Structural and functional characterization of FabG4 from Mycolicibacterium smegmatis
The rise in antimicrobial resistance is a global health crisis and necessitates the development of novel strategies to treat infections. For example, in 2022 tuberculosis (TB) was the second leading infectious killer after COVID-19, with multi-drug-resistant strains of TB having an ∼ 40% fatality rate. Targeting essential biosynthetic pathways in pathogens has proven to be successful for the development of novel antimicrobial treatments. Fatty-acid synthesis (FAS) in bacteria proceeds via the type II pathway, which is substantially different from the type I pathway utilized in animals. This makes bacterial fatty-ac...
Source: Acta Crystallographica Section F - April 24, 2024 Category: Biochemistry Authors: Ran, X. Parikh, P. Abendroth, J. Arakaki, T.L. Clifton, M.C. Edwards, T.E. Lorimer, D.D. Mayclin, S. Staker, B.L. Myler, P. McLaughlin, K.J. Tags: Mycobacterium FabG structural genomics Seattle Structural Genomics Center for Infectious Disease NIAID oxidoreductases HMwFabG Mycolicibacterium smegmatis Mycobacterium smegmatis Mycobacterium tuberculosis research communications Source Type: research
Beyond publishing: introducing Interviews with authors
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 1, 2024 Category: Biochemistry Authors: Nonato, M.C. van Raaij, M.J. Agirre, J. Tags: interviews with authors publishing early career researchers editorial Source Type: research
Cryo-EM sample preparation for high-resolution structure studies
High-resolution structures of biomolecules can be obtained using single-particle cryo-electron microscopy (SPA cryo-EM), and the rapidly growing number of structures solved by this method is encouraging more researchers to utilize this technique. As with other structural biology methods, sample preparation for an SPA cryo-EM data collection requires some expertise and an understanding of the strengths and limitations of the technique in order to make sensible decisions in the sample-preparation process. In this article, common strategies and pitfalls are described and practical advice is given to increase the chances of su...
Source: Acta Crystallographica Section F - March 26, 2024 Category: Biochemistry Authors: Wang, L. Zimanyi, C.M. Tags: cryo-electron microscopy specimen preparation high-resolution structure determination single-particle analysis topical reviews Source Type: research
The unbearable burden of peer review?
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 1, 2024 Category: Biochemistry Authors: van Raaij, M.J. Tags: peer review editorial Source Type: research
Crystallization and biochemical studies of the NYN domain of human KHNYN
KHNYN is composed of an N-terminal KH-like RNA-binding domain and a C-terminal PIN/NYN endoribonuclease domain. It forms a complex with zinc-finger antiviral protein (ZAP), leading to the degradation of viral or cellular RNAs depending on the ZAP isoform. Here, the production, crystallization and biochemical analysis of the NYN domain (residues 477 – 636) of human KHNYN are presented. The NYN domain was crystallized with a heptameric single-stranded RNA from the AU-rich elements of the 3 ′ -UTR of interferon lambda 3. The crystal belonged to space group P4132, with unit-cell parameters a = b = c = 111.3 Å , ...
Source: Acta Crystallographica Section F - February 20, 2024 Category: Biochemistry Authors: Hong, S. Choe, J. Tags: KHNYN ZAP RNases antivirals research communications Source Type: research
Expression, purification and crystallization of the photosensory module of phytochrome B (phyB) from Sorghum bicolor
This study describes the development of an efficient heterologous overproduction system which allows the production of large quantities of various holoprotein constructs, along with purification and crystallization procedures. Crystals of the Pr (red-light-absorbing) forms of NPGP, PGP and PG (residues 1 – 655, 114 – 655 and 114 – 458, respectively), each C-terminally tagged with His6, were successfully produced. While NPGP crystals did not diffract, those of PGP and PG diffracted to 6 and 2.1 Å resolution, respectively. Moving the tag to the N-terminus and replacing phytochromobilin with phycocyanobilin as the ...
