Article
Plant Sciences
Thomas Asensio, Cyril Dian, Jean-Baptiste Boyer, Frederic Riviere, Thierry Meinnel, Carmela Giglione
Summary: The text introduces the characteristics of protein N-acetyltransferases and a new high-throughput assay that can better understand the substrate specificity and activity of any GNAT.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Mengxue Xu, Xia Liu, Xiaoyan Li, Lin Chen, Shengzhe Li, Bo Sun, Dongqing Xu, Tingting Ran, Weiwu Wang
Summary: Acetylation is a widely conserved modification catalyzed by acetyltransferases that participate in diverse biological processes. In this study, the crystal structure of the putative GCN5-N-acetyltransferase PgbP in complex with CoA was determined. The structure analysis revealed the presence of two CoA-binding cavities in the PgbP dimer. Moreover, the biochemical studies demonstrated that PgbP is a prodigiosin-binding protein with high thermal stability. This study provides new insights into the multifunctionality of GNAT family members and the biological activities of prodigiosin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Plant Sciences
Aiste Ivanauskaite, Marjaana Rantala, Laura Laihonen, Minna M. Konert, Naike Schwenner, Jens S. Muehlenbeck, Iris Finkemeier, Paula Mulo
Summary: This study reveals the important role of the GNAT gene family in chloroplast-related metabolism and photosynthesis in Arabidopsis thaliana. The results show that GNAT enzymes affect the accumulation of chloroplast-related compounds and amino acids and their derivatives. The loss of GNAT enzymes leads to increased levels of nucleic acids and nucleases in the chloroplasts, but does not have significant effects on carbon assimilation.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Multidisciplinary Sciences
P. Shirmast, S. M. Ghafoori, R. M. Irwin, J. Abendroth, S. J. Mayclin, D. D. Lorimer, Thomas E. Edwards, Jade K. Forwood
Summary: GNAT enzymes play important roles in biological processes by catalyzing acetylation of various substrates. This study characterized the high-resolution structure of a GNAT enzyme bound with acetyl-CoA, revealing a new dimer interface and suggesting diverse oligomeric assemblies. The structure presented in this study can be utilized for future computational docking and structure-activity studies.
SCIENTIFIC REPORTS
(2021)
Review
Genetics & Heredity
Onyekachi E. Ononye, Michael Downey
Summary: This review summarizes the types and functions of posttranslational modifications that regulate Gcn5 in both yeast and human cells. Common themes, unanswered questions, and strategies for future research are also outlined.
Article
Biochemistry & Molecular Biology
Jackson T. Baumgartner, Thahani S. Habeeb Mohammad, Mateusz P. Czub, Karolina A. Majorek, Xhulio Arolli, Cillian Variot, Madison Anonick, Wladek Minor, Miguel A. Ballicora, Daniel P. Becker, Misty L. Kuhn
Summary: Enzymes in the GNAT superfamily play crucial roles in cellular processes, with recent studies showing their capability of catalyzing various reactions beyond acetyl transfer. This study on the Pseudomonas aeruginosa PA3944 enzyme reveals the use of a nucleophilic serine residue and a hybrid ping-pong mechanism for catalysis, challenging the traditional acid/base mechanism attributed to GNATs. The findings suggest that different active site residues are utilized by these enzymes to achieve a range of catalytic reactions, questioning the current paradigm of GNAT mechanisms.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Van Thi Bich Le, Sofiya Tsimbalyuk, Ee Qi Lim, Allan Solis, Darwin Gawat, Paloma Boeck, Ee Qing Lim, Rosselini Renolo, Jade K. Forwood, Misty L. Kuhn
Summary: Polyamines play crucial roles in regulating various biological processes, with SSATs acting as catabolic enzymes that acetylate polyamines to maintain intracellular homeostasis. The bacterial SSAT protein SpeG, found in pathogens like Vibrio cholerae, has a unique dodecameric structure with an allosteric site. This study identified specific structural elements, such as the allosteric loop and beta 6-beta 7 elements, as critical for the enzyme kinetic activity of SpeG, providing insights into the structure/function relationship and evolutionary aspects of GNAT family members.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Cell Biology
Sofiya Tsimbalyuk, Aleksander Shornikov, Parul Srivastava, Van Thi Bich Le, Imani Warren, Yogesh B. B. Khandokar, Misty L. L. Kuhn, Jade K. K. Forwood
Summary: Polyamines play diverse roles in numerous pathogenic and non-pathogenic organisms, affecting the transcription and translation of key genes and proteins. The bacterial SpeG enzyme exhibits a unique structure and function compared to other SSATs, and its role in different bacterial pathogens varies. This study provides new insight into the structure and function of the SpeG enzyme, shedding light on its molecular role in pathogenic and non-pathogenic bacteria.
