4.4 Review

Molecular mechanisms of processive glycoside hydrolases underline catalytic pragmatism

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biotechnology & Applied Microbiology

Carbohydrate-binding modules of ChiB and ChiC promote the chitinolytic system of Serratia marcescens BWL1001

Jiawen Liu et al.

Summary: This study reveals the effects of carbohydrate-binding modules (CBMs) on the enzymatic characteristics of chitinases and their contributions to the overall efficiency of chitinolytic systems during synergistic hydrolysis.

ENZYME AND MICROBIAL TECHNOLOGY (2023)

Review Biotechnology & Applied Microbiology

Controlled processivity in glycosyltransferases: A way to expand the enzymatic toolbox

Chiara Guidi et al.

Summary: Glycosyltransferases (GT) catalyze the biosynthesis of complex carbohydrates, playing important roles in many cellular mechanisms. Understanding the mechanism of GTs is valuable for studying the structure-function relationships and improving enzyme engineering for various applications. This review focuses on the recent advances in understanding processive enzymes and their engineering strategies, as well as the chain length-controlling mechanisms in both eukaryotic and prokaryotic enzymes.

BIOTECHNOLOGY ADVANCES (2023)

Article Biochemistry & Molecular Biology

Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non-productive binding: insights from crystal structures and MD simulation

Topi Haataja et al.

Summary: In this study, the hydrolysis characteristics of two model enzymes in the CBH family 7 were examined using enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies. The results revealed that the strength of non-productive binding is a key determinant for the activity characteristics of these enzymes on different substrates.

FEBS JOURNAL (2023)

Article Biochemistry & Molecular Biology

The carbohydrate-active enzyme database: functions and literature

Elodie Drula et al.

Summary: The CAZy database, freely available for browsing and download, is deeply rooted in human curation and plays a crucial role in maintaining and updating family classification, classifying new sequences, and presenting functional information. Over the past 8 years, there has been an increase in novel families and extensive annotations conducted, highlighting the significant amount of work involved in analyzing and reporting biochemical data from the literature.

NUCLEIC ACIDS RESEARCH (2022)

Article Multidisciplinary Sciences

Deciphering the mechanism of processive ssDNA digestion by the Dna2-RPA ensemble

Jiangchuan Shen et al.

Summary: The key nuclease Dna2 interacts with the ssDNA binding protein RPA in two ways to protect the integrity of single stranded DNA and facilitate double strand break repair.

NATURE COMMUNICATIONS (2022)

Article Chemistry, Physical

Processive binding mechanism of Cel9G from Clostridium cellulovorans: molecular dynamics and free energy landscape investigations

Penghui Li et al.

Summary: This study investigates the processive binding mechanism of cellulase family 9 (Cel9G) to polysaccharides. The simulations reveal that the binding of the cellulose chain exhibits several local minima, which are influenced by the CH/pi interactions between sugar rings and aromatic residues. Y520 is found to be critical for processive binding, and the straight-line morphology of the substrate is observed after the formation of the slide mode. The study proposes a four-step catalytic cycle for Cel9G.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)

Article Multidisciplinary Sciences

Lytic polysaccharide monooxygenase increases cellobiohydrolases activity by promoting decrystallization of cellulose surface

Taku Uchiyama et al.

Summary: Efficient depolymerization of crystalline cellulose requires the cooperative action of multiple cellulolytic enzymes. This study demonstrates that the synergistic activity between cellobiohy-drolases and a lytic polysaccharide monooxygenase can enhance the activity and performance of the enzymes by producing chain breaks and amorphizing the crystalline surface of cellulose.

SCIENCE ADVANCES (2022)

Article Biochemistry & Molecular Biology

New insight into the mode of action of a GH74 xyloglucanase on tamarind seed xyloglucan: Action pattern and cleavage site

Mingrui Chen et al.

Summary: This study provides important information for the structural analysis of plant cell wall xyloglucan and cell wall processing by studying the mode of action and cleavage site of xyloglucanase.