Source: Acta Crystallographica Section F - February 20, 2024 Category: Biochemistry Authors: Shenkutie, S.M. Nagano, S. Hughes, J. Tags: Sorghum bicolor phytochrome B maturity crystallization diffraction quality research communications Source Type: research
Structure of the GDP-bound state of the SRP GTPase FlhF
This study presents the X-ray structure of FlhF in its GDP-bound state at a resolution of 2.28 Å . The structure exhibits the classical N- and G-domain fold, consistent with related SRP GTPases such as Ffh and FtsY. Comparative analysis with GTP-loaded FlhF elucidates the conformational changes associated with GTP hydrolysis. These topological reconfigurations are similarly evident in Ffh and FtsY, and play a pivotal role in regulating the functions of these hydrolases. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 20, 2024 Category: Biochemistry Authors: Dornes, A. Mais, C.-N. Bange, G. Tags: flagellar assembly SRP GTPases FlhF nucleotides research communications Source Type: research
Private glycan investigations and public video content
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 1, 2024 Category: Biochemistry Authors: van Raaij, M.J. Tags: video content Privateer carbohydrate structural biology editorial Source Type: research
Crystal structure and biophysical characterization of IspD from Burkholderia thailandensis and Mycobacterium paratuberculosis
The methylerythritol phosphate (MEP) pathway is a metabolic pathway that produces the isoprenoids isopentyl pyrophosphate and dimethylallyl pyrophosphate. Notably, the MEP pathway is present in bacteria and not in mammals, which makes the enzymes of the MEP pathway attractive targets for discovering new anti-infective agents due to the reduced chances of off-target interactions leading to side effects. There are seven enzymes in the MEP pathway, the third of which is IspD. Two crystal structures of Burkholderia thailandensis IspD (BtIspD) were determined: an apo structure and that of a complex with cytidine triphosphate (C...
Source: Acta Crystallographica Section F - January 31, 2024 Category: Biochemistry Authors: Pierce, P.G. Hartnett, B.E. Laughlin, T.M. Blain, J.M. Mayclin, S.J. Bolejack, M.J. Myers, J.B. Higgins, T.W. Dranow, D.M. Sullivan, A. Lorimer, D.D. Edwards, T.E. Hagen, T.J. Horn, J.R. Myler, P.J. Tags: IspD Burkholderia thailandensis Mycobacterium paratuberculosis transferases cytidylyltransferases structural genomics Seattle Structural Genomics Center for Infectious Disease SSGCID research communications Source Type: research
Crystal structure of the RNA-recognition motif of Drosophila melanogaster tRNA (uracil-5-)-methyltransferase homolog A
Human tRNA (uracil-5-)-methyltransferase 2 homolog A (TRMT2A) is the dedicated enzyme for the methylation of uridine 54 in transfer RNA (tRNA). Human TRMT2A has also been described as a modifier of polyglutamine (polyQ)-derived neuronal toxicity. The corresponding human polyQ pathologies include Huntington's disease and constitute a family of devastating neurodegenerative diseases. A polyQ tract in the corresponding disease-linked protein causes neuronal death and symptoms such as impaired motor function, as well as cognitive impairment. In polyQ disease models, silencing of TRMT2A reduced polyQ-associated cell death and p...
Source: Acta Crystallographica Section F - January 25, 2024 Category: Biochemistry Authors: Witzenberger, M. Janowski, R. Niessing, D. Tags: RRMs TRMT2A methyltransferases X-ray crystallography Drosophila melanogaster neurodegenerative disease research communications Source Type: research
Online carbohydrate 3D structure validation with the Privateer web app
Owing to the difficulties associated with working with carbohydrates, validating glycan 3D structures prior to deposition into the Protein Data Bank has become a staple of the structure-solution pipeline. The Privateer software provides integrative methods for the validation, analysis, refinement and graphical representation of 3D atomic structures of glycans, both as ligands and as protein modifiers. While Privateer is free software, it requires users to install any of the structural biology software suites that support it or to build it from source code. Here, the Privateer web app is presented, which is always up to dat...
