Article
Biochemistry & Molecular Biology
Kedar Sharma, Carlos M. G. A. Fontes, Shabir Najmudin, Arun Goyal
Summary: The alpha-L-arabinofuranosidase from Clostridium thermocellum displays a modular architecture, enhancing catalytic efficiency. Molecular dynamics simulation analysis reveals higher flexibility in its C-terminal module. Small angle X-ray scattering analysis indicates an elongated structure of the enzyme.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Multidisciplinary
Nicholas G. S. McGregor, Joan Coines, Valentina Borlandelli, Satoko Amaki, Marta Artola, Alba Nin-Hill, Daniel Linzel, Chihaya Yamada, Takatoshi Arakawa, Akihiro Ishiwata, Yukishige Ito, Gijsbert A. van der Marel, Jeroen D. C. Codee, Shinya Fushinobu, Herman S. Overkleeft, Carme Rovira, Gideon J. Davies
Summary: The discovery of zinc-dependent retaining glycoside hydrolases presents unresolved mechanistic questions, particularly the controversy surrounding the proposed mechanism involving a zinc-coordinated cysteine nucleophile and a thioglycosyl enzyme intermediate. A synthesized beta-l-arabinofuranosidase inhibitor reacts exclusively with the cysteine thiol catalytic nucleophiles of GH families 127 and 146, supporting further research into the breakdown of the thioglycosyl enzyme intermediate. X-ray crystal structures and simulations provide insight into the mechanisms of zinc-coordinated cysteine as the catalytic nucleophile and the energetics of this unique metalloenzyme clan.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Raja Bhaiyya, Sukesh Chander Sharma, Ravindra Pal Singh
Summary: Human consumption of larch arabinogalactan enhances probiotic microflora and promotes the production of short-chain fatty acids in the gut. This study explores the biochemistry of a bacterial member of the Lachnospiraceae family, B. producta ATCC 27340, and identifies an enzyme (Bp0469) that plays a role in utilizing non-cellulosic fiber in the gut. The findings contribute to understanding the nutritional perspective of B. producta ATCC 27340 and its potential industrial applications in producing important arabinogalactan oligosaccharides (AGOs).
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Samkelo Malgas, Mpho S. Mafa, Brian N. Mathibe, Brett I. Pletschke
Summary: Understanding the compatibility of different GH family combinations is crucial for efficient depolymerization of biomass into fermentable sugars. Synergistic enzyme cocktails for biomass saccharification should take into consideration the GH family affiliations of the CAZymes used.
Article
Chemistry, Physical
Jorick Franceus, Jolien Lormans, Lore Cools, Matthias D'hooghe, Tom Desmet
Summary: The study demonstrates significant phosphorylase activity can be established in GH3 glycoside hydrolases through single-site substitutions and further optimized through mutational paths. These findings suggest new insights into developing phosphorylases and provide a novel approach for future research in this field.
Review
Biochemistry & Molecular Biology
Xi Jiang, Qing Yang
Summary: Glycoside hydrolase family 20 (GH20) and GH84 are involved in glycoprotein modification, metabolism, and degradation, with potential applications in disease treatment and plant protection. The challenges lie in designing highly selective inhibitors due to the similarity of their active sites. Understanding the catalytic mechanism and substrate binding mode of Hex and OGA provides crucial information for inhibitor design.