CARBOHYDRATE RESEARCH (2022)

Article Chemistry, Physical

Model of Processive Catalysis with Site Clustering and Blocking and Its Application to Cellulose Hydrolysis

Zdenek Petrasek et al.

Summary: Interactions between particles moving on a linear track and obstacles can lead to crowding, hindering transport kinetics. Cellulose hydrolysis by enzymes on cellulose chains is an example. The exact role and mechanism of crowding and blocking in cellulose hydrolysis are not clear. This study proposes a simple model that incorporates crowding and blocking effects by distinguishing between binding and non-binding sites on the chain. The model reproduces experimental results related to the early phase of cellulose hydrolysis and suggests periodic desorption and rebinding of enzyme molecules as a strategy to enhance the rate of cellulose hydrolysis.

JOURNAL OF PHYSICAL CHEMISTRY B (2022)

Article Mechanics

Processive and distributive non-equilibrium networks discriminate in alternate limits

Gaurav G. Venkataraman et al.

Summary: We study biochemical reaction networks inspired by biological proofreading mechanisms. By introducing a measure that can be computed directly from the biochemical rate constants, we provide a condition for optimizing discrimination schemes in a broad class of models.

JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT (2022)

Article Multidisciplinary Sciences

The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases

Sukanya Luang et al.

Summary: In this study, the researchers investigate the binding and conformational behavior of beta-D-glucosides in the barley beta-D-glucan glucohydrolase. They find that the Trp286/Trp434 clamp plays a crucial role in substrate hydrolysis. Mutations in the clamp affect processive catalysis, and phylogenomic analysis reveals the evolutionary advantage of the tryptophan clamp.

NATURE COMMUNICATIONS (2022)

Article Chemistry, Physical

Enzyme Synergy in Transient Clusters of Endo- and Exocellulase Enables a Multilayer Mode of Processive Depolymerization of Cellulose

Krisztina Zajki-Zechmeister et al.

Summary: This study reveals the formation of transient clusters of endo-and exocellulases on the cellulose surface, leading to directed ablation of single microfibrils through a multilayer processive mode. The cooperativity between endo-and exocellulases enables faster degradation of structurally organized polymer materials.

ACS CATALYSIS (2022)

Article Multidisciplinary Sciences

Processive cleavage of substrate at individual proteolytic active sites of the Lon protease complex

Shanshan Li et al.

Summary: Lon protease is able to degrade protein substrates in a processive fashion at each of its six proteolytic active sites, forming a deep groove that encloses the substrate polypeptide chain and allows for continuous cleavage in the C-to-N direction. An acidic residue at the binding groove exit is identified as essential for the proteolytic activity, likely promoting processive proteolysis through carboxyl-carboxylate interactions with cleaved intermediates. These findings reveal a previously unrecognized mechanism for processive substrate degradation by the Lon protease.

SCIENCE ADVANCES (2021)

Review Biochemistry & Molecular Biology

Processivity in Bacterial Glycosyltransferases

Liubov Yakovlieva et al.

ACS CHEMICAL BIOLOGY (2020)

Article Chemistry, Multidisciplinary

The CH-π Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification

Josef Houser et al.

CHEMISTRY-A EUROPEAN JOURNAL (2020)

Article Multidisciplinary Sciences

Convergent evolution of processivity in bacterial and fungal cellulases

Taku Uchiyama et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemistry & Molecular Biology

GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm

Jose-Emilio Sanchez-Aparicio et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Article Biochemistry & Molecular Biology

Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74

Gregory Arnal et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2019)

Article Multidisciplinary Sciences

Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site

Victor A. Streltsov et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

The dissociation mechanism of processive cellulases

Josh V. Vermaas et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin

Akihiko Nakamura et al.

NATURE COMMUNICATIONS (2018)

Article Chemistry, Physical

Sabatier Principle for Interfacial (Heterogeneous) Enzyme Catalysis

Jeppe Kari et al.

ACS CATALYSIS (2018)

Article Multidisciplinary Sciences

Human Chitotriosidase Is an Endo-Processive Enzyme

Silja Kuusk et al.