Article
Microbiology
Kristen M. Jew, Van Thi Bich Le, Kiana Amaral, Allysa Ta, Nina M. Nguyen May, Melissa Law, Nicole Adelstein, Misty L. Kuhn
Summary: Acetylation is a protein post-translational modification that can influence cellular processes. Two mechanisms of N epsilon-acetylation have been identified in bacteria - non-enzymatic/chemical acetylation and enzymatic acetylation. This study focused on determining the 3D location of lysine residues that are acetylated by E. coli enzymes and investigating their conservation in homologs. The results revealed discrepancies between linear amino acid sequences and 3D structures in assessing lysine residue conservation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biology
Dominik Layer, Juergen Kopp, Miriam Fontanillo, Maja Koehn, Karine Lapouge, Irmgard Sinning
Summary: Layer et al. present a crystal structure of Naa20, the catalytic subunit of an N-terminal acetyltransferase NatB, in complex with its competitive inhibitor CoA-Ac-MDEL. They find that Naa20 alone can acetylate NatB in vitro while Naa25, the auxiliary subunit of Naa20, increases the substrate affinity of Naa20. This study provides insights into the development of NAT inhibitors.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Qing Wang, Lingxin Kong, Xiaoqing Zheng, Jufang Shen, Junbo Wang, Dashan Zhang, Yongjian Qiao, Jinjin Wang, Zixin Deng, Delin You
Summary: The study revealed that anil catalyzes acylation of the hydroxyl group of the pyrrolidine ring and is tolerant of diverse acyl donors and acceptors, making the biosynthesis of compound 1 and its derivatives more efficient. The overexpression of anil serves as a successful example of genetic manipulation for high production of final products, setting the stage for future metabolic engineering.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Cillian Variot, Daniel Capule, Xhulio Arolli, Jackson Baumgartner, Cory Reidl, Charles Houseman, Miguel A. Ballicora, Daniel P. Becker, Misty L. Kuhn
Summary: In this study, we investigated how the PA3944 enzyme from Pseudomonas aeruginosa recognizes different acceptor substrates and identified critical residues for substrate specificity. By mutating seven amino acid residues to alanine, we determined their effects on the kinetic parameters of PA3944. We found that certain residues improved the affinity and catalytic efficiency of PA3944 towards NANMO and/or polymyxin B. Additionally, one mutant (R106A) showed substrate inhibition towards NANMO, and we propose potential reasons for this inhibition based on further substrate docking studies with R106A.
Article
Microbiology
Emily Hsieh, Derek H. A. Janssens, Patrick J. E. Paddison, Edward P. A. Browne, Steve E. Henikoff, Molly A. OhAinle, Michael E. Emerman
Summary: By developing a new CRISPR screening strategy called "Latency HIV-CRISPR", we gained insights into the mechanisms controlling the latency of HIV-1. Our study found that the ING3 component of the NuA4 HAT complex acts in synergy with AZD5582 to activate latent HIV-1 proviruses. This research is important for understanding the maintenance mechanisms of HIV-1 latency.
