Article
Biochemistry & Molecular Biology
Melanie Paul, Melissa Teubner, Benjamin Grimm-Lebsanft, Soeren Buchenau, Alexander Hoffmann, Michael Ruebhausen, Sonja Herres-Pawlis
Summary: The study describes the tyrosinase-like activity of hybrid guanidine-stabilized bis(mu-oxido) dicopper(III) complexes. Aromatic hybrid guanidine amine ligands with varying amine donor function were developed and their copper(I) complexes were analyzed for their ability to activate dioxygen. The resulting bis(mu-oxido) species showed remarkable activity in catalytic oxygenation reactions of polycyclic aromatic alcohols, while maintaining selectivity in the hydroxylation reactions of challenging phenolic substrates.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Melanie Paul, Alexander Hoffmann, Sonja Herres-Pawlis
Summary: The development of copper(I) guanidine halide complexes capable of activating molecular oxygen at room temperature for catalytic hydroxylation reactions on polycyclic aromatic alcohols under mild conditions is highlighted. The selective formation of reactive quinones provides a promising tool for designing phenazine derivatives with medical applications. This research represents a significant advancement in the development of synthetic catalysts inspired by natural enzymes for organic transformation reactions.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2021)
Article
Chemistry, Inorganic & Nuclear
Yaru Liu, Yongjun Liu
Summary: This study investigates the catalytic mechanism of PqqB by combining QM/MM calculations. The results show that PqqB first catalyzes the first hydroxylation step using a highly reactive FeIV-oxo species, followed by the second hydroxylation step using a Fe-O2 species. The bidentate coordination of the catechol moiety to iron plays a crucial role in the one-electron oxidation of the substrate and the superoxide radical attack, and Asp90 and His240 act as acid-base catalysts in the proton transfer and orientation of the superoxide.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Jane M. Donnelly, Frederik Lermyte, Juliusz A. Wolny, Marc Walker, Ben G. Breeze, Russell J. Needham, Christina S. Muller, Peter B. O'Connor, Volker Schunemann, Joanna F. Collingwood, Peter J. Sadler
Summary: A stable square-planar Cu(iii) complex, [bis(toluene-3,4-dithiolato)copper(iii)][NEt3H], has been synthesised and characterised using various analytical techniques. Interestingly, a unique [(toluene-3,4-dithiolato)Cu(iii)(peroxide)](-) complex is formed when the complex is fragmented in FTICR-MS upon reaction with oxygen. Additionally, natural 1,2-dithiolenes known to bind molybdenum may play a role in stabilising Cu(iii) in vivo.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Yasuyuki Matoba, Kosuke Oda, Yoshimi Muraki, Taro Masuda
Summary: The study showed that the presence of metallochaperone caddie protein (Cad) enables tyrosinase (Ty) to catalyze the catecholase reaction more effectively than the phenolase reaction. Mutations at the N191 residue can decrease the inherent ratio of phenolase versus catecholase activity. The increased basicity of the water molecule may be necessary for inhibiting the proton transfer in the catalytic cycle.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Laurel Pegram, Demian Riccardi, Natalie Ahn
Summary: Using long molecular dynamics simulations, this study reveals the unexpected flexibility of the A-loop in ERK2 kinase and its coupling with the active site dynamics. The simulations show distinct conformational states of the A-loop in both phosphorylated and unphosphorylated forms, with the phosphorylated form exhibiting restrained dynamics and reduced mobility in the active site. These findings enhance our understanding of ERK2 regulation.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Ioannis Kipouros, Agnieszka Stanczak, Jake W. Ginsbach, Prokopis C. Andrikopoulos, Lubomir Rulsek, Edward I. Solomon
Summary: Melanins are important biopolymer pigments that provide photoprotection, and their biosynthesis involves the catalytic role of tyrosinase (Ty). This study combines spectroscopic, kinetic, and computational methods to investigate the mechanism of the rate-limiting step in melanin biosynthesis. The results provide insights into the O-2 activation and reactivity by the active sites of coupled binuclear copper, with implications in biocatalysis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Yao Wu, Cong Zhao, Yanzhuang Su, Sason Shaik, Wenzhen Lai
Summary: The copper-dependent formylglycine-generating enzyme (FGE) catalyzes the oxygen-dependent oxidation of specific peptidyl-cysteine residues to formylglycine. Our QM/MM calculations provide a likely mechanism for this transformation, suggesting the involvement of a triplet Cu-II-superoxide complex and a Cu-I-alkylperoxo intermediate. The results also indicate that the aldehyde oxygen of the final product originates from O-2.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Inorganic & Nuclear
