Article
Chemistry, Physical
Phebe H. van Langevelde, Errikos Kounalis, Lars Killian, Emily C. Monkcom, Daniel L. J. Broere, Dennis G. H. Hetterscheid
Summary: This study reports a dinuclear copper complex inspired by the active site of multicopper oxidases (MCOs), which undergoes a proton-coupled electron transfer pathway during its electrochemical reduction process, resulting in a larger overpotential. The study also reveals the role of metal-metal cooperativity and the constraints of a rigid ligand framework in catalysis, leading to an improved selectivity for the oxygen reduction reaction (ORR) due to better stabilization of reaction intermediates between the copper centers.
Article
Biochemistry & Molecular Biology
Murillo Peterlini Tavares, Thiago Rodrigues Dutra, Tulio Morgan, Rafaela Zandonade Ventorim, Rafaela Ines de Souza Ladeira Azar, Ednilson Mascarenhas Varela, Roberta Corsino Ferreira, Tiago Antonio de Oliveira Mendes, Sebastiao Taveres de Rezende, Valeria Monteze Guimaraes
Summary: The genome of the phytopathogenic fungus Chrysoporthe cubensis contains distinct groups of multicopper oxidase (MCO) coding genes, including laccases, which have potential for biotechnological applications. In this study, the complete genomic arsenal of MCOs from C. cubensis was identified and characterized. Laccases were induced, purified, and tested for improving sugarcane bagasse saccharification. The fungal cultivation in different lignocellulosic biomass yielded more efficient enzymatic extracts than commercial preparations, with the highest laccase activity detected in the crude extract of the fungus cultivated on wheat bran and orange peel (3:1).
PROCESS BIOCHEMISTRY
(2022)
Article
Chemistry, Inorganic & Nuclear
Irene R. A. M. Ogutu, Richard C. Holz, Brian Bennett
Summary: Research has shown that an eight amino acid peptide based on the metal binding motif of Co-type nitrile hydratase from Pseudonocardia thermophilia can coordinate Fe(II) under anaerobic conditions. Exposure to air results in the formation of a low-spin Fe(III)-peptide complex, similar to the nitrile hydratase from Rhodococcus equi TG328-2.
INORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Alina K. Bakunova, Alena Yu. Nikolaeva, Tatiana V. Rakitina, Tatiana Y. Isaikina, Maria G. Khrenova, Konstantin M. Boyko, Vladimir O. Popov, Ekaterina Yu. Bezsudnova
Summary: This study elucidated a new D-amino acid transaminase with high specificity towards D-amino acids and their analogs, demonstrating unique active site residues compared to previously studied transaminases. The presence of critical residues for catalytic activity and the suggestion of arginine residues' functions based on structural analysis, mutagenesis, and modeling indicate a novel insight into the substrate specificity of this enzyme. The characteristics of Halhy contribute to our understanding of substrate specificity and structure-function relationships in D-amino acid transaminases.
Article
Biochemical Research Methods
Christos Kosinas, Anastasia Zerva, Evangelos Topakas, Maria Dimarogona
Summary: This study focuses on understanding the structure-function determinants of a novel laccase-like multicopper oxidase, TtLMCO1, from the thermophilic fungus Thermothelomyces thermophila. The crystal structure of TtLMCO1, determined using an AlphaFold2 model, revealed a three-domain laccase with two copper sites, lacking the C-terminal plug observed in other ascolaccases. Analysis of solvent tunnels identified crucial amino acids for proton transfer, while docking simulations provided structural evidence for the enzyme's promiscuity in oxidizing ortho-substituted phenols.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Zhenwei Zhang, Norbert Rigo, Olexandr Dybkov, Jean-Baptiste Fourmann, Cindy L. Will, Vinay Kumar, Henning Urlaub, Holger Stark, Reinhard Luehrmann
Summary: During the splicing process, the integration of U2 small nuclear ribonucleoprotein into the spliceosomal A complex is facilitated by the DEAD-box helicase Prp5. Research reveals that the RNA duplex formed by U2 small nuclear RNA is proofread by Prp5, and the U2-BS helix is formed in the pre-A complex. The study further shows a large-scale remodelling of U1 and U2 snRNPs and how the binding of Hsh155(HEAT) triggers closure, disrupting Prp5 binding.