Article
Materials Science, Multidisciplinary
Kseniya Girel, Aliaksandr Burko, Aliaksei Barysiuk, Sergey Dubkov, Dmitry Gromov, Hanna Bandarenka
Summary: We propose a method to identify the time point of Ag particle formation with prominent SERS activity during Ag wet electroless deposition on macro-PS by measuring the decrease in surface potential. The most intense SERS spectra of DTNB were collected on macro-PS covered with Ag particles for 20 minutes. We claim a TNB detection limit of 2 x 10(-9) M by considering the chemisorption of monomolecular TNB layer on the surface of Ag structures. The analytical enhancement factor was calculated to be approximately 0.7 x 10(7).
CURRENT APPLIED PHYSICS
(2023)
Article
Biotechnology & Applied Microbiology
Antonio Garcia-Moyano, Yuleima Diaz, Jose Navarro, David Almendral, Pal Puntervoll, Manuel Ferrer, Gro Elin Kjaereng Bjerga
Summary: To support the development of environment-friendly processes and products in the bio-based industry, an optimal toolbox of biocatalysts is crucial. Functional screen of (meta)genomic libraries can potentially identify new enzymes, but discovering enzymes that meet industry compliance demands remains challenging, especially in the case of proteases. This study demonstrated the use of six industry-relevant animal and plant by-products as complementary substrates in functional screens, suggesting temperature as a screening parameter to potentially discover new broad-substrate range and robust proteases.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Marek Grabowski, Joanna M. Macnar, Marcin Cymborowski, David R. Cooper, Ivan G. Shabalin, Miroslaw Gilski, Dariusz Brzezinski, Marcin Kowiel, Zbigniew Dauter, Bernhard Rupp, Alexander Wlodawer, Mariusz Jaskolski, Wladek Minor
Summary: In response to the global mobilization to combat the current pandemic, a large amount of new structural data has emerged, leading to the development of multiple resources for evaluating the quality of data. A method is described to evaluate these data, which can be used in large-scale initiatives in future biomedical crises, enhancing the reproducibility of biomedical research.
Article
Biochemistry & Molecular Biology
Jackson T. Baumgartner, Thahani S. Habeeb Mohammad, Mateusz P. Czub, Karolina A. Majorek, Xhulio Arolli, Cillian Variot, Madison Anonick, Wladek Minor, Miguel A. Ballicora, Daniel P. Becker, Misty L. Kuhn
Summary: Enzymes in the GNAT superfamily play crucial roles in cellular processes, with recent studies showing their capability of catalyzing various reactions beyond acetyl transfer. This study on the Pseudomonas aeruginosa PA3944 enzyme reveals the use of a nucleophilic serine residue and a hybrid ping-pong mechanism for catalysis, challenging the traditional acid/base mechanism attributed to GNATs. The findings suggest that different active site residues are utilized by these enzymes to achieve a range of catalytic reactions, questioning the current paradigm of GNAT mechanisms.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Editorial Material
Biochemistry & Molecular Biology
Wladek Minor, Mariusz Jaskolski, Seamus J. Martin, Zbigniew Dauter
Summary: This tribute honors Alexander Wlodawer for his contributions to the community of structural biology researchers, focusing on his dedication to crystallography and structural science, as well as his outstanding contributions to the success of the FEBS Journal.
Editorial Material
Biochemistry & Molecular Biology
Mariusz Jaskolski, Alexander Wlodawer, Zbigniew Dauter, Wladek Minor, Bernhard Rupp
Article
Biochemistry & Molecular Biology
Wladek Minor, Marcin Cymborowski, Dominika Borek, David R. Cooper, Maksymilian Chruszcz, Zbyszek Otwinowski
Summary: The HKL-3000 system integrates various steps of structure determination and has been proven to be valuable in determining high-quality structures. The optimization of the heuristic approach increases the likelihood of successful structure determination with challenging data.
Article
Chemistry, Multidisciplinary
Joanna Loch, Jakub Barciszewski, Joanna Sliwiak, Piotr Bonarek, Paulina Wrobel, Kinga Pokrywka, Ivan G. Shabalin, Wladek Minor, Mariusz Jaskolski, Krzysztof Lewinski
Summary: This study identified alternative ligand-binding sites in the beta-lactoglobulin molecule, providing important evidence through crystal structure analysis. The importance of shape complementarity for ligand recognition and selectivity was highlighted in the analysis.