PLOS ONE (2017)

Review Chemistry, Multidisciplinary

Artificial molecular motors

Salma Kassem et al.

CHEMICAL SOCIETY REVIEWS (2017)

Article Biochemistry & Molecular Biology

Insights into the structure and function of membrane-integrated processive glycosyltransferases

Yunchen Bi et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2015)

Article Chemistry, Physical

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

Yinglong Miao et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Multidisciplinary Sciences

Self-organization of waves and pulse trains by molecular motors in cellular protrusions

A. Yochelis et al.

SCIENTIFIC REPORTS (2015)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Chemistry, Multidisciplinary

Processive Catalysis

Stijn F. M. van Dongen et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)

Review Biochemical Research Methods

Towards a molecular-level theory of carbohydrate processivity in glycoside hydrolases

Gregg T. Beckham et al.

CURRENT OPINION IN BIOTECHNOLOGY (2014)

Article Biochemistry & Molecular Biology

Key amino acid residues for the endo-processive activity of GH74 xyloglucanase

Tomohiko Matsuzawa et al.

FEBS LETTERS (2014)

Article Multidisciplinary Sciences

Two-way traffic of glycoside hydrolase family 18 processive chitinases on crystalline chitin

Kiyohiko Igarashi et al.

NATURE COMMUNICATIONS (2014)

Review Biochemistry & Molecular Biology

Fungal Beta-Glucosidases: A Bottleneck in Industrial Use of Lignocellulosic Materials

Annette Sorensen et al.

BIOMOLECULES (2013)

Article Biochemistry & Molecular Biology

Processivity and substrate-binding in family 18 chitinases

Morten Sorlie et al.

BIOCATALYSIS AND BIOTRANSFORMATION (2012)

Article Biochemistry & Molecular Biology

Hallmarks of Processivity in Glycoside Hydrolases from Crystallographic and Computational Studies of the Serratia marcescens Chitinases

Christina M. Payne et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2012)

Article Multidisciplinary Sciences

Molecular crowding creates traffic jams of kinesin motors on microtubules

Cecile Leduc et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biotechnology & Applied Microbiology

Processivity, Synergism, and Substrate Specificity of Thermobifida fusca Cel6B

Thu V. Vuong et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Article Microbiology

Processive Endoglucanases Mediate Degradation of Cellulose by Saccharophagus degradans

Brian J. Watson et al.

JOURNAL OF BACTERIOLOGY (2009)

Article Chemistry, Multidisciplinary

Carbohydrate-π Interactions: What Are They Worth?

Zachary R. Laughrey et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

Article Chemistry, Multidisciplinary

On the role of aromatic-sugar interactions in the molecular recognition of carbohydrates:: A 3D view by using NMR

M. Dolores Diaz et al.

PURE AND APPLIED CHEMISTRY (2008)

Article Multidisciplinary Sciences

Costs and benefits of processivity in enzymatic degradation of recalcitrant polysaccharides

Svein J. Horn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Chemistry, Physical

PELE: Protein energy landscape exploration. A novel Monte Carlo based technique

KW Borrelli et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)

Article Multidisciplinary Sciences

Mapping glycoside hydrolase substrate subsites by isothermal titration calorimetry

G Zolotnitsky et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemistry & Molecular Biology

Structural basis for broad substrate specificity in higher plant β-D-glucan glucohydrolases

M Hrmova et al.

PLANT CELL (2002)

Review Biochemistry & Molecular Biology

A structural basis for processivity

WA Breyer et al.

PROTEIN SCIENCE (2001)

Review Biochemistry & Molecular Biology

Structure-function relationships of beta-D-glucan endo- and exohydrolases from higher plants

M Hrmova et al.

PLANT MOLECULAR BIOLOGY (2001)

Article Biochemistry & Molecular Biology

Site-directed mutation of noncatalytic residues of Thermobifida fusca exocellulase Cel6B

S Zhang et al.

EUROPEAN JOURNAL OF BIOCHEMISTRY (2000)