Article
Biochemistry & Molecular Biology
Tetsuya Miyamoto, Shinya Fushinobu, Yasuaki Saitoh, Masae Sekine, Masumi Katane, Kumiko Sakai-Kato, Hiroshi Homma
Summary: This study identified a new D-serine metabolizing activity of the enzyme serine hydroxymethyltransferase (SHMT) in bacteria and mammals. Additionally, it was found that human and E. coli SHMTs have D-serine dehydratase activity. The D-serine dehydratase activity of SHMT is physiologically important for the growth of E. coli.
Article
Chemistry, Multidisciplinary
Robert W. Harkness, Zev A. Ripstein, Justin M. Di Trani, Lewis E. Kay
Summary: DegP is a periplasmic protein involved in the transport of pathogenicity-related virulence factors. It functions as a bi-functional protease and chaperone to maintain protein homeostasis in Gram-negative bacteria under stress conditions. It forms cage-like structures by reorganizing high-order preformed apo oligomers, which can encapsulate clients of various sizes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Ken-ichi Miyazono, Keiko Kubota, Kenji Takahashi, Masaru Tanokura
Summary: Proteases are vital enzymes for life and have significant industrial importance. Understanding the substrate recognition mechanisms of proteases is crucial for enhancing their applications. This study determined the crystal structure of the prolyl endoprotease PEP and revealed the importance of its unique catalytic pocket structure in recognizing protein substrates.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Natalia Stach, Abdulkarim Karim, Przemyslaw Golik, Radoslaw Kitel, Katarzyna Pustelny, Natalia Gruba, Katarzyna Groborz, Urszula Jankowska, Sylwia Kedracka-Krok, Benedykt Wladyka, Marcin Drag, Adam Lesner, Grzegorz Dubin
Summary: By studying the substrate specificity and structure of SplF, it was found that the enzyme has a strict preference for long aliphatic sidechains at the P1 subsite and significant selectivity for aromatic residues at P3, with its crystal structure defining the structural basis of this substrate specificity. Comparisons with other Spl proteases suggest that the spl operon encodes a unique extracellular proteolytic system.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ryushi Kawakami, Tatsuya Ohshida, Junji Hayashi, Kazunari Yoneda, Toshio Furumoto, Toshihisa Ohshima, Haruhiko Sakuraba
Summary: The Orn-AT activity of the enzyme encoded by the PH1423 gene from Pyrococcus horikoshii OT-3 was detected. Crystal structures of this novel archaeal omega-aminotransferase were determined in complex with pyridoxal 5'-phosphate (PLP), in complex with PLP and L-ornithine (L-Orn), and in complex with N-(5'-phosphopyridoxyl)-L-glutamate (PLP-L-Glu). The P. horikoshii OrnAT monomer showed notable similarity to that of human Orn-AT. However, the residues recognizing the alpha-amino group of L-Orn differed between the two enzymes. Asp93* was found to play a critical role in maintaining high affinity for the substrate. The structure of the enzyme with the reaction-intermediate analogue PLP-L-Glu bound provided the first structural evidence for the Glu switch mechanism in the dual substrate specificity of Orn-AT.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Multidisciplinary
Manuel Cordova, Lyndon Emsley
Summary: The determination of the molecular solid structure using NMR crystallography relies on generating a comprehensive set of candidate crystal structures and comparing computed chemical shifts with experimental values. However, exploring the polymorph landscape of molecular solids requires a significant computational power, leading to a bottleneck in candidate crystal generation. This study constructs three-dimensional interaction maps using a crystal structure database with associated chemical shifts to identify structural constraints for accelerating crystal structure prediction protocols, without requiring DFT-level chemical shift computations.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Microbiology
Yi Ding, Laiyin Nie, Xiao-Chen Yang, Yang Li, Ying-Yi Huo, Zhengyang Li, Yan Gao, Heng-Lin Cui, Jixi Li, Xue-Wei Xu
Summary: This study identified and characterized an alkalophilic esterase, E53, from a marine bacterium. The crystal structures of E53 and its variants were solved using X-ray diffraction, and functional studies revealed the role of different regions in the catalytic reaction and pH pattern of E53.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Medicine, General & Internal
Masataka Kawamura, Atsushi Hesaka, Ayumu Taniguchi, Shigeaki Nakazawa, Toyofumi Abe, Makoto Hirata, Ryuichi Sakate, Masaru Horio, Shiro Takahara, Norio Nonomura, Yoshitaka Isaka, Ryoichi Imamura, Tomonori Kimura
Summary: This study explored the potential of D-serine clearance as a measure of GFR, showing that D-serine underestimated C-in levels but combining D-serine and creatinine measurements can reduce this bias, providing a more accurate method for GFR measurement.