BIOORGANIC CHEMISTRY
(2024)
Article
Biotechnology & Applied Microbiology
Zhenyuan Si, Yang Cai, Lang Zhao, Lu Han, Feng Wang, Xiaobing Yang, Xiangdong Gao, Meiling Lu, Wei Liu
Summary: In this study, an arabinofuranosidase (ThAbf1) belonging to the glycoside hydrolase 51 (GH51) family was expressed, characterized, and functionally determined from the genome of the white-rot fungus Trametes hirsuta. It was found that ThAbf1 synergized with commercial xylanase (XYL) and increased the saccharification efficiency of arabinoxylan.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Physical
Shubha Singh, Jebin Ahmed, Parmeshwar Vitthal Gavande, Carlos M. G. A. Fontes, Arun Goyal
Summary: This study investigated the structure and function of family 30 glycoside hydrolase from Ruminococcus flavefaciens. The results revealed the catalytic residues and ligand binding characteristics of the enzyme. Experimental techniques were used to validate the structural features and stability of the enzyme, providing various conformational information in solution.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Biotechnology & Applied Microbiology
Hao Shi, Feng Gao, Xing Yan, Qingfei Li, Xinling Nie
Summary: This study characterized a glycoside hydrolase 51 family alpha-L-arabinofuranosidase (TtAbf51) from thermophile Thermoanaerobacterium thermosaccharolyticum DSM 571. The enzyme showed optimal activity at 55℃ and pH 5.5, and exhibited stability at pH 5.0-8.0 and up to 60℃. It was inhibited by Cu2+, Zn2+, and SDS. The enzyme had residual activity in the presence of arabinose and showed good catalytic effect for both synthesized and natural substrates.
Article
Biology
Alsu Nazipova, Olga Makshakova, Liudmila Kozlova
Summary: Plant alpha-l-arabinofuranosidases, belonging to the glycoside hydrolase (GH) family 51, play a role in removing terminal arabinose from arabinose-containing substrates in plants. The presence of a CBM4-like domain at the N-terminus is a characteristic feature of GH51 family proteins and is found in almost 90% of plant sequences. However, mutations in the catalytic site of GH51 proteins in Poales may render them inactive. Analyzing transcription and translation data, it was found that arabinoxylan is a more favorable ligand for maize GH51 enzymes than arabinan.
Article
Biotechnology & Applied Microbiology
Mpho S. Mafa, Samkelo Malgas, Brett I. Pletschke
Summary: The study found that the feruloyl esterase can work in synergy with GH10 xylanases to efficiently degrade arabinoxylans in cereal feedstocks, offering potential applications in industries such as animal feeds and baking.
Article
Biochemistry & Molecular Biology
Casey Crooks, Nathan J. Bechle, Franz J. St John
Summary: This study characterized a non-reducing terminal (NRT)-specific xylobiohydrolase AcXbh30A, which strictly cleaves xylobiose from the NRT with minimal other hydrolysis products under optimized reaction conditions. This new xylobiohydrolase may be useful for commercial production of industrial quantities of xylobiose.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Medicinal
Dianyi Li, Zheng Wang, Yong Yu, Huirong Li, Wei Luo, Bo Chen, Guoqing Niu, Haitao Ding
Summary: A novel GH2 beta-galactosidase from Marinomonas sp. BSi20584 was successfully expressed in E. coli and showed stable soluble form. The purified enzyme had a specific activity of 96.827 U mg(-1) at 30 degrees C using ONPG as a substrate. It had an optimum pH of 7.0 and an optimum temperature of 50 degrees C. The enzyme's activity was enhanced by some divalent cations and inhibited by EDTA. Despite being derived from a cold-adapted strain, the enzyme exhibited considerable stability against various physical and chemical elements. It also showed activity towards rare substrates. The enzyme is a promising candidate for the industrial application of beta-galactosidase.
