Endo-alpha-1-4-polygalactosaminidases and their homologues: structure and evolution

Endo-alpha-1,4-polygalactosaminidase is a rare enzyme. Its catalytic domain belongs to the GH114 family of glycoside hydrolases. Phylogenetic analysis of the family proteins allowed us to show an important role of duplications, eliminations, and horizontal transfer in the evolution of their genes. Domain structure, the secondary structure, and proposed structure of the active center of the endo-alpha-1,4-polygalactosaminidases are discussed. Evolutionary connections of the GH114 family with GH13, GH18, GH20, GH27, GH29, GH31, GH35, GH36, and GH66 families of glycoside hydrolases, as well as, with COG1306, COG1649, COG2342, GHL3, and GHL4 families of enzymatically uncharacterized proteins have been revealed by iterative screening of the protein database. The unclassified homologues have been grouped into 13 new families of hypothetical glycoside hydrolases: GHL5 - GHL15, GH36J, and GH36K.     

GHL1-GHL15: new families of hypothetical glycoside hydrolases

Domains of fifteen recently found families of hypothetical glycoside hydrolases (GHL1-GHL15) have been used for iterative screening of the protein database. Evolutionary connections between representatives of these families were revealed. Also, their relationship with members of the following known families of protein domains were found: GH5, GH13, GH13_33, GH17, GH18, GH20, GH27, GH29, GH31, GH35, GH36A, GH36B, GH36C, GH36D, GH36E, GH36F, GH36G, GH36H, GH36J, GH36K, GH39, GH42, GH53, GH66, GH97, GH101, GH107, GH112, GH114, COG1082, COG1306, COG1649, COG2342, DUF3111, and PF00962. The unclassified homologues were grouped into 35 new families of hypothetical glycoside hydrolases: GHL16-GHL50. Position of GHL1-GHL15 families in the hierarchical classification of glycoside hydrolases and their homologues is discussed. Several new superfamilies of protein domains are suggested.     

Endo-α-1,4-polygalactosaminidases and their homologs: Structure and evolution

Endo-α-1,4-polygalactosaminidase is a rare enzyme. Its catalytic domain belongs to the GH114 family of glycoside hydrolases. It is shown by phylogenetic analysis that the evolution of the corresponding genes involved duplications, elimination, and horizontal transfer. The domain and secondary structures of endo-α-1,4-polygalactosaminidases are discussed. A hypothesis is put forward as to the structure of the active center of the enzyme. Iterative screening of a protein database reveals evolutionary relationships of the GH114 family with the GH13, GH18, GH20, GH27, GH29, GH31, GH35, GH36, and GH66 families of glycoside hydrolases and with the COG1306, COG1649, COG2342, GHL3, and GHL4 families of proteins with unknown enzymatic functions. Unclassified homologs are grouped into 13 new families of hypothetical glycoside hydrolases: GHL5-GHL15, GH36J, and GH36K.     

GHL1-GHL15: New families of the hypothetical glycoside hydrolases

The domains of 15 recently discovered families of the hypothetical glycoside hydrolases GHL1-GHL15 were used for iterative screening of the protein database. The evolutionary relationships between these families were revealed, as well as their relationship with the previously known families of protein domains: GH5, GH13, GH13-33, GH17, GH18, GH20, GH27, GH29, GH31, GH35, GH36A, GH36B, GH36C, GH36D, GH36E, GH36F, GH36G, GH36H, GH36J, GH36K, GH39, GH42, GH53, GH66, GH97, GH101, GH107, GH112, GH114, COG1082, COG1306, COG1649, COG2342, DUF3111, and PF00962. The unclassified homologues were grouped in 35 new families of the hypothetical glycoside hydrolases: GHL16-GHL50. The position of the families GHL1-GHL15 in the hierarchical classification of glycoside hydrolases and their homologues is discussed. Several new superfamilies of protein domains are proposed.     