Article
Chemistry, Physical
Daiqiang Li, Lian Wang, Yuqin Lu, Hua Deng, Zhilin Zhang, Yingjie Wang, Ying Ma, Tingting Pan, Qian Zhao, Yulong Shan, Xiaoyan Shi, Jinzhu Ma, Hong He
Summary: In this study, regulation of active sites in zeolites with different Si/Al ratios was used to achieve Pt/Beta catalysts with different valence states, locations, and dispersion of Pt for toluene oxidation. The Pt/Beta catalysts with high silica showed better catalytic oxidation performance than those with low silica, due to the stronger activation ability towards O2 and more facile oxygen replenishment of Pt0. Moreover, Pt0 was found to be more conducive to the benzene ring opening reaction.
APPLIED CATALYSIS B-ENVIRONMENTAL
(2023)
Article
Biochemistry & Molecular Biology
Guolyu Xu, Huizhao Su, Lining Lu, Xiaomeng Liu, Liang Zhao, Bo Tang, Zhenhua Ming
Summary: This study reports the structural characteristics of ubiquitin-specific protease 34 (USP34) and the mechanism of ubiquitin recognition. The results show that upon binding with ubiquitin, the conformation of USP34 changes, and the catalytic triad is rearranged. This structural transition is closely related to the gripping of ubiquitin by the fingertips of USP34.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Physical
Vania Brissos, Patricia T. Borges, Reyes Nunez-Franco, Maria Fatima Lucas, Carlos Frazao, Emanuele Monza, Laura Masgrau, Tiago N. Cordeiro, Ligia O. Martins
Summary: This study characterizes the molecular features of the evolution of a hyperthermostable metallo-oxidase from the multicopper oxidase family into a laccase by combining mutagenesis with structural, kinetic, and in silico analyses. The results show that residue replacements and distal mutations modulate substrate binding and catalysis, and allosterically coupled, long-range dynamic networks favor catalytically competent conformational states.
Article
Environmental Sciences
Efstratios Nikolaivits, Romanos Siaperas, Andreas Agrafiotis, Jamal Ouazzani, Antonios Magoulas, Anastasia Giot, Evangelos Topakas
Summary: This study screened novel fungal strains isolated as symbionts of marine invertebrates for their ability to remove 2,4,5-trichlorobiphenyl (PCB29) and isolated two enzymes exhibiting laccase activity, with one of them showing improved ability to remove PCB29 in the presence of mediators. RNAseq analysis of the strain revealed a diverse repertoire of multicopper oxidases involved in laccase activities.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Nanoscience & Nanotechnology
Yue Ding, Yong Shi, Wei Xiong, Jian Heng Sun, Cheng Li, Ya Qi Zhang, Jing Guo
Summary: In this study, a CuFe-N/C bimetallic catalyst was prepared and applied for CO selective catalytic reduction of NO. The synergistic effect of bimetallic Cu-Fe sites was revealed, providing insights into the electron transfer mechanism and laying the foundation for understanding N-coordinated bimetallic site synergy and designing highly active catalysts.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Chemistry, Physical
Leilei Dai, Nan Zhou, Kirk Cobb, Paul Chen, Yunpu Wang, Yuhuan Liu, Rongge Zou, Hanwu Lei, Badr A. Mohamed, Yanling Cheng, Roger Ruan
Summary: This study investigates the effects of acid density and pore structure on the catalytic performance. The results show that the Bronsted acid site density has a profound impact on catalyst lifetime and aromatic selectivity, with a non-linear correlation. Additionally, an increase in mesoporosity extends the catalyst lifetime.