Source: Acta Crystallographica Section F - January 24, 2024 Category: Biochemistry Authors: Dialpuri, J.S. Bagdonas, H. Schofield, L.C. Pham, P.T. Holland, L. Bond, P.S. S á nchez Rodr í guez, F. McNicholas, S.J. Agirre, J. Tags: Privateer validation polysaccharides carbohydrates N-glycosylation N-glycans web apps methods communications Source Type: research
Structure of the outer membrane porin OmpW from the pervasive pathogen Klebsiella pneumoniae
Conjugation is the process by which plasmids, including those that carry antibiotic-resistance genes, are mobilized from one bacterium (the donor) to another (the recipient). The conjugation efficiency of IncF-like plasmids relies on the formation of mating-pair stabilization via intimate interactions between outer membrane proteins on the donor (a plasmid-encoded TraN isoform) and recipient bacteria. Conjugation of the R100-1 plasmid into Escherichia coli and Klebsiella pneumoniae (KP) recipients relies on pairing between the plasmid-encoded TraN α in the donor and OmpW in the recipient. Here, the crystal structure of K....
Source: Acta Crystallographica Section F - January 1, 2024 Category: Biochemistry Authors: Seddon, C. Frankel, G. Beis, K. Tags: Klebsiella pneumoniae outer membrane porin OmpW bacterial conjugation β -barrel research communications Source Type: research
Biochemical and structural characterization of a class A β -lactamase from Nocardia cyriacigeorgica
In this study, the expression, purification and preliminary biochemical characterization of an ABL from an N. cyriacigeorgica (NCY-1) clinical strain are reported. The crystallization and the very high resolution crystal structure of NCY-1 are also described. The sequence and structural analysis of the protein demonstrate that NCY-1 belongs to the class A1 β -lactamases and show its very high conservation with ABLs from other human-pathogenic Nocardia. In addition, the presence of one molecule of citrate tightly bound in the catalytic site of the enzyme is described. This structure may provide a solid basis for future dru...
Source: Acta Crystallographica Section F - January 1, 2024 Category: Biochemistry Authors: Feuillard, J. Couston, J. Benito, Y. Hodille, E. Dumitrescu, O. Blaise, M. Tags: Nocardia cyriacigeorgica class A β -lactamases -lactam resistance antibiotic resistance -lactams research communications Source Type: research
High-resolution double vision of the allosteric phosphatase PTP1B
Protein tyrosine phosphatase 1B (PTP1B) plays important roles in cellular homeostasis and is a highly validated therapeutic target for multiple human ailments, including diabetes, obesity and breast cancer. However, much remains to be learned about how conformational changes may convey information through the structure of PTP1B to enable allosteric regulation by ligands or functional responses to mutations. High-resolution X-ray crystallography can offer unique windows into protein conformational ensembles, but comparison of even high-resolution structures is often complicated by differences between data sets, including no...
Source: Acta Crystallographica Section F - December 22, 2023 Category: Biochemistry Authors: Sharma, S. Skaist Mehlman, T. Sagabala, R.S. Boivin, B. Keedy, D.A. Tags: protein tyrosine phosphatase 1B allosteric regulation conformational heterogeneity high-resolution crystallography research communications Source Type: research
Direct relationship between dimeric form and activity in the acidic copper – zinc superoxide dismutase from lemon
The copper – zinc superoxide dismutase (CuZnSOD) from lemon (SOD_CL) is active in an acidic environment and resists proteolytic degradation. The enzyme occurs as a dimer, which has an indirect effect on the enzyme activity as the monomer retains only ∼ 35% of the activity. Here, the crystal structure of SOD_CL at 1.86 Å resolution is reported that may explain this peculiarity. The crystal belonged to space group P21, with unit-cell parameters a = 61.11, b = 74.55, c = 61.69 Å , β = 106.86 ° , and contained four molecules in the asymmetric unit. The overall structure of SOD_CL resembles that of CuZn...
Source: Acta Crystallographica Section F - December 1, 2023 Category: Biochemistry Authors: Utami, R.A. Yoshida, H. Kartadinata, L.H. Abdillah, V.A. Faratilla, C.R. Retnoningrum, D.S. Ismaya, W.T. Tags: copper – zinc superoxide dismutases Citrus limon lemon stabilization research communications Source Type: research
