8 research outputs found
Structural and functional characterization of PL28 family ulvan lyase NLR48 from Nonlabens ulvanivorans
International audienc
Structure–function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism
International audienc
New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture
Ulvan
is a complex sulfated polysaccharide biosynthesized by green
seaweed and contains predominantly rhamnose, xylose, and uronic acid
sugars. Ulvan-degrading enzymes have only recently been identified
and added to the CAZy (www.cazy.org) database as family PL24, but neither their structure nor catalytic
mechanism(s) are yet known. Several homologous, new ulvan lyases,
have been discovered in <i>Pseudoalteromonas</i> sp. strain
PLSV, <i>Alteromonas LOR</i>, and <i>Nonlabens ulvanivorans</i>, defining a new family PL25, with the lyase encoded by the gene
PLSV_3936 being one of them. This enzyme cleaves the glycosidic bond
between 3-sulfated rhamnose (R3S) and glucuronic acid (GlcA) or iduronic
acid (IdoA) via a β-elimination mechanism. We report the crystal
structure of PLSV_3936 and its complex with a tetrasaccharide substrate.
PLSV_3936 folds into a seven-bladed β-propeller, with each blade
consisting of four antiparallel β-strands. Sequence conservation
analysis identified a highly conserved region lining at one end of
a deep crevice on the protein surface. The putative active site was
identified by mutagenesis and activity measurements. Crystal structure
of the enzyme with a bound tetrasaccharide substrate confirmed the
identity of base and acid residues and allowed determination of the
catalytic mechanism and also the identification of residues neutralizing
the uronic acid carboxylic group. The PLSV_3936 structure provides
an example of a convergent evolution among polysaccharide lyases toward
a common active site architecture embedded in distinct folds
Conformational flexibility of PL12 family heparinases: structure and substrate specificity of heparinase III from <em>Bacteroides thetaiotaomicron</em> (BT4657)
International audienceGlycosaminoglycans (GAGs) are linear polysaccharides comprised of disaccharide repeat units, a hexuronic acid, glucuronic acid or iduronic acid, linked to a hexosamine, N-acetylglucosamine (GlcNAc) or N-acetylgalactosamine. GAGs undergo further modification such as epimerization and sulfation. These polysaccharides are abundant in the extracellular matrix and connective tissues. GAGs function in stabilization of the fibrillar extracellular matrix, control of hydration, regulation of tissue, organism development by controlling cell cycle, cell behavior and differentiation. Niche adapted bacteria express enzymes called polysaccharide lyases (PL), which degrade GAGs for their nutrient content. PL have been classified into 24 sequence-related families. Comparison of 3D structures of the prototypic members of these families allowed identification of distant evolutionary relationships between lyases that were unrecognized at the sequence level, and identified occurrences of convergent evolution. We have characterized structurally and enzymatically heparinase III from Bacteroides thetaiotaomicron (BtHepIII; gene BT4657), which is classified within the PL12 family. BtHepIII is a 72.5 kDa protein. We present the X-ray structures of two crystal forms of BtHepIII at resolution 1.8 and 2.4 angstrom. BtHepIII contains two domains, the N-terminal alpha-helical domain forming a toroid and the C-terminal beta-sheet domain. Comparison with recently determined structures of two other heparinases from the same PL12 family allowed us to identify structural flexibility in the arrangement of the domains indicating open-close movement. Based on comparison with other GAG lyases, we identified Tyr301 as the main catalytic residue and confirmed this by site-directed mutagenesis. We have characterized substrate preference of BtHepIII toward sulfate-poor heparan sulfate substrate
Conformational flexibility of PL12 family heparinases: structure and substrate specificity of heparinase III from Bacteroides thetaiotaomicron
Glycosaminoglycans (GAGs) are linear polysaccharides comprised of disaccharide repeat units, a hexuronic acid, glucuronic acid or iduronic acid, linked to a hexosamine, N-acetylglucosamine (GlcNAc) or N-acetylgalactosamine. GAGs undergo further modification such as epimerization and sulfation. These polysaccharides are abundant in the extracellular matrix and connective tissues. GAGs function in stabilization of the fibrillar extracellular matrix, control of hydration, regulation of tissue, organism development by controlling cell cycle, cell behavior and differentiation. Niche adapted bacteria express enzymes called polysaccharide lyases (PL), which degrade GAGs for their nutrient content. PL have been classified into 24 sequence-related families. Comparison of 3D structures of the prototypic members of these families allowed identification of distant evolutionary relationships between lyases that were unrecognized at the sequence level, and identified occurrences of convergent evolution. We have characterized structurally and enzymatically heparinase III from Bacteroides thetaiotaomicron (BtHepIII; gene BT4657), which is classified within the PL12 family. BtHepIII is a 72.5 kDa protein. We present the X-ray structures of two crystal forms of BtHepIII at resolution 1.8 and 2.4 Å. BtHepIII contains two domains, the N-terminal α-helical domain forming a toroid and the C-terminal β-sheet domain. Comparison with recently determined structures of two other heparinases from the same PL12 family allowed us to identify structural flexibility in the arrangement of the domains indicating open–close movement. Based on comparison with other GAG lyases, we identified Tyr301 as the main catalytic residue and confirmed this by site-directed mutagenesis. We have characterized substrate preference of BtHepIII toward sulfate-poor heparan sulfate substrate
Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2
International audienceABSTRACT We report here the first genome sequence of the white-rot fungus Obba rivulosa (Polyporales, Basidiomycota), a polypore known for its lignin-decomposing ability. The genome is based on the homokaryon 3A-2 originating in Finland. The genome is typical in size and carbohydrate active enzyme (CAZy) content for wood-decomposing basidiomycetes