Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1
Superoxide dismutase (SOD) is an essential and ubiquitous antioxidant protein that is widely present in biological systems. The anhydrobiotic tardigrades are some of the toughest micro-animals. They have an expanded set of genes for antioxidant proteins such as SODs. These proteins are thought to play an essential role in oxidative stress resistance in critical situations such as desiccation, although their functions at the molecular level have yet to be explored. Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. I...
Source: Acta Crystallographica Section F - June 26, 2023 Category: Biochemistry Authors: Sim, K.-S. Inoue, T. Tags: superoxide dismutases SODs CuZnSODs Ramazzottius varieornatus strain YOKOZUNA-1 tardigrades research communications Source Type: research
AlphaFold and the future of structural biology
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 26, 2023 Category: Biochemistry Authors: Read, R.J. Baker, E.N. Bond, C.S. Garman, E.F. van Raaij, M.J. Tags: AlphaFold protein structure prediction crystallography cryo-EM editorial Source Type: research
Crystal structure of thermostable acetaldehyde dehydrogenase from the hyperthermophilic archaeon Sulfolobus tokodaii
In this study, crystals of recombinant thermostable ALDH from S. tokodaii were prepared and the crystal structure of its holo form was determined. A crystal of the enzyme was prepared and its structure in complex with NADP was determined at a resolution of 2.2 Å . This structural analysis may facilitate further studies on catalytic mechanisms and applications. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - May 25, 2023 Category: Biochemistry Authors: Mine, S. Nakabayashi, M. Ishikawa, K. Tags: thermostability acetaldehyde dehydrogenase aldehydes archaea Sulfolobus tokodaii research communications Source Type: research
Crystal structure of a putative 3-hydroxypimelyl-CoA dehydrogenase, Hcd1, from Syntrophus aciditrophicus strain SB at 1.78 Å resolution
Syntrophus aciditrophicus strain SB is a model syntroph that degrades benzoate and alicyclic acids. The structure of a putative 3-hydroxypimelyl-CoA dehydrogenase from S. aciditrophicus strain SB (SaHcd1) was resolved at 1.78 Å resolution. SaHcd1 contains sequence motifs and structural features that belong to the short-chain dehydrogenase/reductase (SDR) family of NADPH-dependent oxidoreductases. SaHcd1 is proposed to concomitantly reduce NAD+ or NADP+ to NADH or NADPH, respectively, while converting 3-hydroxypimelyl-CoA to 3-oxopimeyl-CoA. Further enzymatic studies are needed to confirm the function of SaHcd1. (Sourc...
Source: Acta Crystallographica Section F - May 25, 2023 Category: Biochemistry Authors: Dinh, D.M. Thomas, L.M. Karr, E.A. Tags: SDR-family proteins Hcd1 syntrophy fatty-acid metabolism Syntrophus aciditrophicus research communications Source Type: research
Bacterial structural genomics target enabled by a recently discovered potent fungal acetyl-CoA synthetase inhibitor
The compound ethyl-adenosyl monophosphate ester (ethyl-AMP) has been shown to effectively inhibit acetyl-CoA synthetase (ACS) enzymes and to facilitate the crystallization of fungal ACS enzymes in various contexts. In this study, the addition of ethyl-AMP to a bacterial ACS from Legionella pneumophila resulted in the determination of a co-crystal structure of this previously elusive structural genomics target. The dual functionality of ethyl-AMP in both inhibiting ACS enzymes and promoting crystallization establishes its significance as a valuable resource for advancing structural investigations of this class of protein...
Source: Acta Crystallographica Section F - May 25, 2023 Category: Biochemistry Authors: DeBouver, N.D. Bolejack, M.J. Esan, T.E. Krysan, D.J. Hagen, T.J. Abendroth, J. Tags: SSGCID acetyl-coenzyme A synthetase Legionella pneumophila structural genomics ligases research communications Source Type: research
Crystal structure of a three-tetrad, parallel, K+-stabilized human telomeric G-quadruplex at 1.35 Å resolution
The crystal structure of the G-rich human telomeric DNA Tel22 has been determined at 1.35 Å resolution in space group P6. Tel22 forms a non-canonical DNA structure called the G-quadruplex. The space group and unit-cell parameters are comparable to those in the crystal structures with PDB codes 6ip3 (1.40 Å resolution) and 1kf1 (2.15 Å resolution). The G-quadruplexes are highly similar in all of the structures. However, this structure of Tel22 displays clear density for polyethylene glycol and two potassium ions, which are located outside the ion channel in the G-quadruplex and play an important role in stabi...
