Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus

Among the extensive repertoire of carbohydrate-active enzymes, lytic polysaccharide monooxygenases (LPMOs) have a key role in recalcitrant biomass degradation. LPMOs are copper-dependent enzymes that catalyze oxidative cleavage of glycosidic bonds in polysaccharides such as cellulose and chitin. Several LPMOs contain carbohydrate-binding modules (CBMs) that are known to promote LPMO efficiency. However, structural and functional properties of some CBMs remain unknown, and it is not clear why some LPMOs, like CjLPMO10A from the soil bacterium Cellvibrio japonicus, have multiple CBMs (CjCBM5 and CjCBM73). Here, we studied substrate binding by these two CBMs to shine light on their functional variation and determined the solution structures of both by NMR, which constitutes the first structure of a member of the CBM73 family. Chitin-binding experiments and molecular dynamics simulations showed that, while both CBMs bind crystalline chitin with K_d values in the micromolar range, CjCBM73 has higher affinity for chitin than CjCBM5. Furthermore, NMR titration experiments showed that CjCBM5 binds soluble chitohexaose, whereas no binding of CjCBM73 to this chitooligosaccharide was detected. These functional differences correlate with distinctly different arrangements of three conserved aromatic amino acids involved in substrate binding. In CjCBM5, these residues show a linear arrangement that seems compatible with the experimentally observed affinity for single chitin chains. On the other hand, the arrangement of these residues in CjCBM73 suggests a wider binding surface that may interact with several chitin chains. Taken together, these results provide insight into natural variation among related chitin-binding CBMs and the possible functional implications of such variation.

Identification and characterization of the glycoside hydrolase family 18 genes from the entomopathogenic fungus Isaria cicadae genome

Fungal chitinases play essential roles in chitin degradation, cell wall remodeling, chitin recycling, nutrition acquisition, autolysis, and virulence. In this study, 18 genes of the glycoside hydrolase 18 (GH18) family were identified in the Isaria cicadae genome. Seventeen of the genes belonged to chitinases and one was an endo-β-N-acetylglucosaminidase (ENGase). According to phylogenetic analysis, the 17 chitinases were designated as subgroups A (7 chitinases), B (7), and C (3). The exon-intron organizations of these genes were analyzed. The conserved regions DxxDxDxE and S/AxGG and the domains CBM1, CBM18, and CBM50 were detected in I. cicadae chitinases and ENGase. The results of analysis of expression patterns showed that genes ICchiA1, ICchiA6, ICchiB1, and ICchiB4 had high transcript levels in the different growth conditions or developmental stages. Subgroup A chitinase genes had higher transcript levels than the genes of all other chitinases. Subgroup B chitinase genes (except ICchiB7) presented higher transcript levels in chitin medium compared with other conditions. ICchiC2 and ICchiC3 were mainly transcribed in autolysis medium and in blastospores, respectively. Moreover, ICchiB1 presented higher transcript levels than genes of other chitinases. This work provides an overview of the GH18 chitinases and ENGase in I. cicadae and provides a context for the chitinolytic potential, functions, and biological controls of these enzymes of entomopathogenic fungi.

Structural Insights into the Molecular Evolution of the Archaeal Exo-β-d-Glucosaminidase

The archaeal exo-β-d-glucosaminidase (GlmA), a thermostable enzyme belonging to the glycosidase hydrolase (GH) 35 family, hydrolyzes chitosan oligosaccharides into monomer glucosamines. GlmA is a novel enzyme in terms of its primary structure, as it is homologous to both GH35 and GH42 β-galactosidases. The catalytic mechanism of GlmA is not known. Here, we summarize the recent reports on the crystallographic analysis of GlmA. GlmA is a homodimer, with each subunit comprising three distinct domains: a catalytic TIM-barrel domain, an α/β domain, and a β1 domain. Surprisingly, the structure of GlmA presents features common to GH35 and GH42 β-galactosidases, with the domain organization resembling that of GH42 β-galactosidases and the active-site architecture resembling that of GH35 β-galactosidases. Additionally, the GlmA structure also provides critical information about its catalytic mechanism, in particular, on how the enzyme can recognize glucosamine. Finally, we postulate an evolutionary pathway based on the structure of an ancestor GlmA to extant GH35 and GH42 β-galactosidases.

