5 research outputs found
MOESM1 of The impact of hydrogen peroxide supply on LPMO activity and overall saccharification efficiency of a commercial cellulase cocktail
Additional file 1. The impact of hydrogen peroxide supply on LPMO activity and overall saccharification efficiency of a commercial cellulase cocktail. Figure S1. Stability of Glc4gemGlc and its impact on the results presented in this paper. Figure S2. Degradation of Glc4gemGlc during incubation under conditions similar to those during biomass saccharification in bioreactors
How a Lytic Polysaccharide Monooxygenase Binds Crystalline Chitin
Lytic
polysaccharide monooxygenases (LPMOs) are major players in
biomass conversion, both in Nature and in the biorefining industry.
How the monocopper LPMO active site is positioned relative to the
crystalline substrate surface to catalyze powerful, but potentially
self-destructive, oxidative chemistry is one of the major questions
in the field. We have adopted a multidisciplinary approach, combining
biochemical, spectroscopic, and molecular modeling methods to study
chitin binding by the well-studied LPMO from <i>Serratia marcescens
Sm</i>AA10A (or CBP21). The orientation of the enzyme on a single-chain
substrate was determined by analyzing enzyme cutting patterns. Building
on this analysis, molecular dynamics (MD) simulations were performed
to study interactions between the LPMO and three different surface
topologies of crystalline chitin. The resulting atomistic models showed
that most enzymeâsubstrate interactions involve the polysaccharide
chain that is to be cleaved. The models also revealed a constrained
active site geometry as well as a tunnel connecting the bulk solvent
to the copper site, through which only small molecules such as H<sub>2</sub>O, O<sub>2</sub>, and H<sub>2</sub>O<sub>2</sub> can diffuse.
Furthermore, MD simulations, quantum mechanics/molecular mechanics
calculations, and electron paramagnetic resonance spectroscopy demonstrate
that rearrangement of Cu-coordinating water molecules is necessary
when binding the substrate and also provide a rationale for the experimentally
observed C1 oxidative regiospecificity of <i>Sm</i>AA10A.
This study provides a first, experimentally supported, atomistic view
of the interactions between an LPMO and crystalline chitin. The confinement
of the catalytic center is likely crucially important for controlling
the oxidative chemistry performed by LPMOs and will help guide future
mechanistic studies
How a Lytic Polysaccharide Monooxygenase Binds Crystalline Chitin
Lytic
polysaccharide monooxygenases (LPMOs) are major players in
biomass conversion, both in Nature and in the biorefining industry.
How the monocopper LPMO active site is positioned relative to the
crystalline substrate surface to catalyze powerful, but potentially
self-destructive, oxidative chemistry is one of the major questions
in the field. We have adopted a multidisciplinary approach, combining
biochemical, spectroscopic, and molecular modeling methods to study
chitin binding by the well-studied LPMO from <i>Serratia marcescens
Sm</i>AA10A (or CBP21). The orientation of the enzyme on a single-chain
substrate was determined by analyzing enzyme cutting patterns. Building
on this analysis, molecular dynamics (MD) simulations were performed
to study interactions between the LPMO and three different surface
topologies of crystalline chitin. The resulting atomistic models showed
that most enzymeâsubstrate interactions involve the polysaccharide
chain that is to be cleaved. The models also revealed a constrained
active site geometry as well as a tunnel connecting the bulk solvent
to the copper site, through which only small molecules such as H<sub>2</sub>O, O<sub>2</sub>, and H<sub>2</sub>O<sub>2</sub> can diffuse.
Furthermore, MD simulations, quantum mechanics/molecular mechanics
calculations, and electron paramagnetic resonance spectroscopy demonstrate
that rearrangement of Cu-coordinating water molecules is necessary
when binding the substrate and also provide a rationale for the experimentally
observed C1 oxidative regiospecificity of <i>Sm</i>AA10A.
This study provides a first, experimentally supported, atomistic view
of the interactions between an LPMO and crystalline chitin. The confinement
of the catalytic center is likely crucially important for controlling
the oxidative chemistry performed by LPMOs and will help guide future
mechanistic studies
Molecular Design of Non-Leloir Furanose-Transferring Enzymes from an αâlâArabinofuranosidase: A Rationale for the Engineering of Evolved Transglycosylases
The vast biodiversity of glycoside
hydrolases (GHs) constitutes
a reservoir of readily available carbohydrate-acting enzymes that
employ simple substrates and hold the potential to perform highly
stereopecific and regioselective glycosynthetic reactions. However,
most GHs preferentially hydrolyze glycosidic bonds and are thus characterized
by a hydrolysis/transglycosylation partition in favor of hydrolysis.
Unfortunately, current knowledge is insufficient to rationally modify
this partition, specifically mutating key molecular determinants to
tip the balance toward transglycosylation. In this study, in the absence
of precise knowledge concerning the hydrolysis/transglycosylation
partition in a hydrolytic GH51 α-l-arabinofuranosidase,
we describe how an iterative protein engineering approach has been
used to create the first ânon-Leloirâ transarabinofuranosylases.
In the first step, random mutagenesis yielded a point mutation (R69H)
at a position that is highly conserved in clan GH-A. Characterization
of R69H revealed that this enzyme displays high transglycosylation
activity but severely reduced (61-fold) activity on <i>p</i>NP-α-l-arabinofuranoside. Upon recombination of R69H
with other point mutations selected using semirational or <i>in silico</i> approaches, transfer rates close to 100% and transarabinofuranosylation
yields of the main (1â2)-linked oligosaccharide product of
80% (vs 11% for the wild-type) were obtained. Combining data presented
here with knowledge drawn from the literature, we suggest that the
creation of non-Leloir transglycosylases necessarily involves the
destabilization of the highly developed transition states that characterize
the predominantly hydrolytic <i>exo</i>-acting GHs; this
is an efficient way to prevent ubiquitous water molecules from performing
the deglycosylation step
Multipoint Precision Binding of Substrate Protects Lytic Polysaccharide Monooxygenases from Self-Destructive Off-Pathway Processes
Lytic polysaccharide
monooxygenases (LPMOs) play a crucial role
in the degradation of polysaccharides in biomass by catalyzing powerful
oxidative chemistry using only a single copper ion as a cofactor.
Despite the natural abundance and importance of these powerful monocopper
enzymes, the structural determinants of their functionality have remained
largely unknown. We have used site-directed mutagenesis to probe the
roles of 13 conserved amino acids located on the flat substrate-binding
surface of CBP21, a chitin-active family AA10 LPMO from <i>Serratia
marcescens</i>, also known as <i>Sm</i>LPMO10A. Single
mutations of residues that do not interact with the catalytic copper
site, but rather are involved in substrate binding had remarkably
strong effects on overall enzyme performance. Analysis of product
formation over time showed that these mutations primarily affected
enzyme stability. Investigation of protein integrity using proteomics
technologies showed that loss of activity was caused by oxidation
of essential residues in the enzyme active site. For most enzyme variants,
reduced enzyme stability correlated with a reduced level of binding
to chitin, suggesting that adhesion to the substrate prevents oxidative
off-pathway processes that lead to enzyme inactivation. Thus, the
extended and highly evolvable surfaces of LPMOs are tailored for precise
multipoint substrate binding, which provides the confinement that
is needed to harness and control the remarkable oxidative power of
these enzymes. These findings are important for the optimized industrial
use of LPMOs as well as the design of LPMO-inspired catalysts