Furanosidase superfamily: Search of homologues

The furanosidase superfamily contains the GH32, GH43, GH62, GH68, GH117, DUF377 (GH130), and DUF1861 families of glycoside hydrolases and their homologues. Catalytic domains of these families have five-bladed β-propeller tertiary structure. Iterative screening of the protein database supports of their relationship as well as evolutionary connections with domains from GH33 and GH93 families of glycoside hydrolases. The latter two have the structure of the six-bladed β-propeller. Among detected homologues we found 441 unclassified proteins. These proteins are combined into 39 groups based on homology: FURAN1-FURAN39. FURAN8 and FURAN36 can be considered as separate subfamilies within the GH43 and GH32 families of glycoside hydrolases, respectively. The remaining 37 groups are new families of hypothetical glycoside hydrolases.     

Furanosidase superfamily: search of homologues

The furanosidase superfamily contains GH32, GH43, GH62, GH68, GH117, DUF377, and DUF1861 families of glycoside hydrolases and their homologues. Catalytic domains of these families have five-bladed beta-propeller tertiary structure. Iterative screening of the protein database allowed to support their relationship as well as evolutionary connections with domains from GH33 and GH93 families of glycoside hydrolases. The latter two have structure of the six-bladed beta-propeller. Among revealed homologues we found 441 unclassified proteins. These proteins are combined into 39 groups based on homology: FURAN1-FURAN39. FURAN8 and FURAN36 can be considered as separate subfamilies within GH43 and GH32 families of glycoside hydrolases, respectively. The remaining 37 groups are new families of hypothetical glycoside hydrolases.     

Multiple lateral transfers and duplications of genes as sources of diversity of α-L-rhamnosidases in Clostridium methylpentosum DSM5476

α-L-Rhamnosidases are an important group of glycoside hydrolases represented in many organisms from various prokaryotic phyla. Based on the homology of catalytic domains, all these proteins are assigned to the GH78 and GH106 families of glycoside hydrolases. However, most prokaryotic genomes contain no genes encoding proteins from these two families. We found that the unique genome of Clostridium methylpentosum DSM5476 contains 83 genes of proteins from these families and undertook investigation of their phylogeny. The absence of homologous genes in most of strains of the genus Clostridium suggests an important ecological role of these genes, in C. methylpentosum in particular. Phylogenetic analysis revealed multiple lateral transfers and duplications of the corresponding genes.     

Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain.

The alpha-amylase family (glycoside hydrolase family 13; GH 13) contains enzymes with approximately 30 specificities. Six types of enzyme from the family can possess a C-terminal starch-binding domain (SBD): alpha-amylase, maltotetraohydrolase, maltopentaohydrolase, maltogenic alpha-amylase, acarviose transferase, and cyclodextrin glucanotransferase (CGTase). Such enzymes are multidomain proteins and those that contain an SBD consist of four or five domains, the former enzymes being mainly hydrolases and the latter mainly transglycosidases. The individual domains are labelled A [the catalytic (beta/alpha)8-barrel], B, C, D and E (SBD), but D is lacking from the four-domain enzymes. Evolutionary trees were constructed for domains A, B, C and E and compared with the 'complete-sequence tree'. The trees for domains A and B and the complete-sequence tree were very similar and contain two main groups of enzymes, an amylase group and a CGTase group. The tree for domain C changed substantially, the separation between the amylase and CGTase groups being shortened, and a new border line being suggested to include the Klebsiella and Nostoc CGTases (both four-domain proteins) with the four-domain amylases. In the 'SBD tree' the border between hydrolases (mainly alpha-amylases) and transglycosidases (principally CGTases) was not readily defined, because maltogenic alpha-amylase, acarviose transferase, and the archaeal CGTase clustered together at a distance from the main CGTase cluster. Moreover the four-domain CGTases were rooted in the amylase group, reflecting sequence relationships for the SBD. It appears that with respect to the SBD, evolution in GH 13 shows a transition in the segment of the proteins C-terminal to the catalytic (beta/alpha)8-barrel(domain A).     