Review
Psychiatry
Amir Meftah, Hiroshi Hasegawa, Joshua T. Kantrowitz
Summary: D-Serine, a potential treatment for psychiatric and neurological conditions, has been limited in human studies due to concerns of nephrotoxicity observed in rats. However, D-serine induced nephrotoxicity has not been reported in other species and only one subject in human studies showed abnormal renal values, which resolved after stopping treatment. DAAO inhibitors may have nephroprotective effects.
FRONTIERS IN PSYCHIATRY
(2021)
Article
Chemistry, Inorganic & Nuclear
Zhehui Weng, Xiaohua Zhou, Jie Ling, Pengzhi Xiang, Yao Huang, Haidong Ju, Shengchun Chen, Zhihui Zhang
Summary: Five new coordination assemblies of substituted zinc(II) isophthalates and H(2)pbbp linkers have been synthesized under hydrothermal conditions, exhibiting different layer structures and supramolecular networks. The properties of these compounds, including thermal stability, powder X-ray diffractions, infrared spectra and luminescence, have been investigated.
JOURNAL OF SOLID STATE CHEMISTRY
(2022)
Article
Chemistry, Physical
Taro Udagawa, Hinata Yabushita, Hikaru Tanaka, Kazuaki Kuwahata, Masanori Tachikawa
Summary: Curcumin and its derivatives have intramolecular low-barrier hydrogen bonds for intramolecular proton transfer. The pi-delocalization in the OCCCO framework of the hydrogen bond in these compounds is reorganized concomitantly with the proton transfer. Path integral molecular dynamics simulations were performed to characterize the hydrogen bond and pi-delocalization, revealing a weak correlation between proton migration and reorganization of the pi-delocalized structure.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Dunlu Yuan, Jiaqing Li, Min Guo, Qing Yang, Jingjing Huang, Jingwen Nie, Ruomei Li, Qing Li
Summary: This study investigated the expression of fibroblast growth factor 23 (FGF23) and D-serine in maintenance hemodialysis (MHD) patients with hearing impairment, and explored the correlation between FGF23/D-serine and hearing impairment. The results showed that MHD patients with hearing impairment had significantly higher levels of FGF23 and D-serine compared to those with normal hearing and normal controls. Elevated FGF23 and D-serine were identified as risk factors for hearing impairment in end-stage renal disease (ESRD).
Article
Microbiology
Fa Dai, Ming Guo, Yina Shao, Chenghua Li
Summary: The study identified a novel T3SS effector protein, STPKLRR, in Vibrio splendidus AJ01. It was found that STPKLRR could phosphorylate AjTmod and promote cytoskeleton rearrangement, leading to self-internalization of the bacteria.
Article
Biochemistry & Molecular Biology
Ju Hyeong Kim, Gwan Hee Lee, Jae-Hee Jeong, Yeon-Gil Kim, Hyun Ho Park
Summary: Protein quality control mechanisms are crucial for cellular integrity, and the HtrA family of serine proteases plays a key role in folding stress in the prokaryotic periplasm. This study presents the structure of MucD from Pseudomonas syringae, revealing its similarities and differences with other HtrA family members. The study also provides a model of psMucD's catalytic process.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Patrick Cottingham, Richard L. Brutchey
Summary: We investigated the local structure of BaTiO3 nanocrystals using pair distribution function analysis, and found that the Ti4+ displacements in the local structure have the same coherence length as the overall perovskite structure.
