Publications by authors named "Alexandra Holinski"

Biocuration involves a variety of teams and individuals across the globe. However, they may not self-identify as biocurators, as they may be unaware of biocuration as a career path or because biocuration is only part of their role. The lack of a clear, up-to-date profile of biocuration creates challenges for organisations like ELIXIR, the ISB and GOBLET to systematically support biocurators and for biocurators themselves to develop their own careers.

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It is important to identify hotspot residues that determine protein-protein interactions in interfaces of macromolecular complexes. We have applied a combination of ancestral sequence reconstruction and protein design to identify hotspots within imidazole glycerol phosphate synthase (ImGPS). ImGPS is a key metabolic enzyme complex, which links histidine and de novo purine biosynthesis and consists of the cyclase subunit HisF and the glutaminase subunit HisH.

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Article Synopsis
  • We studied the structure and function of YbiB, a protein from E. coli belonging to the uncharacterized TrpD2 family, revealing new insights into its binding properties and potential roles.
  • YbiB shows strong similarity to proteins involved in anthranilate metabolism and can bind nucleic acids with high affinity, but without specificity for sequence, suggesting it interacts cooperatively with DNA.
  • This protein forms a homodimer, meaning it has two binding sites, but exhibits negative cooperativity, leading to only one site binding DNA in lab experiments; it may play a role in the bacterial SOS response controlled by the LexA protein.
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Due to the lack of macromolecular fossils, the enzymatic repertoire of extinct species has remained largely unknown to date. In an attempt to solve this problem, we have characterized a cyclase subunit (HisF) of the imidazole glycerol phosphate synthase (ImGP-S), which was reconstructed from the era of the last universal common ancestor of cellular organisms (LUCA). As observed for contemporary HisF proteins, the crystal structure of LUCA-HisF adopts the (βα)8-barrel architecture, one of the most ancient folds.

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