Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut

The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta) genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an α-xylosidase, a β-glucosidase, and two α-L-arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins

Structure and activity of the Streptococcus pyogenes family GH1 6-phospho β-glycosidase, Spy1599

The group A streptococcus Streptococcus pyogenes is the causative agent of a wide spectrum of invasive infections, including necrotizing fasciitis, scarlet fever and toxic shock syndrome. In the context of its carbohydrate chemistry, it is interesting that S. pyogenes (in this work strain M1 GAS SF370) displays a spectrum of oligosaccharide-processing enzymes that are located in close proximity on the genome but that the in vivo function of these proteins remains unknown. These proteins include different sugar transporters (SPy1593 and SPy1595), both GH125 -1,6- and GH38 -1,3-mannosidases (SPy1603 and SPy1604), a GH84 -hexosaminidase (SPy1600) and a putative GH2 -galactosidase (SPy1586), as well as SPy1599, a family GH1 `putative -glucosidase'. Here, the solution of the three-dimensional structure of SPy1599 in a number of crystal forms complicated by unusual crystallographic twinning is reported. The structure is a classical (/)8-barrel, consistent with CAZy family GH1 and other members of the GH-A clan. SPy1599 has been annotated in sequence depositions as a -glucosidase (EC 3.2.1.21), but no such activity could be found; instead, three-dimensional structural overlaps with other enzymes of known function suggested that SPy1599 contains a phosphate-binding pocket in the active site and has possible 6-phospho--glycosidase activity. Subsequent kinetic analysis indeed showed that SPy1599 has 6-phospho--glucosidase (EC 3.2.1.86) activity. These data suggest that SPy1599 is involved in the intracellular degradation of 6-phosphoglycosides, which are likely to originate from import through one of the organism's many phosphoenolpyruvate phosphotransfer systems (PEP-PTSs)

The molecular and cellular characterisation of the first glycocin, plantaricin KW30 : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry at Massey University, Palmerston North, New Zealand

Bacteriocins, typically secreted by Gram-positive and -negative bacteria, are ribosomally synthesised antimicrobial peptides which inhibit the growth of competing bacteria. We have purified a 43 amino acid bacteriocin, plantaricin KW30 (PlnKW30) produced by Lactobacillus plantarum KW30, that has little amino acid sequence similarity to any other characterised bacteriocin. The gene encoding plnKW30 is in a cluster with the genes required for maturation and export of, and immunity to, the bacteriocin. This arrangement of genes is similar to the genomic context of bacteriocin genes in other lactic acid bacteria. The plnKW30 gene cluster comprises six genes encoding a glycosyltransferase, a proteolytic ABC-transporter, two putative thioredoxins, a response regulator and PlnKW30 itself. PlnKW30 was found to possess two unusual post-translational modifications: an O-glycosylated serine and an unprecedented S-glycosylation of the C-terminal cysteine. The modified serine is located on an eight residue loop that is tethered by a disulfide bridge. Bothmodifications have been identified as N-acetylglucosamines (GlcNAc), making PlnKW30 the first described class IV bacteriocin. A post-translational modification with S-linked GlcNAc is unprecedented in bacteriocins as well as in all genera. The antimicrobial activity of PlnKW30 on L. plantarum ATCC 8014 was analysed using enzymatic dissection coupled with bioassays. It was found to be concentration dependent and both the N-and C-terminalfragments are necessary for activity. Furthermore, reduction of the disulfide bonds results in abolishment of antimicrobial activity and it appears that deglycosylation of the serine 18 decreases the antimicrobial activity by about two thirds. These results show that all posttranslational modifications contribute to the antimicrobial activity of PlnKW30. The addition of N-acetylglucosamine to cultures of the indicator strain L. plantarum ATCC 8014 protects it from the antimicrobial effect of the added PlnKW30. PlnKW30 probably targets an N-acetylglucosamine transporter in the target cell membrane, similar to the mannose phosphotransferase system targeted by lactococcin A

Combined inhibitor free-energy landscape and structural analysis reports on the mannosidase conformational coordinate

Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence‐based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X‐ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole‐type inhibitors are energetically poised to report faithfully on mannosidase transition‐state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including β‐mannanases from families GH26 and GH113. Isofagomine‐type inhibitors are poor mimics of transition‐state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar‐shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active‐site residues involved in substrate recognition

Ribosomally synthesized and post-translationally modified peptide natural products:overview and recommendations for a universal nomenclature

<p>This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.</p>