Article
Biochemistry & Molecular Biology
Kotaro Koiwai, Kazue Inaba, Kana Morohashi, Sora Enya, Reina Arai, Hirotatsu Kojima, Takayoshi Okabe, Yuuta Fujikawa, Hideshi Inoue, Ryunosuke Yoshino, Takatsugu Hirokawa, Koichiro Kato, Kaori Fukuzawa, Yuko Shimada-Niwa, Akira Nakamura, Fumiaki Yumoto, Toshiya Senda, Ryusuke Niwa
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biochemical Research Methods
Ryuichi Kato, Masahiko Hiraki, Yusuke Yamada, Mikio Tanabe, Toshiy Senda
Summary: The PXS system is a fully automated protein crystallization and monitoring system that can automatically set up crystallization plates, transfer, observe, and monitor crystallization drops. As time has passed, user demands have changed, requiring screening with smaller amounts of proteins, and membrane proteins have become a primary target for X-ray crystallography.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Evdokia-Anastasia Giannopoulou, Miki Senda, Maharani Pertiwi Koentjoro, Naruhiko Adachi, Naoto Ogawa, Toshiya Senda
Summary: LTTRs are a large family of transcriptional regulators in bacteria, typically homo-tetrameric proteins that interact with promoter DNA. Studies show that LTTR binding to promoter DNA bends the DNA, and upon inducer binding, the tetrameric LTTR undergoes structural changes leading to transcription activation. The crystal structure of full-length LTTR CbnR in complex with its promoter DNA reveals the mechanism of quaternary structure changes necessary for promoter region-binding.
Article
Entomology
Kotaro Koiwai, Kana Morohashi, Kazue Inaba, Kana Ebihara, Hirotatsu Kojima, Takayoshi Okabe, Ryunosuke Yoshino, Takatsugu Hirokawa, Taiki Nampo, Yuuta Fujikawa, Hideshi Inoue, Fumiaki Yumoto, Toshiya Senda, Ryusuke Niwa
Summary: The development of IGRs involves elucidating the molecular mechanisms of insect-specific biological events, with insect molting and metamorphosis controlled by ecdysteroids serving as targets for IGR development. The conserved Nobo plays a crucial role in ecdysteroid biosynthesis, and novel non-steroidal DmNobo inhibitors have been identified as potential seed compounds for IGR development. Crystal structure analysis revealed dynamic alterations in amino acid residues upon inhibitor binding, indicating the potential for developing IGRs with greater Nobo inhibitory activity.
JOURNAL OF PESTICIDE SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Yohei Katsuyama, Kaoru Sone, Ayaka Harada, Seiji Kawai, Naoki Urano, Naruhiko Adachi, Toshio Moriya, Masato Kawasaki, Kazuo Shin-ya, Toshiya Senda, Yasuo Ohnishi
Summary: The study determined the structure of FmoA3 using X-ray crystallography and cryogenic electron microscopy, revealing the accommodation of alpha-methyl-l-serine in the active site. The Cy domains of FmoA2 and FmoA3 catalyze different reactions, with the Cy domain of FmoA3 potentially losing its donor PCP binding activity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biology
Yoshihisa Hirakawa, Miki Senda, Kodai Fukuda, Hong Yang Yu, Masaki Ishida, Masafumi Taira, Kazushi Kinbara, Toshiya Senda
Summary: COG4337 proteins are a novel metal-independent variant of iota-class carbonic anhydrases, which accelerate CO2 hydration and are localized in organelles for CO2 metabolism. They share structural features with iota-class CAs but exhibit activity without reliance on metals.
Article
Biology
Miho Watanabe-Takahashi, Masakazu Tamada, Miki Senda, Masahiro Hibino, Eiko Shimizu, Akiko Okuta, Atsuo Miyazawa, Toshiya Senda, Kiyotaka Nishikawa
Summary: The study identified a tetravalent peptide and a monomeric peptide that can inhibit Shiga toxin (Stx) by targeting its receptor-binding and inhibiting catalytic activity, respectively. These peptides demonstrate potent inhibition of two functionally distinct subunits of Stx, providing a potential intervention for the pathogenic mechanism of enterohemorrhagic Escherichia coli.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Takamasa Teramoto, Takeshi Koyasu, Naruhiko Adachi, Masato Kawasaki, Toshio Moriya, Tomoyuki Numata, Toshiya Senda, Yoshimitsu Kakuta
Summary: The study of Aquifex RNase P homologs showed that Aq880 enzyme consists of nuclease and protruding helical domains, forming dimers and dodecamers. The cryo-EM structure revealed that Aq880's active site is similar to eukaryotic PRORPs, and its mechanism for processing pre-tRNA resembles that of PRORPs and ribonucleoprotein RNase P.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Naruhiko Adachi, Takahide Yamaguchi, Toshio Moriya, Masato Kawasaki, Kotaro Koiwai, Akira Shinoda, Yusuke Yamada, Fumiaki Yumoto, Takamitsu Kohzuma, Toshiya Senda