APPLIED CATALYSIS B-ENVIRONMENTAL
(2022)
Review
Chemistry, Inorganic & Nuclear
Bashir Adegbemiga Yusuf, Waleed Yaseen, Suci Meng, Jimin Xie, Funmilayo O. Fapohunda, Rosalynn Nankya, Atika Ibrahim Muhammad, Meng Xie, Yuanguo Xu
Summary: In recent years, research interest in electrocatalytic CO2 reduction reaction (CO2RR) has grown due to its potential to recycle CO2 into valuable chemicals. However, determining the catalytic active centers and understanding structure-performance relationships in catalysts, such as copper-based catalysts, is challenging due to their intrinsic variation during operation. This review focuses on identifying electroactive centers in the CO2RR and discusses the dynamic evolution characteristics, operando characterization methodologies, and the potential of the CO2 pulse-mode electrolysis process.
COORDINATION CHEMISTRY REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Hanzhong Deng, Mingming Qin, Zhijun Liu, Ying Yang, Yefei Wang, Lishan Yao
Summary: Conformational dynamics plays a crucial role in enzyme catalysis, and engineering these dynamics to improve catalytic efficiency remains challenging. In this study, a new strategy is developed to enhance the activity of yeast cytosine deaminase by modulating its conformational dynamics. By extending the C-terminal helix, which serves as an active site lid, the product release rate and overall catalytic rate are significantly increased. The favorable activation entropy change is identified as the main contributor to the improved catalytic efficiency. This study introduces a novel dynamics engineering approach that accelerates catalysis through an entropy-driven mechanism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Nirupa Nagaratnam, Silvia L. Delker, Rebecca Jernigan, Thomas E. Edwards, Janey Snider, Darren Thifault, Dewight Williams, Brent L. Nannenga, Mary Stofega, Lidia Sambucetti, James J. Hsieh, Andrew J. Flint, Petra Fromme, Jose M. Martin-Garcia
Summary: Taspase1 is an Ntn-hydrolase overexpressed in primary human cancers, with its activity closely related to the proliferation, invasion, and metastasis of cancer cells. This study reveals the structure and function of the active site of Taspase1, providing a potential target for the development of anticancer therapeutics.
Article
Chemistry, Applied
Takeshi Hiromoto, Koji Nishikawa, Taro Tamada, Yoshiki Higuchi
Summary: X-ray crystallography is a powerful tool for obtaining structural information of protein molecules, but it cannot accurately determine the positions of hydrogen atoms. Neutron crystallography, on the other hand, enables direct identification of hydrogen positions, aiding in understanding the physiological functions of enzymes and catalytic reaction mechanisms.
TOPICS IN CATALYSIS
(2021)
Article
Microbiology
Kentaro Miyazaki, Natsuko Tokito
Summary: The complete genome of Thermus thermophilus strain TMY was resequenced using a hybrid assembly of long-read data from Oxford Nanopore Technologies and short-read data from MGI. Correction of errors in the previously reported genome sequence obtained solely from PacBio technology enabled high-quality comparative genomic analysis of closely related T. thermophilus genomes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Kentaro Miyazaki, Natsuki Tomariguchi, Yuko Ueno
Summary: The four Thermus thermophilus strains isolated from Arima Hot Spring in Japan showed high nucleotide identity to each other and those from the same spot, but lower identity to strains from geographically different spots, indicating habitat-specific genomic conservation.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Kentaro Miyazaki
Summary: In this study, extremely thermophilic strains belonging to the genus Thermus were isolated from Senami Hot Spring in Japan. The complete genome sequences of these strains, including five Thermus thermophilus strains and one Thermus brockianus strain, were obtained using a combination of Oxford Nanopore long-read and DNBSEQ or Illumina short-read sequencing data.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Microbiology
Kentaro Miyazaki, Kae Hosoya
Summary: Four Parageobacillus strains were isolated from soil in Japan and their genomes were fully sequenced. Three of the strains showed high nucleotide identity (>=98.9%) to Parageobacillus caldoxylosilyticus 51812, while one strain, designated KH3-4, showed the highest nucleotide identity (91%) to Parageobacillus thermantarcticus M1, suggesting the novelty of the species KH3-4.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Chemistry, Multidisciplinary
Naoki Shibata, Yoshiki Higuchi, Bernhard Krautler, Tetsuo Toraya