Thomas Rotaermel, Pascal Specht, Jonathan Becker, Adam Neuba, Siegfried Schindler
Summary: In the active site of copper monooxygenases, thioether residues coordinate through the sulfur atom. The reaction between dioxygen and copper(I) complexes with thioether groups was investigated, and the formation of labile intermediates and copper(II) complexes was detected. The finding of increased stability in the formed superoxido copper complex by replacing the ethyl group with a methyl group in a specific derivative was particularly interesting. Ozone measurements were conducted to explore alternative ways to obtain and stabilize labile intermediates.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2023)
Article
Crystallography
Larisa A. A. Varfolomeeva, Anastasia Yu. Solovieva, Nikolai S. S. Shipkov, Olga G. G. Kulikova, Natalia I. I. Dergousova, Tatiana V. V. Rakitina, Konstantin M. M. Boyko, Tamara V. V. Tikhonova, Vladimir O. O. Popov
Summary: This study investigates the role of F436 residue in the copper center formation and catalytic process of Thiocyanate dehydrogenase (TcDH). Through mutant construction and crystal structure analysis, it was found that F436 plays a structural role in the active site of TcDH, rather than participating in copper ion binding. This has significant implications for understanding the catalytic mechanism of TcDH.
Article
Chemistry, Multidisciplinary
Ryan P. Sweeney, Phillip M. Danby, Andreas Geissner, Ryan Karimi, Jesper Brask, Stephen G. Withers
Summary: Efforts have been made to find better amylase mutants through high-throughput screening, aided by the development of efficient active site titration reagents for quantitation of active mutants in crude cell lysates. The designed reagent incorporates a highly reactive fluorogenic leaving group onto unsaturated cyclitol ethers, providing a convenient titrant for alpha-amylases down to low nanomolar levels.
Article
Biochemistry & Molecular Biology
Jessica Alves Nunes, Rodrigo Santos Aquino de Araujo, Fabricia Nunes da Silva, Joanna Cytarska, Krzysztof Z. Laczkowski, Silvia Helena Cardoso, Francisco Jaime Bezerra Mendonca-Junior, Edeildo Ferreira da Silva-Junior
Summary: Cancer is a serious global health problem, with melanoma as the most aggressive and fatal type of skin cancer. Coumarin-based compounds, such as FN-19, have shown potential as anti-melanoma agents and tyrosinase inhibitors. The study demonstrated that FN-19 exhibited potent anti-tyrosinase activity, acting as a mixed inhibitor, and its binding with tyrosinase was stabilized by van der Waals interactions. The data obtained from this study will be valuable for the development of novel coumarin-based analogs targeting the tyrosinase enzyme.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Kathryn H. Gunn, Saskia B. Neher
Summary: Lipoprotein lipase (LPL) hydrolyzes triglycerides from circulating lipoproteins, and the structure of an active LPL dimer reveals a hydrophobic pore adjacent to the active site. The dimerization interface and pore may play a role in substrate specificity and acyl chain release from LPL.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Inorganic & Nuclear
Pascal Specht, Alexander Petrillo, Jonathan Becker, Siegfried Schindler
Summary: The intramolecular ligand hydroxylation of copper(I) imine complexes during their reaction with dioxygen was systematically studied, revealing three different reaction pathways depending on the ligand system. The clip-and-cleave concept offers a facile way to oxygenate aldehydes or ketones. The mechanism and outcome of the reaction are strongly influenced by factors such as steric effects, chelate ring size, and coordination number of the ligand system.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2021)
Article
Chemistry, Physical
Matthew N. Podgorski, Joshua S. Harbort, Joel H. Z. Lee, Giang T. H. Nguyen, John B. Bruning, William A. Donald, Paul Bernhardt, Jeffrey R. Harmer, Stephen G. Bell
Summary: In this study, it was found that mutating a highly conserved threonine residue in CYP199A4 to glutamate can convert it to a peroxygenase and improve its peroxygenase activity. The crystal structure of the mutant demonstrated a change in spin state upon substrate binding, which was linked to the modification of the oxygen-binding groove and the retention of the iron-bound aqua ligand. The detailed characterization of this engineered heme peroxygenase will aid in the development of new methods for the selective C-H bond activation using heme enzymes.
