4.2 Article

New insights into the catalytic active-site structure of multicopper oxidases

出版社

WILEY-BLACKWELL
DOI: 10.1107/S1399004713033051

关键词

-

资金

  1. Ministry of Education, Science, Sports and Culture of Japan [23580131]
  2. fund for Kagawa University Young Scientists
  3. Grants-in-Aid for Scientific Research [24651231, 24119515, 23380197, 23580131, 24657077] Funding Source: KAKEN

向作者/读者索取更多资源

Structural models determined by X-ray crystallography play a central role in understanding the catalytic mechanism of enzymes. However, X-ray radiation generates hydrated electrons that can cause significant damage to the active sites of metalloenzymes. In the present study, crystal structures of the multicopper oxidases (MCOs) CueO from Escherichia coli and laccase from a metagenome were determined. Diffraction data were obtained from a single crystal under low to high X-ray dose conditions. At low levels of X-ray exposure, unambiguous electron density for an O atom was observed inside the trinuclear copper centre (TNC) in both MCOs. The gradual reduction of copper by hydrated electrons monitored by measurement of the Cu K-edge X- ray absorption spectra led to the disappearance of the electron density for the O atom. In addition, the size of the copper triangle was enlarged by a two-step shift in the location of the type III coppers owing to reduction. Further, binding of O-2 to the TNC after its full reduction was observed in the case of the laccase. Based on these novel structural findings, the diverse resting structures of the MCOs and their four-electron O-2-reduction process are discussed.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.2
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Chemistry, Applied

The Challenge of Visualizing the Bridging Hydride at the Active Site and Proton Network of [NiFe]-Hydrogenase by Neutron Crystallography

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

Complete Genome Resequencing of Thermus thermophilus Strain TMY by Hybrid Assembly of Long- and Short-Read Sequencing Technologies

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

Complete Genome Sequences of Four Halophilic Thermus thermophilus Strains Isolated from Arima Hot Spring in Japan

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

Complete Genome Sequences of Thermus Strains Isolated from Senami Hot Spring in Japan

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

Complete Genome Sequences of Four Parageobacillus Strains Isolated from Soil in Japan

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

Structural Insights into the Very Low Activity of the Homocoenzyme B12 Adenosylmethylcobalamin in Coenzyme B12-Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase

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

Genetic Perturbation Alters Functional Substates in Alkaline Phosphatase

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

Chitin- and Streptavidin-Mediated Affinity Purification Systems: A Screening Platform for Enzyme Discovery

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

Genetic Perturbation Alters Functional Substates in Alkaline Phosphatase

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

Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region

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.

RSC ADVANCES (2021)

Article Microbiology

Complete Genome Sequences of Thermus thermophilus Strains HB5002 and HB5008, Isolated from Mine Hot Spring in Japan

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

Complete Genome Sequence of Thermus thermophilus Strain HB5018, Isolated from Mine Hot Spring in Japan

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

Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater

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

Complete Genome Sequence of Geobacillus sp. Strain E55-1, Isolated from Mine Geyser in Japan

Kentaro Miyazaki, Erina Hase, Natsuko Tokito

MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2020)

Article Microbiology

Complete Genome Sequence of Pseudomonas otitidis Strain MrB4, Isolated from Lake Biwa in Japan

Kentaro Miyazaki, Erina Hase, Tomomasa Maruya

MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2020)

暂无数据