Article
Chemistry, Multidisciplinary
Mateusz P. Czub, Alan J. Stewart, Ivan G. Shabalin, Wladek Minor
Summary: Serum albumin is a highly conserved circulatory transport protein in mammals that plays an important role in pharmacokinetics. However, this study reveals that ketoprofen exhibits different binding-site preferences when interacting with human serum albumin compared to other mammalian albumins, despite the conservation of binding sites across species. This work emphasizes the importance of understanding organism-dependent differences when assessing the suitability of albumins for structural or biochemical studies.
Article
Biochemistry & Molecular Biology
Michal Gucwa, Joanna Lenkiewicz, Heping Zheng, Marcin Cymborowski, David R. Cooper, Krzysztof Murzyn, Wladek Minor
Summary: Metal ions bound to macromolecules play a vital role in cellular processes, but their unique nature makes them challenging to model and refine, resulting in misidentification or poor refinement in the PDB. CheckMyMetal (CMM) is a widely accepted validation tool for researchers studying metal-macromolecule complexes. The enhanced functionalities of CMM provide additional information and allow for on-the-fly refinement of metal binding sites, improving the reproducibility of biomedical research.
Article
Chemistry, Physical
Joanna Lenkiewicz, Vanessa Bijak, Shrisha Poonuganti, Michal Szczygiel, Michal Gucwa, Krzysztof Murzyn, Wladek Minor
Summary: During the pandemic, structural biologists have collaborated closely with vaccine and treatment development groups. However, relying only on in vitro and clinical studies might not be enough to guide the development of vaccines, treatments, and healthcare policies during virus mutations or peak infections and fatalities. Therefore, it is crucial to track statistical data on the number of infections, deaths, and vaccinations in specific regions and present it in an easily understandable way.
STRUCTURAL DYNAMICS-US
(2023)
Review
Pharmacology & Pharmacy
Vanessa Bijak, Michal Szczygiel, Joanna Lenkiewicz, Michal Gucwa, David R. Cooper, Krzysztof Murzyn, Wladek Minor
Summary: The integration of artificial intelligence into X-ray crystallography has shown great promise in automating and accelerating the analysis of complex structural data, further improving the efficiency and accuracy of structure determination. This is crucial for drug discovery and structural bioinformatics.
EXPERT OPINION ON DRUG DISCOVERY
(2023)
Article
Chemistry, Multidisciplinary
Dongmei Wu, Michal Gucwa, Mateusz P. Czub, David R. Cooper, Ivan G. Shabalin, Remi Fritzen, Swati Arya, Ulrich Schwarz-Linek, Claudia A. Blindauer, Wladek Minor, Alan J. Stewart
Summary: Serum albumin-Co2+ interactions are clinically important and play a role in cobalt toxicity and the diagnosis of myocardial ischemia. Crystallographic structures of human and equine serum albumin in complex with Co2+ were obtained, revealing prominent metal-binding sites. Mutagenesis and ITC studies characterized the Co2+ binding sites on human serum albumin and showed the presence of weak-affinity Co2+ binding sites. Fatty acids were found to reduce the Co2+ binding affinity. These findings provide a comprehensive understanding of Co2+ binding to serum albumin.
Meeting Abstract
Chemistry, Multidisciplinary
Michal Gucwa, Joanna Lenkiewicz, Heping Zheng, Marcin Cymborowski, David Cooper, Krzysztof Murzyn, Wladek Minor
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2022)
Meeting Abstract
Chemistry, Multidisciplinary
Marek Grabowski, Marcin Cymborowski, David Cooper, Przemyslaw Porebski, Wladek Minor
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2021)
Meeting Abstract
Chemistry, Multidisciplinary
Wladek Minor, Marek Grabowski, David Cooper, Ivan Shabalin, Zbigniew Dauter, Marcin Cymborowski, Dariusz Brzezinski, Joanna M. Macnar
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2021)
Meeting Abstract
Chemistry, Multidisciplinary
Wladek Minor
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2021)