Article
Biotechnology & Applied Microbiology
Erandika H. Hemamali, Laksiri P. Weerasinghe, Hideaki Tanaka, Genji Kurisu, Inoka C. Perera
Summary: The utilization of genetically engineered bacterial strains for hydrocarbon degradation is a sustainable solution for pollution treatment and industrial applications. This study focuses on a putative transcriptional regulator named LcaR, which affects the expression of alkB2 and lcaR genes and has potential applications in bioengineering.
Article
Biophysics
Stanislav D. Zakharov, Sergei Savikhin, Yuko Misumi, Genji Kurisu, William A. Cramer
Summary: This study confirms the absence of a significant interaction between FNR and the b(6)f complex through thermodynamic analysis. It also provides a precedent for considering protein-detergent interactions in ITC analyses.
BIOPHYSICAL JOURNAL
(2022)
Review
Biochemistry & Molecular Biology
Genji Kurisu
Summary: Protein Data Bank (PDB) is the only global archive of experimentally determined biological macromolecular structures, and deposition to PDB is mandatory for publication of structural articles. The archive contains many structures from Asian institutions, with Japan being the first Asian country to have a structure deposited in PDB. The long-term collaboration between PDB and the Journal of Biochemistry (J. Biochem) allowed for statistical analysis of structural reports in various aspects such as yearly distribution, resolution, structure quality, target protein type, and citation.
JOURNAL OF BIOCHEMISTRY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Genji Kurisu, Tomitake Tsukihara
Summary: This article presents the X-ray structure of a ferredoxin from Spirulina platensis, providing valuable insights into the structural research of the photosynthetic electron transport chain.
JOURNAL OF BIOCHEMISTRY
(2022)
Article
Chemistry, Physical
Toru Kondo, Risa Mutoh, Shun Arai, Genji Kurisu, Hirozo Oh-Oka, Satoru Fujiyoshi, Michio Matsushita
Summary: This study investigates the polarization dependence and role of red-Bchl g in the photosynthetic reaction center. A candidate molecule for red-Bchl g is proposed based on fluorescence spectra and structural data. The study finds that while the energy transfer network in the reaction center can be perturbed by local conformational dynamics, the overall energy transfer efficiency remains relatively stable.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Gert-Jan Bekker, Masashi Yokochi, Hirofumi Suzuki, Yasuyo Ikegawa, Takeshi Iwata, Takahiro Kudou, Kei Yura, Toshimichi Fujiwara, Takeshi Kawabata, Genji Kurisu
Summary: Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB), has continuously improved and expanded its query search interface and services over the past 20 years, making significant contributions to the acceptance, processing, and distribution of experimentally determined biological macromolecular structures. During the COVID-19 pandemic, PDBj has also provided feature pages for COVID-19 related entries and outreach content for high school students and teachers.
Review
Biochemistry & Molecular Biology
John D. Westbrook, Jasmine Y. Young, Chenghua Shao, Zukang Feng, Vladimir Guranovic, Catherine L. Lawson, Brinda Vallat, Paul D. Adams, John M. Berrisford, Gerard Bricogne, Kay Diederichs, Robbie P. Joosten, Peter Keller, Nigel W. Moriarty, Oleg Sobolev, Sameer Velankar, Clemens Vonrhein, David G. Waterman, Genji Kurisu, Helen M. Berman, Stephen K. Burley, Ezra Peisach
Summary: PDBx/mmCIF is a data standard for structural biology, used for storing and disseminating three-dimensional structures of biological macromolecules. Developed collaboratively over three decades, involving contributions from multiple scientific disciplines, it accelerates the pace of scientific discovery.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Microscopy
Christoph Gerle, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi, Orkun coruh, Fumiaki Makino, Tomoko Miyata, Akihiro Kawamoto, Ken Yokoyama, Keiichi Namba, Genji Kurisu, Takayuki Kato
Summary: Progress in structural membrane biology has been greatly enhanced by the "Resolution Revolution" in cryo-electron microscopy (cryo-EM), particularly the use of single-particle analysis for determining atomic models of multisubunit membrane protein complexes. However, there is a growing need for new and affordable cryo-electron microscopes to meet the increasing demand for cryo-EM machine time.