Source: Acta Crystallographica Section F - May 24, 2023 Category: Biochemistry Authors: Chen, E.V. Nicoludis, J.M. Powell, B.M. Li, K.S. Yatsunyk, L.A. Tags: three tetrads parallel G-quadruplex propeller loops human telomeric DNA polyethylene glycol research communications Source Type: research
The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis
Streptococcus mutans, found in the human oral cavity, is a significant contributor to the pathogenesis of dental caries. This bacterium expresses three genetically distinct types of glucosyltransferases named GtfB (GTF-I), GtfC (GTF-SI) and GtfD (GTF-S) that play critical roles in the development of dental plaque. The catalytic domains of GtfB, GtfC and GtfD contain conserved active-site residues for the overall enzymatic activity that relate to hydrolytic glycosidic cleavage of sucrose to glucose and fructose, release of fructose and generation of a glycosyl-enzyme intermediate in the reducing end. In a subsequent transgl...
Source: Acta Crystallographica Section F - May 5, 2023 Category: Biochemistry Authors: Schormann, N. Patel, M. Thannickal, L. Purushotham, S. Wu, R. Mieher, J.L. Wu, H. Deivanayagam, C. Tags: glucansucrases glycosyltransferases catalytic domains soluble and insoluble glucans GtfB GtfC GtfD dental plaque Streptococcus mutans SRCR1 binding research communications Source Type: research
Crystal structure of MbnF: an NADPH-dependent flavin monooxygenase from Methylocystis strain SB2
Methanobactins (MBs) are ribosomally produced and post-translationally modified peptides (RiPPs) that are used by methanotrophs for copper acquisition. The signature post-translational modification of MBs is the formation of two heterocyclic groups, either an oxazolone, pyrazinedione or imidazolone group, with an associated thioamide from an X-Cys dipeptide. The precursor peptide (MbnA) for MB formation is found in a gene cluster of MB-associated genes. The exact biosynthetic pathway of MB formation is not yet fully understood, and there are still uncharacterized proteins in some MB gene clusters, particularly those that p...
Source: Acta Crystallographica Section F - May 5, 2023 Category: Biochemistry Authors: Stewart, A. Dershwitz, P. Stewart, C. Sawaya, M.R. Yeates, T.O. Semrau, J.D. Zischka, H. DiSpirito, A.A. Bobik, T.A. Tags: methanobactins MbnF flavin monooxygenases Methylocystis sp. strain SB2 Wilson's disease research communications Source Type: research
Crystal structure of MAB_4123, a putative flavin-dependent monooxygenase from Mycobacterium abscessus
In this study, the crystal structure of the uncharacterized MAB_4123 protein from the human pathogen Mycobacterium abscessus is presented. The structure solved at high resolution displays high similarity to homologs from Rhodococcus, Paenibacillus and Pseudomonas species. In silico docking approaches suggest that MAB_4123 binds FMN and may use it as a cofactor. Structural analysis strongly suggests that MAB_4123 is a two-component flavin-dependent monooxygenase that could act as a detoxifying enzyme of organosulfur compounds in mycobacteria. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - May 3, 2023 Category: Biochemistry Authors: Ung, K.L. Poussineau, C. Couston, J. Alsarraf, H.M.A.B. Blaise, M. Tags: Mycobacterium abscessus organosulfur compounds two-component flavin-dependent monooxygenases MAB_4123 research communications Source Type: research
Crystal structure of the engineered endolysin mtEC340M
Endolysins produced by bacteriophages play essential roles in the release of phage progeny by degrading the peptidoglycan layers of the bacterial cell wall. Bacteriophage-encoded endolysins have emerged as a new class of antibacterial agents to combat surging antibiotic resistance. The crystal structure of mtEC340M, an engineered endolysin EC340 from the PBEC131 phage that infects Escherichia coli, was determined. The crystal structure of mtEC340M at 2.4 Å resolution consists of eight α -helices and two loops. The three active residues of mtEC340M were predicted by structural comparison with peptidoglycan-degradin...
