølgaard and Larsen 2002). Homology modeling of RGAE from Bacillus subtilis (BsYesT) (Martínez-Martínez et al. 2008) and Bacillus halodurans (BhRGAE) (Navarro-Fernández et al. 2008) using the AaRGAE as the template shows similar structural features. As per SUPERFAMILY library (Gough et al. 2001), AaRGAE along with hypothetical protein YXIM_BACsu from Bacillus subtilis (PDB ID: 2O14, unpublished data) (Bolvig et al. 2003), putative protein YesY and YesT from Bacillus subtilis (Martínez-Martínez et al. 2008), esterase from Streptomyces scabies (SsEst) (PDB ID: 1ESC) (Wei et al. 1995), Bos taurus Platelet-activating factor acetylhydrolase (Ho et al. 1997), haemagglutinin-esterase-fusion protein (HEF) of influenza C virus (PDB ID: 1FLC) (Rosenthal et al. 1998), Hypothetical lipase protein alr1529 from Nostoc sp. (PDB ID: 1Z8H, unpublished data), Bacillus sp. KCCM10143 cephalosporin C deacetylase (CCD) (Choi et al. 2000), Erwinia chrysanthemi PAE (PaeY) (Mølgaard et al. 2000) are classified as members of SGNH-hydrolase family. The characteristic features that distinguish SGNH-hydrolase family from α/β hydrolase family are: central five-stranded parallel β-sheets, conserved residue blocks (GDS, G, GXND, and DXXHP), nucleophilic serine at C-terminal of β-strand1, close proximity of aspartate and histidine, absence of nucleophilic elbow motif (Martínez-Martínez et al. 2008; Mølgaard et al. 2000).

Fig. 11
figure 11

The (α/β/α)-Sandwich fold a schematic representation of overall structure of Aspergillus aculeatus RGAE (PDB ID: 1DEO); b active site of RGAE showing three catalytic residues, S9, H195, and D192

Full size image

Concluding remarks and prospectives

The emergence of structural information leads to a better comprehension of structure–function correlation. Based on structural analysis, pectinase can be classified as right-handed β-helix, (α/α)n-barrel, β-sandwich + β-sheets, β-sandwich + (α/α)n-barrel, β-propeller, and α/β/α-sandwich. These enzymes display high selectivity towards specific bonds and work via hydrolysis/β-elimination and de-esterification reaction mechanism. Functionally conserved patches, NxD, G/QDD, HG, and RxK, determine the catalytic activity among GH28 family, except few residues in RGH. PGs, RGH, and endo-XGH exhibit a single displacement inverting reaction mechanism involving two aspartate residues at the active site. PME catalyzes reactions through double-displacement mechanisms which also involves two catalytic aspartates rather than serine as seen in other carbohydrate esterases. Despite the structural differences in right-handed β-helix, (α/α)3/7-barrel, and β-propeller class, the β-elimination mechanism utilizes metal (Ca2+/Mn2+)- assisted neutralization involving arginine or lysine as proton abstractor and water as a proton donor. Interestingly, RGLs of the PL4 and PL26 family, which displays β-sandwich + β-sheets and β-sandwich + (α/α)6-barrel topology, respectively, eliminates the requirement of ions during the β-elimination mechanism. Sequence and structural exploration reveal RGAE, which belong to SGNH-hydrolase family, adopts α/β/α-sandwich fold with the catalytic triad: serine-aspartate-histidine.

Although significant progress on the structures of pectinase has been done, still ample of scope available to explore structures from different sources which are not yet known. Current structural knowledge could be used to establish the three-dimensional structure of other pectinases using computational modeling approach and for an in-depth understanding of the structure–function association at the molecular level.