Summary: The X-ray structures of coenzyme B-12 (AdoCbl)-dependent eliminating isomerases complexed with adenosylmethylcobalamin (AdoMeCbl) have been determined. The Co-C bond in diol dehydratase (DD) is not activated even in the presence of substrate. In ethanolamine ammonia-lyase (EAL), the bond is elongated in the absence of substrate, and in the presence of substrate, the complex likely exists in both pre- and post-homolysis states. The flexibility and rigidity of the active sites in the two enzymes may reflect the tightness of adenine binding.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Morito Sakuma, Shingo Honda, Hiroshi Ueno, Kazuhito V. Tabata, Kentaro Miyazaki, Nobuhiko Tokuriki, Hiroyuki Noji
Summary: Enzymes display heterogeneity in their conformational and functional states, which is crucial for the evolution of new functions. A single-molecule enzyme assay was used to analyze functional substates in wild-type and mutant alkaline phosphatase. Mutant enzymes exhibited significantly heterogeneous functional substates, while the wild-type enzyme showed a highly homogeneous substate. The degree of functional substates correlated with the improvement in promiscuous activities. The findings highlight the importance of functional substates in enzyme evolution.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Shunsuke Kato, Koki Takeuchi, Motonao Iwaki, Kentaro Miyazaki, Kohsuke Honda, Takashi Hayashi
Summary: Affinity purification of recombinant proteins is an essential technique in biotechnology. However, current methods are costly, limiting their versatile use. To address this issue, we developed the CSAP system, using commercially available chitin powder as a chromatography matrix for low-cost purification of Strep-tag II fusion proteins. We demonstrated the system's effectiveness in protein screening using 96-well format, identifying potential candidates for an abiotic carbene transfer reaction.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Morito Sakuma, Shingo Honda, Hiroshi Ueno, Kazuhito V. Tabata, Kentaro Miyazaki, Nobuhiko Tokuriki, Hiroyuki Noji
Summary: Enzymes have inherent heterogeneity in their conformational and functional states, which is key to the evolution of new functions. Single-molecule enzyme assays allow direct observation of these multiple functional substates. We analyzed functional substates in wild-type and mutant Escherichia coli alkaline phosphatase and found that mutant enzymes exhibited significantly heterogeneous functional substates, while the wild-type enzyme showed a highly homogeneous substate. Our study provides comprehensive evidence that functional substates can be easily altered by mutations and that the evolution towards new catalytic activities may involve modulation of these substates.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Cheng Xie, Hiromitsu Shimoyama, Masaru Yamanaka, Satoshi Nagao, Hirofumi Komori, Naoki Shibata, Yoshiki Higuchi, Yasuteru Shigeta, Shun Hirota
Summary: Research has shown that enhancing the hydrogen bond network at the hinge region can stabilize the structure of myoglobin dimer, further supporting the connection between myoglobin dimer and monomer through 3D domain swapping.
Article
Microbiology
Kentaro Miyazaki, Toshiyuki Moriya, Natsuko Tokito, Tairo Oshima, Kei Yura, Yoshitaka Bessho
Summary: The Thermus thermophilus strains isolated from the same spot in Mine Hot Spring, Japan, showed a higher level of genetic similarity compared to strains from geographically different places in Japan.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Kentaro Miyazaki, Toshiyuki Moriya, Naoki Nemoto, Tairo Oshima, Kei Yura, Yoshitaka Bessho
Summary: The Thermus thermophilus strain HB5018 isolated from Mine Hot Spring in Japan has a 99.1% average nucleotide identity with the type strain HB8, indicating strict species conservation in the habitat over the past 50 years.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Kentaro Miyazaki, Hikaru Suenaga, Mamoru Oshiki, Shuichi Kawano, Toshikazu Fukushima
Summary: Thiohalobacter sp. strain COW1, a bacterium capable of degrading thiocyanate, was isolated from activated sludge treating coke oven wastewater, and its complete genome sequence was determined to contain a single circular chromosome with 2,788 protein-coding genes, 39 tRNA genes, and 3 rRNA genes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Kentaro Miyazaki, Erina Hase, Natsuko Tokito
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)
Article
Microbiology
Kentaro Miyazaki, Erina Hase, Tomomasa Maruya
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)