Comprehensive Analysis of Carbohydrate-Active Enzymes from the Filamentous Fungus <Emphasis Type="Italic">Scytalidium candidum</Emphasis> 3C

Complete enzymatic degradation of plant polysaccharides is a result of combined action of various carbohydrate-active enzymes (CAZymes). In this paper, we demonstrate the potential of the filamentous fungus Scytalidium candidum 3C for processing of plant biomass. Structural annotation of the improved assembly of S. candidum 3C genome and functional annotation of CAZymes revealed putative gene sequences encoding such proteins. A total of 190 CAZyme-encoding genes were identified, including 104 glycoside hydrolases, 52 glycosyltransferases, 28 oxidative enzymes, and 6 carbohydrate esterases. In addition, 14 carbohydrate-binding modules were found. Glycoside hydrolases secreted during the growth of S. candidum 3C in three media were analyzed with a variety of substrates. Mass spectrometry analysis of the fungal culture liquid revealed the presence of peptides identical to 36 glycoside hydrolases, three proteins without known enzymatic function belonging to the same group of families, and 11 oxidative enzymes. The activity of endohemicellulases was determined using specially synthesized substrates in which the glycosidic bond between monosaccharide residues was replaced by a thiolinkage. During analysis of the CAZyme profile of S. candidum 3C, four β-xylanases from the GH10 family and two β-glucanases from the GH7 and GH55 families were detected, partially purified, and identified.     

Function and structure studies of GH family 31 and 97 α-glycosidases

A huge number of glycoside hydrolases are classified into the glycoside hydrolase family (GH family) based on their amino-acid sequence similarity. The glycoside hydrolases acting on α-glucosidic linkage are in GH family 4, 13, 15, 31, 63, 97, and 122. This review deals mainly with findings on GH family 31 and 97 enzymes. Research on two GH family 31 enzymes is described: clarification of the substrate recognition of Escherichia coli α-xylosidase, and glycosynthase derived from Schizosaccharomyces pombe α-glucosidase. GH family 97 is an aberrant GH family, containing inverting and retaining glycoside hydrolases. The inverting enzyme in GH family 97 displays significant similarity to retaining α-glycosidases, including GH family 97 retaining α-glycosidase, but the inverting enzyme has no catalytic nucleophile residue. It appears that a catalytic nucleophile has been eliminated during the molecular evolution in the same way as a man-made nucleophile mutant enzyme, which catalyzes the inverting reaction, as in glycosynthase and chemical rescue.     

Function and Structure Studies of GH Family 31 and 97 α-Glycosidases

A huge number of glycoside hydrolases are classified into the glycoside hydrolase family (GH family) based on their amino-acid sequence similarity. The glycoside hydrolases acting on α-glucosidic linkage are in GH family 4, 13, 15, 31, 63, 97, and 122. This review deals mainly with findings on GH family 31 and 97 enzymes. Research on two GH family 31 enzymes is described: clarification of the substrate recognition of Escherichia coli α-xylosidase, and glycosynthase derived from Schizosaccharomyces pombe α-glucosidase. GH family 97 is an aberrant GH family, containing inverting and retaining glycoside hydrolases. The inverting enzyme in GH family 97 displays significant similarity to retaining α-glycosidases, including GH family 97 retaining α-glycosidase, but the inverting enzyme has no catalytic nucleophile residue. It appears that a catalytic nucleophile has been eliminated during the molecular evolution in the same way as a man-made nucleophile mutant enzyme, which catalyzes the inverting reaction, as in glycosynthase and chemical rescue.     

Enzyme diversity of the cellulolytic system produced by Clostridium cellulolyticum explored by two-dimensional analysis: identification of seven genes encoding new dockerin-containing proteins

The enzyme diversity of the cellulolytic system produced by Clostridium cellulolyticum grown on crystalline cellulose as a sole carbon and energy source was explored by two-dimensional electrophoresis. The cellulolytic system of C. cellulolyticum is composed of at least 30 dockerin-containing proteins (designated cellulosomal proteins) and 30 noncellulosomal components. Most of the known cellulosomal proteins, including CipC, Cel48F, Cel8C, Cel9G, Cel9E, Man5K, Cel9M, and Cel5A, were identified by using two-dimensional Western blot analysis with specific antibodies, whereas Cel5N, Cel9J, and Cel44O were identified by using N-terminal sequencing. Unknown enzymes having carboxymethyl cellulase or xylanase activities were detected by zymogram analysis of two-dimensional gels. Some of these enzymes were identified by N-terminal sequencing as homologs of proteins listed in the NCBI database. Using Trap-Dock PCR and DNA walking, seven genes encoding new dockerin-containing proteins were cloned and sequenced. Some of these genes are clustered. Enzymes encoded by these genes belong to glycoside hydrolase families GH2, GH9, GH10, GH26, GH27, and GH59. Except for members of family GH9, which contains only cellulases, the new modular glycoside hydrolases discovered in this work could be involved in the degradation of different hemicellulosic substrates, such as xylan or galactomannan.     