Article
Biochemistry & Molecular Biology
Keizo Yamamoto, Hideaki Tanaka, Genji Kurisu, Ryuichi Nakano, Hisakazu Yano, Hiromi Sakai
Summary: IMP-type metallo-beta-lactamases confer resistance to carbapenems and a broad spectrum of beta-lactam antibiotics. The difference in amino acid at position 262 alters the flexibility of the loop region, affecting substrate specificity and affinity. This may result in treatment failure.
JOURNAL OF BIOCHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Toshiyuki Sasaki, Takanori Nakane, Akihiro Kawamoto, Tomohiro Nishizawa, Genji Kurisu
Summary: Solid-state grinding can produce mechano-distinctive co-crystals not obtainable from solutions. In this study, the structure of a powdered mechano-distinctive co-crystal of 2-aminopyrimidine and succinic acid in a 2:1 molar ratio was determined using microcrystal electron diffraction.
Article
Biochemistry & Molecular Biology
Tomoki Nakayoshi, Yusuke Ohnishi, Hideaki Tanaka, Genji Kurisu, Hiroko X. Kondo, Yu Takano
Summary: In this study, molecular dynamics simulations were used to investigate the differences between oxidized and reduced models of plant-type ferredoxins (Fds). The simulations showed no significant differences in global conformation, but the reduction of the active center affected the hydrogen-bond network and compactness of surrounding residues, leading to increased flexibility of a key side chain.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jeffrey C. Hoch, Kumaran Baskaran, Harrison Burr, John Chin, Hamid R. Eghbalnia, Toshimichi Fujiwara, Michael R. Gryk, Takeshi Iwata, Chojiro Kojima, Genji Kurisu, Dmitri Maziuk, Yohei Miyanoiri, Jonathan R. Wedell, Colin Wilburn, Hongyang Yao, Masashi Yokochi
Summary: BMRB is an international open data repository for biomolecular NMR data, which has applications in various research fields. Advances in technology have led to the increasing use of NMR data in the biosciences.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Seolmin Ko, Akiyuki Toda, Hideaki Tanaka, Jian Yu, Genji Kurisu
Summary: In this study, the X-ray crystal structure of the human inner-arm dynein-d (DNAH1) stalk region was determined, revealing differences in the conformation and diverse orientations in the microtubule-binding domain (MTBD). A "spike shoe model" was proposed to explain the interaction between IAD-d and microtubules at an altered stepping angle. The findings provide insights into the isoform-specific functions of axonemal dynein stalk MTBDs.
Letter
Biochemical Research Methods
Wenqing Xu, Sameer Velankar, Ardan Patwardhan, Jeffrey C. Hoch, Stephen K. Burley, Genji Kurisu
Summary: The Protein Data Bank (PDB) is a global archive of atomic-level, three-dimensional structures of biological macromolecules. Recently, there has been an increase in new structure depositions from Asia. In 2022, Protein Data Bank China (PDBc) joined the Worldwide Protein Data Bank (wwPDB) as an Associate Member. This letter discusses the history of wwPDB, the mechanisms for adding new data centers, and the processes for incorporating PDBc into the partnership.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Ryusei Matsumoto, Saho Yoshioka, Miho Yuasa, Yoshitsugu Morita, Genji Kurisu, Nobutaka Fujieda
Summary: We repurposed a cupin superfamily protein's metal-binding site into a 2-His-1-carboxylate facial triad to create artificial metalloenzymes capable of catalyzing new reactions. The Cu2+-H52A/H58E variant was able to catalyze a stereoselective Michael addition reaction and had a flexible metal-binding site in its crystal structure. Additionally, the H52A/H58E/F104W mutant accommodated a water molecule, leading to high stereoselectivity through hydrogen bonding. Thus, the 2-His-1-carboxylate facial triad is a versatile and promising metal-binding motif for both abiological and canonical biological reactions.