Source: Acta Crystallographica Section F - May 1, 2023 Category: Biochemistry Authors: Wang, J.-M. Seok, S.-H. Yoon, W.-S. Kim, J.-H. Seo, M.-D. Tags: Gram-negative bacteria endolysin mtEC340M endolysins antibacterial agents crystal structure research communications Source Type: research
Introduction to the virtual thematic issue on room-temperature biological crystallography
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 31, 2023 Category: Biochemistry Authors: Steiner, R.A. Tags: room-temperature crystallography synchrotron radiation serial crystallography protein dynamics editorial Source Type: research
A partially open conformation of an androgen receptor ligand-binding domain with drug-resistance mutations
Mutations in the androgen receptor (AR) ligand-binding domain (LBD) can cause resistance to drugs used to treat prostate cancer. Commonly found mutations include L702H, W742C, H875Y, F877L and T878A, while the F877L mutation can convert second-generation antagonists such as enzalutamide and apalutamide into agonists. However, pruxelutamide, another second-generation AR antagonist, has no agonist activity with the F877L and F877L/T878A mutants and instead maintains its inhibitory activity against them. Here, it is shown that the quadruple mutation L702H/H875Y/F877L/T878A increases the soluble expression of AR LBD in complex...
Source: Acta Crystallographica Section F - March 30, 2023 Category: Biochemistry Authors: Doamekpor, S.K. Peng, P. Xu, R. Ma, L. Tong, Y. Tong, L. Tags: androgen receptors ligand-binding domain DHT drug resistance prostate cancer COVID-19 pruxelutamide enzalutamide research communications Source Type: research
Structural and enzymatic characterization of the sialidase SiaPG from Porphyromonas gingivalis
The sialidases, which catalyze the hydrolysis of sialic acid from extracellular glycoconjugates, are a group of major virulence factors in various pathogenic bacteria. In Porphyromonas gingivalis, which causes human periodontal disease, sialidase contributes to bacterial pathogenesis via promoting the formation of biofilms and capsules, reducing the ability for macrophage clearance, and providing nutrients for bacterial colonization. Here, the crystal structure of the P. gingivalis sialidase SiaPG is reported at 2.1 Å resolution, revealing an N-terminal carbohydrate-binding domain followed by a canonical C-terminal ca...
Source: Acta Crystallographica Section F - March 30, 2023 Category: Biochemistry Authors: Dong, W.-B. Jiang, Y.-L. Zhu, Z.-L. Zhu, J. Li, Y. Xia, R. Zhou, K. Tags: sialidases Porphyromonas gingivalis crystallography kinetic analysis human periodontal disease research communications Source Type: research
Monomeric crystal structure of the vaccine carrier protein CRM197 and implications for vaccine development
CRM197 is a genetically detoxified mutant of diphtheria toxin (DT) that is widely used as a carrier protein in conjugate vaccines. Protective immune responses to several bacterial diseases are obtained by coupling CRM197 to glycans from these pathogens. Wild-type DT has been described in two oligomeric forms: a monomer and a domain-swapped dimer. Their proportions depend on the chemical conditions and especially the pH, with a large kinetic barrier to interconversion. A similar situation occurs in CRM197, where the monomer is preferred for vaccine synthesis. Despite 30 years of research and the increasing application of CR...
Source: Acta Crystallographica Section F - March 30, 2023 Category: Biochemistry Authors: Gallagher, D.T. Oganesyan, N. Lees, A. Tags: carriers conjugate vaccines CRM197 diphtheria toxin domain swapping toxoids research communications Source Type: research
Expression, purification and crystallization of N-acetyl-(R)- β -phenylalanine acylases derived from Burkholderia sp. AJ110349 and Variovorax sp. AJ110348 and structure determination of the Burkholderia enzyme
In this study, structural analyses were carried out in order to investigate the structure – function relationships of the enzymes derived from both organisms. The recombinant N-acetyl-(R)- β -phenylalanine acylases were crystallized by the hanging-drop vapor-diffusion method under multiple crystallization solution conditions. The crystals of the Burkholderia enzyme belonged to space group P41212, with unit-cell parameters a = b = 112.70 – 112.97, c = 341.50 – 343.32 Å , and were likely to contain two subunits in the asymmetric unit. The crystal structure was solved by the Se-SAD method, suggesting that two subu...
Source: Acta Crystallographica Section F - February 23, 2023 Category: Biochemistry Authors: Kato, Y. Kawasaki, H. Nakamatsu, T. Matsuda, N. Natsume, R. Tags: N-acetyl-(R)- β -phenylalanine acylase enantiomer-specific amidohydrolysis Burkholderia sp. AJ110349 Variovorax sp. AJ110348 research communications Source Type: research