Beta-helical catalytic domains in glycoside hydrolase families 49, 55 and 87: domain architecture,modelling and assignment of catalytic residues

X-ray crystallography and bioinformatics studies reveal a tendency for the right-handed β-helix domain architecture to be associated with carbohydrate binding proteins. Here we demonstrate the presence of catalytic β-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 β-helices, as well as an unexpected pair of β-helix domains in GH family 55.     

Mannose foraging by Bacteroides thetaiotaomicron: structure and specificity of the beta-mannosidase, BtMan2A

The human colonic bacterium Bacteroides thetaiotaomicron, which plays an important role in maintaining human health, produces an extensive array of exo-acting glycoside hydrolases (GH), including 32 family GH2 glycoside hydrolases. Although it is likely that these enzymes enable the organism to utilize dietary and host glycans as major nutrient sources, the biochemical properties of these GH2 glycoside hydrolases are currently unclear. Here we report the biochemical properties and crystal structure of the GH2 B. thetaiotaomicron enzyme BtMan2A. Kinetic analysis demonstrates that BtMan2A is a beta-mannosidase in which substrate binding energy is provided principally by the glycone binding site, whereas aglycone recognition is highly plastic. The three-dimensional structure, determined to a resolution of 1.7 A, reveals a five-domain structure that is globally similar to the Escherichia coli LacZ beta-galactosidase. The catalytic center is housed mainly within a (beta/alpha)8 barrel although the N-terminal domain also contributes to the active site topology. The nature of the substrate-binding residues is quite distinct from other GH2 enzymes of known structure, instead they are similar to other clan GH-A enzymes specific for manno-configured substrates. Mutagenesis studies, informed by the crystal structure, identified a WDW motif in the N-terminal domain that makes a significant contribution to catalytic activity. The observation that this motif is invariant in GH2 mannosidases points to a generic role for these residues in this enzyme class. The identification of GH-A clan and GH2 specific residues in the active site of BtMan2A explains why this enzyme is able to harness substrate binding at the proximal glycone binding site more efficiently than mannan-hydrolyzing glycoside hydrolases in related enzyme families. The catalytic properties of BtMan2A are consistent with the flexible nutrient acquisition displayed by the colonic bacterium.     

Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron

SusB, an 84-kDa alpha-glucoside hydrolase involved in the starch utilization system (sus) of Bacteroides thetaiotaomicron, belongs to glycoside hydrolase (GH) family 97. We have determined the enzymatic characteristics and the crystal structures in free and acarbose-bound form at 1.6A resolution. SusB hydrolyzes the alpha-glucosidic linkage, with inversion of anomeric configuration liberating the beta-anomer of glucose as the reaction product. The substrate specificity of SusB, hydrolyzing not only alpha-1,4-glucosidic linkages but also alpha-1,6-, alpha-1,3-, and alpha-1,2-glucosidic linkages, is clearly different from other well known glucoamylases belonging to GH15. The structure of SusB was solved by the single-wavelength anomalous diffraction method with sulfur atoms as anomalous scatterers using an in-house x-ray source. SusB includes three domains as follows: the N-terminal, catalytic, and C-terminal domains. The structure of the SusB-acarbose complex shows a constellation of carboxyl groups at the catalytic center; Glu532 is positioned to provide protonic assistance to leaving group departure, with Glu439 and Glu508 both positioned to provide base-catalyzed assistance for inverting nucleophilic attack by water. A structural comparison with other glycoside hydrolases revealed significant similarity between the catalytic domain of SusB and those of alpha-retaining glycoside hydrolases belonging to GH27, -36, and -31 despite the differences in catalytic mechanism. SusB and the other retaining enzymes appear to have diverged from a common ancestor and individually acquired the functional carboxyl groups during the process of evolution. Furthermore, sequence comparison of the active site based on the structure of SusB indicated that GH97 included both retaining and inverting enzymes.     