Summary: Cu-containing nitrite reductases play central roles in denitrification, but structural analysis of their catalytic mechanisms has been impeded by issues such as crystal packing and photoreduction. Cryo-EM structures of Achromobacter cycloclastes NiR at different pH values were obtained, revealing structural changes and crystallographic artifacts in certain residues. The combination of X-ray and cryo-EM structures provides deeper insight into local structural changes of proteins, despite challenges in estimating coordinate errors in cryo-EM structures.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Halilibrahim Ciftci, Hiroshi Tateishi, Kotaro Koiwai, Ryoko Koga, Kensaku Anraku, Kazuaki Monde, Cagdas Dag, Ebru Destan, Busra Yuksel, Esra Ayan, Gunseli Yildirim, Merve Yigin, F. Betul Ertem, Alaleh Shafiei, Omur Guven, Sabri O. Besler, Raymond G. Sierra, Chun Hong Yoon, Zhen Su, Mengling Liang, Burcin Acar, Turkan Haliloglu, Masami Otsuka, Fumiaki Yumoto, Mikako Fujita, Toshiya Senda, Hasan DeMirci
Summary: The oligomerization of Pr55(Gag) is a critical step in the late stage of the HIV life cycle, with the binding of IP6 at the MA domain playing a key role. The crystal structures of the MA domain in complex with IP6 molecules provide insights into the binding mode, while analysis of key residues and interactions with PIP2 reveal a multilayered assembly process involving coordination between IP6 and PIP2 for membrane localization of virion particles. Additionally, a new model is proposed based on the structures, suggesting that IP6 coordinates the oligomerization of MA and CA domains during assembly and budding.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Natsuki Osaka, Yoshihisa Hirota, Doshun Ito, Yoshiki Ikeda, Ryo Kamata, Yuki Fujii, Venkat R. Chirasani, Sharon L. Campbell, Koh Takeuchi, Toshiya Senda, Atsuo T. Sasaki
Summary: The article provides an overview of post-translational modifications in the RAS G4 and G5 motifs, highlighting their role in RAS activation and potential applications in cancer therapy.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Takuto Kumano, Sanae Hori, Satomi Watanabe, Yuzu Terashita, Hong Yang Yu, Yoshiteru Hashimoto, Toshiya Senda, Miki Senda, Michihiko Kobayashi
Summary: The study identified an enzyme named CarA that plays a crucial role in carminic acid metabolism by oxidizing the sugar moiety. Homologs of CarA were found to be widely distributed in soil microorganisms and important for C-glycoside metabolism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Takahiro Mori, Takuto Kumano, Haibing He, Satomi Watanabe, Miki Senda, Toshio Moriya, Naruhiko Adachi, Sanae Hori, Yuzu Terashita, Masato Kawasaki, Yoshiteru Hashimoto, Takayoshi Awakawa, Toshiya Senda, Ikuro Abe, Michihiko Kobayashi
Summary: Through bioinformatics analysis, researchers identified C-glycoside deglycosidase enzymes in intestinal and soil bacteria, characterized them biochemically, determined their structures, and probed catalytic important residues in mutagenesis experiments. These metal-dependent enzymes exhibit broad substrate specificity toward C-glycosides.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Takuo Minato, Takamasa Teramoto, Naruhiko Adachi, Nguyen Khac Hung, Kaho Yamada, Masato Kawasaki, Masato Akutsu, Toshio Moriya, Toshiya Senda, Seiji Ogo, Yoshimitsu Kakuta, Ki-Seok Yoon
Summary: Takuo Minato and colleagues have identified both a conventional hexameric structure and a novel octameric structure in native C-phycocyanin (CPC) from the thermophilic cyanobacterium Thermoleptolyngbya sp. O77. The observation of an unusual dimeric state via analytical ultracentrifugation suggests a key intermediate structure in the assembly of octameric CPC. These findings offer new insights into the assembly processes of CPCs and the mechanism of energy transfer in light-harvesting complexes.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Takuya Miyakawa, Jian Yang, Masato Kawasaki, Naruhiko Adachi, Ayumu Fujii, Yumiko Miyauchi, Tomonari Muramatsu, Toshio Moriya, Toshiya Senda, Masaru Tanokura
Summary: This study solves the cryo-EM structures of CphA1 and reveals the aspartate binding mode and protein dynamics required for cyanophycin elongation. The research also suggests a potential role of protein dynamics in the catalytic efficiency of the arginine condensation reaction.
NATURE COMMUNICATIONS
(2022)