Article
Biochemistry & Molecular Biology
Huitang Qi, Xi Jiang, Yi Ding, Tian Liu, Qing Yang
Summary: Kasugamycin, an aminoglycoside antibiotic, has been found to be a competitive inhibitor of glycoside hydrolase family 18 (GH18) chitinases in various organisms. It was discovered that the electrostatic interaction between kasugamycin and a conserved aspartate in GH18 chitinase is vital for its inhibitory activity. This research not only identifies new molecular targets of kasugamycin but also expands the understanding of GH inhibitor design by utilizing a scaffold unrelated to the substrate.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Agriculture, Multidisciplinary
Laura Plaza-Vinuesa, Oswaldo Hernandez-Hernandez, Ana Sanchez-Arroyo, Jose M. Cumella, Nieves Corzo, Ana M. Munnoz-Labrador, F. Javier Moreno, Blanca de las Rivas, Rosario Munoz
Summary: This study confirmed the myrosinase-like activity of Lactiplantibacillus plantarum WCFS1, indicating that glucosinolates in this strain may undergo phosphorylation and the glycosidases belonging to the GH1 family are involved in the hydrolysis of phosphorylated glucosinolates.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Mariana A. B. Morais, Joan Coines, Mariane N. Domingues, Renan A. S. Pirolla, Celisa C. C. Tonoli, Camila R. Santos, Jessica B. L. Correa, Fabio C. Gozzo, Carme Rovira, Mario T. Murakami
Summary: Family 43 glycoside hydrolases (GH43) are involved in the breakdown of hemicellulose. Functional, structural and computational characterization of a GH43 enzyme, including a snapshot of an active Michaelis complex, reveal the hydrolysis mechanism and suggest two possible reaction pathways.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Valeria R. Turowski, Diego M. Ruiz, Andrey F. Z. Nascimento, Claudia Millan, Massimo D. Sammito, Judith Juanhuix, Aline Sampaio Cremonesi, Isabel Uson, Priscila O. Giuseppe, Mario T. Murakami
Summary: The study revealed potential differences in cargo selection and recognition mechanisms of plant-specific myosins MyoXIs compared to those of animals and fungi, with the unique alpha 5-alpha 6 loop in the GTD potentially serving a structural stabilizing role.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Plinio S. Vieira, Isabela M. Bonfim, Evandro A. Araujo, Ricardo R. Melo, Augusto R. Lima, Melissa R. Fessel, Douglas A. A. Paixao, Gabriela F. Persinoti, Silvana A. Rocco, Tatiani B. Lima, Renan A. S. Pirolla, Mariana A. B. Morais, Jessica B. L. Correa, Leticia M. Zanphorlin, Jose A. Diogo, Evandro A. Lima, Adriana Grandis, Marcos S. Buckeridge, Fabio C. Gozzo, Celso E. Benedetti, Igor Polikarpov, Priscila O. Giuseppe, Mario T. Murakami
Summary: Xyloglucans are polysaccharides found in plant cell walls. The phytopathogenic Xanthomonas bacteria have a xyloglucan depolymerization machinery, and the sugars released by this system induce the expression of key virulence factors driving pathogenesis.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Lucelia Cabral, Gabriela F. Persinoti, Douglas A. A. Paixao, Marcele P. Martins, Mariana A. B. Morais, Mariana Chinaglia, Mariane N. Domingues, Mauricio L. Sforca, Renan A. S. Pirolla, Wesley C. Generoso, Clelton A. Santos, Lucas F. Maciel, Nicolas Terrapon, Vincent Lombard, Bernard Henrissat, Mario T. Murakami
Summary: In this study, Cabral et al. analyzed the gut microbiome of capybara, the largest living rodent, and identified enzymatic mechanisms for the breakdown of lignocellulosic biomass. They also discovered two families of carbohydrate-active enzymes. The findings shed light on the microbial community composition and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, and provide insights into the untapped reservoir of enzymatic mechanisms in the capybara gut microbiota.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Paulla Vieira Rodrigues, Joao Vitor Pereira de Godoy, Beatriz Pelegrini Bosque, Dionisio Pedro Amorim Neto, Katiane Tostes, Soledad Palameta, Sheila Garcia-Rosa, Celisa Caldana Costa Tonoli, Hernandes Faustino de Carvalho, Matheus de Castro Fonseca
Summary: Parkinson's disease is a neurodegenerative disease that can originate in the enteric nervous system and spread to the brain. Enteroendocrine cells in the gut may play a key role in the development of Parkinson's disease. Alpha-synuclein is involved in this process.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Dionisio Pedro Amorim Neto, Beatriz Pelegrini Bosque, Joao Vitor Pereira de Godoy, Paulla Vieira Rodrigues, Dario Donoso Meneses, Katiane Tostes, Celisa Caldana Costa Tonoli, Hernandes Faustino de Carvalho, Christian Gonzalez-Billault, Matheus de Castro Fonseca
Summary: This research found a higher abundance of Akkermansia muciniphila in fecal samples of Parkinson's disease patients and showed that the composition of A. muciniphila conditioned medium is influenced by the strain's ability to degrade mucin. Experimental results indicate that bacterial proteins can induce alpha-synuclein aggregation in enteroendocrine cells, but buffering mitochondrial calcium can reverse the damaging effects.