Conserved sequence motifs in levansucrases and bifunctional beta-xylosidases and alpha-L-arabinases

Comparison of the amino acid sequences of two families of glycosyl hydrolases reveals that they are related in a region in the central part of the sequences. One of these families (GH family 68) includes levansucrases and the other one (glycosyl hydrolase family 43) includes bifunctional beta-xylosidases and alpha-L-arabinofuranosidases. The similarity of the primary structure of proteins from these families allows us to consider the invariant glutamate residue as a component of their active center. It is shown for the first time that glycosyl hydrolases recognizing different glycofuranoside residues can have a common sequence motif.     

Composition and Expression of Genes Encoding Carbohydrate-Active Enzymes in the Straw-Degrading Mushroom Volvariella volvacea

Volvariella volvacea is one of a few commercial cultivated mushrooms mainly using straw as carbon source. In this study, the genome of V. volcacea was sequenced and assembled. A total of 285 genes encoding carbohydrate-active enzymes (CAZymes) in V. volvacea were identified and annotated. Among 15 fungi with sequenced genomes, V. volvacea ranks seventh in the number of genes encoding CAZymes. In addition, the composition of glycoside hydrolases in V. volcacea is dramatically different from other basidiomycetes: it is particularly rich in members of the glycoside hydrolase families GH10 (hemicellulose degradation) and GH43 (hemicellulose and pectin degradation), and the lyase families PL1, PL3 and PL4 (pectin degradation) but lacks families GH5b, GH11, GH26, GH62, GH93, GH115, GH105, GH9, GH53, GH32, GH74 and CE12. Analysis of genome-wide gene expression profiles of 3 strains using 3′-tag digital gene expression (DGE) reveals that 239 CAZyme genes were expressed even in potato destrose broth medium. Our data also showed that the formation of a heterokaryotic strain could dramatically increase the expression of a number of genes which were poorly expressed in its parental homokaryotic strains.     

The crystal structure of a family GH25 lysozyme from Bacillus anthracis implies a neighboring-group catalytic mechanism with retention of anomeric configuration

Lysozymes are found in many of the sequence-based families of glycoside hydrolases (www.cazy.org) where they show considerable structural and mechanistic diversity. Lysozymes from glycoside hydrolase family GH25 adopt a (α/β)₅(β)₃-barrel-like fold with a proposal in the literature that these enzymes act with inversion of anomeric configuration; the lack of a suitable substrate, however, means that no group has successfully demonstrated the configuration of the product. Here we report the 3-D structure of the GH25 enzyme from Bacillus anthracis at 1.4 Å resolution. We show that the active center is extremely similar to those from glycoside hydrolase families GH18, GH20, GH56, GH84, and GH85 implying that, in the absence of evidence to the contrary, GH25 enzymes also act with net retention of anomeric configuration using the neighboring-group catalytic mechanism that is common to this ‘super-family’ of enzymes.     

Identification and analysis of catalytic TIM barrel domains in seven further glycoside hydrolase families

Fold recognition results allocate catalytic triose phosphate isomerase (TIM) barrels to seven previously unassigned glycoside hydrolase (GH) families, numbers 29, 44, 50, 71, 84, 85 and 89, enabling prediction of catalytic residues. Modelling of GH family 50 suggests that it may be the common evolutionary ancestor of families 42 and 14. TIM barrels now comprise the catalytic domains of more than half of the assigned GH families, and catalyse a much larger variety of GH reactions than any other catalytic domain architecture. Only 327 GH sequences still have no structurally identified catalytic domain.     

PSI protein classifier: A new program automating PSI-BLAST search results

A new program, PSI Protein Classifier, generalizing the results of both successive and independent iterations of the PSI-BLAST program was developed. The technical opportunities of the program are described and illustrated by two examples. An iterative screening of the amino acid sequence database detected potential evolutionary relationships between GH5, GH13, GH27, GH31, GH36, GH66, GH101 and GH114 families of glycoside hydrolases. Analysis of the statistically significant sequence similarity (E-value analysis) allowed us to divide the family GH31 into 38 subfamilies.