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Empowering education through structural genomics
Edited by Jon Agirre, Oluwatoyin A. Asojo, Graham Chakafana and Craig L. Smith
This focused issue of Acta Crystallographica Section F, titled Empowering Education through Structural Genomics, features 16 articles authored by early-career researchers, including undergraduates and high-school students. Fifteen of the articles are based on protein structures provided by the Seattle Structural Genomics Center for Infectious Disease (SSGCID). This consortium has deposited over 1800 structures in the Protein Data Bank since its foundation in 2007. While many of these structures previously lacked corresponding publications, a recent initiative by SSGCID has used them as educational tools, providing students with meaningful opportunities to gain research experience and enhance their scientific writing and communication skills. This collection highlights the success of that initiative and the promise of using structural genomics as a foundation for research-based education in structural biology.
Cover illustration: Early career researchers contributing to this focused issue.
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The focused issue on Empowering education through structural genomics is introduced. The virtual issue is available at https://journals.iucr.org/special_issues/2024/educationsg.
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Brucella ovis leucine-, isoleucine-, valine-, threonine- and alanine-binding protein structures have a prototypical bacterial periplasmic amino acid-binding protein topology with a conformationally flexible peptide-binding cavity in the absence of peptide.
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The 2.3 Å resolution ternary structure of the essential P. vivax N-myristoyltransferase with myristoyl-CoA and a peptide-binding domain inhibitor is reported as part of ongoing efforts by the SSGCID for the rational design of new therapeutics for malaria.
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N-terminally hexahistidine-tagged O. volvulus macrophage migration inhibitory factor-1 has a unique jellyfish-like structure with the prototypical macrophage migration inhibitory factor trimer as the `head' and a C-terminal extension as the `tail'.
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Persistent H. pylori infection causes gastric ulcers and cancer, and multidrug resistance is increasing globally. The 2.5 Å resolution structure of H. pylori glutamyl-tRNA synthetase was determined as a first step towards rational drug discovery.
PDB reference: glutamyl-tRNA synthetase, 6b1p
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The production, crystallization and three crystal structures of macrophage migratory inhibitory factor from T. vaginalis are reported.
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The structure of B. cenocepacia short-chain dehydrogenase/reductase (SDR) in complex with NADP+ and benzoic acid is presented. Analysis of the structure reveals a distinctive active-site architecture, suggesting that this protein is part of the divergent SDR subgroup.
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The 1.8 Å resolution ternary structure of P. vivax N-myristoyltransferase in complex with IMP-1088 and myristoyl-CoA is presented. IMP-1088 is an N-myristoyltransferase inhibitor from a family of inhibitors that are under investigation as antimalarials.
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Recombinant N-terminally histidine-tagged H. pylori biotin protein ligase was purified and its 2.25 Å resolution co-crystal structure with biotinyl-5-ATP is reported.
The crystal structure of dihydroorotate dehydrogenase from H. pylori bound to flavin mononucleotide was determined at 2.25 Å resolution in space group P21.
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A high-resolution structure of carboxyspermidine decarboxylase, a member of the PLP-dependent β/α-barrel-fold decarboxylase family, is analyzed.
PDB reference: Clostridium leptum carboxyspermidine decarboxylase, 9eaf
Crystal structures of tryptophanyl-tRNA synthetase from N. gonorrhoeae were solved in both the apo form and in complex with tryptophan to resolutions of 2.25 and 2.5 Å, respectively. These structures reveal conserved catalytic motifs and conformational changes at the active site upon ligand binding. Additionally, structural comparisons suggest that indolmycin may act as a competitive inhibitor, offering potential for antibiotic development.
The co-crystal structures of five sulfonamide ligands bound to the active site of the IspF enzyme from B. psuedomallei are reported. The ligands include the drugs ethoxzolamide, acetazolamide, sulfapyridine and sulfamonomethoxine.
The crystal structure of UmaA from M. tuberculosis was solved to 1.95 Å resolution in space group P3221.
PDB reference: UmaA from Mycobacterium tuberculosis, 7lxi
L. pneumophila serogroup 1 is the causative agent of Legionnaires' disease. Two crystal structures of apo and dUMP-bound deoxyuridine 5′-triphosphate nucleotidohydrolase (dUTPase) were determined to 1.80 and 1.95 Å resolution, respectively. dUTPases have been investigated as a potential druggable target in several pathogens.
Peptide deformylases (PDFs) are of interest as viable drug targets for the development of new antimicrobials. Two crystal structures of PDF from L. pneumophila serogroup 1, the causative agent of Legionnaires' disease, bound to Ni2+ or to actinonin and Zn2+, were solved at 1.5 and 1.65 Å resolution, respectively.
The purification, crystallization and three crystal structures of the putative endoribonuclease L-PSP from E. histolytica are reported.
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