Article
Biochemistry & Molecular Biology
Mariana Abrahao Bueno Morais, Joice Helena Paiva, Mario Tyago Murakami
Summary: Carbohydrate-binding modules (CBMs) are independently folded domains associated with carbohydrate-active enzymes (CAZymes). The high-resolution SAD-solved structure of a CBM from family 3 (BsCBM3) that binds to crystalline cellulose is reported, showing molecular plasticity and structural differences between crystalline forms. Variations in the cellulose binding interface were observed, supporting the idea that family 3 CBMs are structurally dynamic and suggesting a role in polysaccharide recognition and enzyme activity modulation.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Rosa L. Cordeiro, Camila R. Santos, Mariane N. Domingues, Tatiani B. Lima, Renan A. S. Pirolla, Mariana A. B. Morais, Felippe M. Colombari, Renan Y. Miyamoto, Gabriela F. Persinoti, Antonio C. Borges, Marcelo A. de Farias, Fabiane Stoffel, Chao Li, Fabio C. Gozzo, Marin van Heel, Marcelo E. Guerin, Eric J. Sundberg, Lai-Xi Wang, Rodrigo V. Portugal, Priscila O. Giuseppe, Mario T. Murakami
Summary: This study elucidated the key biochemical steps and molecular mechanisms by which Bifidobacterium longum utilizes high-mannose N-glycans, providing insights into the utilization of this perennial carbon and energy source in the intestinal lumen.
NATURE CHEMICAL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Mariana Abrahao Bueno Morais, Alba Nin-Hill, Carme Rovira
Summary: The enzymatic breakdown of carbohydrates is important for biological events and sustainable production of bioproducts and biofuels. Designing efficient inhibitors for glycosidases and engineering carbohydrate-active enzymes is crucial. Computer simulations have provided insights into the atomic details of carbohydrate conformations and catalytic reactions. This review focuses on how the active-site topology and mode of cleavage affect the catalytic mechanisms of glycosidases.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Priscila O. Giuseppe, Isabela M. Bonfim, Mario T. Murakami
Summary: Xanthomonas plant pathogens have developed sophisticated strategies to overcome plant defenses using multiple secretion systems and virulence factors. They possess a diverse repertoire of Carbohydrate-Active enzymes (CAZymes) that not only enable them to utilize complex plant carbohydrates, but also play important roles in virulence and bacterial lifestyle. These CAZymes are often organized in multienzymatic systems similar to Bacteroidetes' Polysaccharide Utilization Loci (PUL) known as CUT systems. Xanthomonas bacteria also produce distinct exopolysaccharides, such as xanthan gum, associated with biofilm formation.
ESSAYS IN BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
V. R. Bevilaqua, Mariele C. Carvalho, Gabriel F. Pelentir, Atilio Tomazini, Mario Murakami, Vadim R. Viviani
Summary: The study demonstrated that deletion of the C-terminal domain significantly affected the overall bioluminescence activities and slightly impacted the oxidative activities of luciferases. The results indicated that the C-terminal plays a crucial role in shielding the active site during the light emitting step, contributing to the adenylation reaction and bioluminescence coloration.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2021)