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Open AccessJournal ArticleDOI

The chitinolytic machinery of Serratia marcescens – a model system for enzymatic degradation of recalcitrant polysaccharides

TLDR
The catalytic mechanisms of these enzymes as well as the structural basis of each enzyme's specific role in the chitin degradation process are discussed, and how knowledge of this enzyme system may be extrapolated to other enzyme systems for conversion of insoluble polysaccharides is discussed.
Abstract
The chitinolytic machinery of Serratia marcescens is one of the best known enzyme systems for the conversion of insoluble polysaccharides This machinery includes four chitin-active enzymes: ChiC, an endo-acting non-processive chitinase; ChiA and ChiB, two processive chitinases moving along chitin chains in opposite directions; and CBP21, a surface-active CBM33-type lytic polysaccharide monooxygenase that introduces chain breaks by oxidative cleavage Furthermore, an N-acetylhexosaminidase or chitobiase converts the oligomeric products from the other enzymes to monomeric N-acetylglucosamine Here we discuss the catalytic mechanisms of these enzymes as well as the structural basis of each enzyme's specific role in the chitin degradation process We also discuss how knowledge of this enzyme system may be extrapolated to other enzyme systems for conversion of insoluble polysaccharides, in particular conversion of cellulose by cellulases and GH61-type lytic polysaccharide monooxygenases

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Chemical and biological catalysis for plastics recycling and upcycling

TL;DR: In this article, the challenges and opportunities associated with the catalytic transformation of waste plastics, looking at both chemical and biological approaches to transforming such spent materials into a resource, are explored and compared.
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Lytic Polysaccharide Monooxygenases in Biomass Conversion

TL;DR: LPMOs offer tremendous promise for further process improvements owing to their ability to boost the activity of biomass-degrading enzyme consortia, and the academic literature in this area is reviewed.
Journal ArticleDOI

Recent insights into copper-containing lytic polysaccharide mono-oxygenases.

TL;DR: 3D structural analyses of lytic polysaccharide mono-oxygenases of both bacterial and fungal enzymes revealed structures with β-sandwich folds containing an active site with a metal coordinated by an N-terminal histidine, indicating copper-dependent oxygenases.
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The Copper Active Site of Cbm33 Polysaccharide Oxygenases.

TL;DR: The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to bio fuels.
Journal ArticleDOI

A rapid quantitative activity assay shows that the Vibrio cholerae colonization factor GbpA is an active lytic polysaccharide monooxygenase.

TL;DR: A method for quantification of C1‐oxidized chitooligosaccharides (aldonic acids) and hence LPMO activity is described, used to quantify the activity of a four‐domain L PMO from Vibrio cholerae, GbpA, which is a virulence factor with no obvious role in biomass processing.
References
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Journal ArticleDOI

The Pfam protein families database

TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
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Pfam: the protein families database.

TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
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The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

TL;DR: The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates and has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation.
Journal ArticleDOI

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

TL;DR: An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences, and a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data.
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CATH – a hierarchic classification of protein domain structures

TL;DR: Analysis of the structural families generated by CATH reveals the prominent features of protein structure space and a database of well-characterised protein structure families will facilitate the assignment of structure-function/evolution relationships to both known and newly determined protein structures.
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