ArticleJournal of biomedicine & biotechnology2012
Computer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function.
Article in Journal of biomedicine & biotechnology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 15 citations in OpenAlex.
- The small molecule regacin binds a conserved pocket in RegA to inhibit the expression of bacterial virulence factors.bioRxiv : the preprint server for biology · 2026Article
- Diversity in Genetic Regulation of Bacterial Fimbriae Assembled by the Chaperone Usher Pathway.International journal of molecular sciences · 2022Review
- Optimised Heterologous Expression and Functional Analysis of theInternational journal of molecular sciences · 2021Article
- A Novel Two-Component System, XygS/XygR, Positively Regulates Xyloglucan Degradation, Import, and Catabolism in Ruminiclostridium cellulolyticum.Applied and environmental microbiology · 2020Article
- Global Transcriptomic Responses ofMicroorganisms · 2020Article
- Identification of Genes Controlled by the Essential YycFG Two-Component System Reveals a Role for Biofilm Modulation inFrontiers in microbiology · 2017Article
- An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry.PloS one · 2016Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Currently, about 20 crystal structures per day are released and deposited in the Protein Data Bank. A significant fraction of these structures is produced by research groups associated with the structural genomics consortium. The biological function of many of these proteins is generally unknown or not validated by experiment. Therefore, a growing need for functional prediction of protein structures has emerged. Here we present an integrated bioinformatics method that combines sequence-based relationships and three-dimensional (3D) structural similarity of transcriptional regulators with computer prediction of their cognate DNA binding sequences. We applied this method to the AraC/XylS family of transcription factors, which is a large family of transcriptional regulators found in many bacteria controlling the expression of genes involved in diverse biological functions. Three putative new members of this family with known 3D structure but unknown function were identified for which a probable functional classification is provided. Our bioinformatics analyses suggest that they could be involved in plant cell wall degradation (Lin2118 protein from Listeria innocua, PDB code 3oou), symbiotic nitrogen fixation (protein from Chromobacterium violaceum, PDB code 3oio), and either metabolism of plant-derived biomass or nitrogen fixation (protein from Rhodopseudomonas palustris, PDB code 3mn2).
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