In silico analysis of ChtBD3 domain to find its role in bacterial pathogenesis and beyond

Chitin binding domain 3, known by the acronym ChtBD3, is a domain in the enzymes and proteins of several pathogenic virus, bacteria and fungi. As this domain is evolutionarily-conserved in virulence factors of these infectious agents, its detailed investigation is of clinical interest. In this regard, the current in silico study analyzed ChtBD3 domain distribution in bacterial proteins present in publicly-available SMART (simple modular architecture research tool) database. Also, the co-occurring domains of ChtBD3 in the studied proteins were mapped to understand positional rearrangement of the domain and consequent functional diversity. Custom-made scripts were used to interpret the data and to derive patterns. As expected, interesting results were obtained. ChtBD3 domain co-occurred with other critical domains like peptidase, glycol_hydrolase, kinase, hemagglutinin-acting, collagen-binding, among others. The findings are expected to be of clinical relevance.

The Structure of an Archaeal β-Glucosaminidase Provides Insight into Glycoside Hydrolase Evolution

The archaeal exo-β-d-glucosaminidase (GlmA) is a dimeric enzyme that hydrolyzes chitosan oligosaccharides into monomer glucosamines. GlmA is a member of the glycosidase hydrolase (GH)-A superfamily-subfamily 35 and is a novel enzyme in terms of its primary structure. Here, we present the crystal structure of GlmA in complex with glucosamine at 1.27 Å resolution. The structure reveals that a monomeric form of GlmA shares structural homology with GH42 β-galactosidases, whereas most of the spatial positions of the active site residues are identical to those of GH35 β-galactosidases. We found that upon dimerization, the active site of GlmA changes shape, enhancing its ability to hydrolyze the smaller substrate in a manner similar to that of homotrimeric GH42 β-galactosidase. However, GlmA can differentiate glucosamine from galactose based on one charged residue while using the "evolutionary heritage residue" it shares with GH35 β-galactosidase. Our study suggests that GH35 and GH42 β-galactosidases evolved by exploiting the structural features of GlmA.

Chitin and chitinase: Role in pathogenicity, allergenicity and health

Chitin, a polysaccharide with particular abundance in fungi, nematodes and arthropods is immunogenic. It acts as a threat to other organisms, to tackle which they have been endowed with chitinase enzyme. Even if this enzyme is not present in all organisms, they possess proteins having chitin-binding domain(s) (ChtBD). Many lethal viruses like Ebola, and HCV (Hepatitis C virus) have these domains to manipulate their carriers and target organisms. In keeping with the basic rule of survival, the self-origin (own body component) chitins and chitinases are protective, but that of non-self origin (from other organisms) are detrimental to health. The exogenous chitins and chitinases provoke human innate immunity to generate a deluge of inflammatory cytokines, which injure organs (leading to asthma, atopic dermatitis etc.), and in persistent situations lead to death (multiple sclerosis, systemic lupus erythromatosus (SLE), cancer, etc.). Unfortunately, chitin-chitinase-stimulated hypersensitivity is a common cause of occupational allergy. On the other hand, chitin, and its deacetylated derivative chitosan are increasingly proving useful in pharmaceutical, agriculture, and biocontrol applications. This critical review discusses the complex nexus of chitin and chitinase and assesses both their pathogenic as well as utilitarian aspects.

Multiple crystal forms of N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus

Native N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus (Pf-Dac) and its selenomethionine derivative (Se-Pf-Dac) were crystallized and analyzed in the presence and absence of cadmium ion. The four crystal structures fell into three different crystal-packing groups, with the cadmium-free Pf-Dac and Se-Pf-Dac belonging to the same space group, with homologous unit-cell parameters. The crystal structures in the presence of cadmium contained distorted octahedral cadmium complexes coordinated by three chlorides, two O atoms and an S or Se atom from the N-terminal methionine or selenomethionine, respectively. The N-terminal cadmium complex was involved in crystal contacts between symmetry-related molecules through hydrogen bonding to the N-termini. While all six N-termini of Se-Pf-Dac were involved in cadmium-complex formation, only two of the Pf-Dac N-termini participated in complex formation in the Cd-containing crystal, resulting in different crystal forms. These differences are discussed in light of the higher stability of the Cd-Se bond than the Cd-S bond. This work provides an example of the contribution of cadmium towards determining protein crystal quality and packing depending on the use of the native protein or the selenomethionine derivative.