Computer-Based Annotation of Putative AraCXylS-Family Transcription Factors of Known Structure but Unknown Function
Joint Authors
Melo, Francisco
Norambuena, Tomás
Almonacid, Leonardo I.
Slater, Alex W.
Cifuentes, Juan J.
Schüller, Andreas
Source
Journal of Biomedicine and Biotechnology
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-14, 14 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-03-13
Country of Publication
Egypt
No. of Pages
14
Main Subjects
Abstract EN
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).
American Psychological Association (APA)
Schüller, Andreas& Slater, Alex W.& Norambuena, Tomás& Cifuentes, Juan J.& Almonacid, Leonardo I.& Melo, Francisco. 2012. Computer-Based Annotation of Putative AraCXylS-Family Transcription Factors of Known Structure but Unknown Function. Journal of Biomedicine and Biotechnology،Vol. 2012, no. 2012, pp.1-14.
https://search.emarefa.net/detail/BIM-446542
Modern Language Association (MLA)
Schüller, Andreas…[et al.]. Computer-Based Annotation of Putative AraCXylS-Family Transcription Factors of Known Structure but Unknown Function. Journal of Biomedicine and Biotechnology No. 2012 (2012), pp.1-14.
https://search.emarefa.net/detail/BIM-446542
American Medical Association (AMA)
Schüller, Andreas& Slater, Alex W.& Norambuena, Tomás& Cifuentes, Juan J.& Almonacid, Leonardo I.& Melo, Francisco. Computer-Based Annotation of Putative AraCXylS-Family Transcription Factors of Known Structure but Unknown Function. Journal of Biomedicine and Biotechnology. 2012. Vol. 2012, no. 2012, pp.1-14.
https://search.emarefa.net/detail/BIM-446542
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-446542