This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.
What are protein domains?
Proteins are made up of different domains. Different proteins have different numbers of domains and different types of domains. A domain is a distinct structural or functional unit of a protein [1]. Some protein domains bind to other proteins, to DNA, to ligands, or to cellular components. These domains are evolutionarily conserved but can evolve, function, and exist independently from the rest of the protein. Proteins are made up of families that share common evolutionary paths, function, and similar sequences [1]. Protein domains are cataloged in database such as: PFAM, SMART, InterPro, or PROSITE. Identifying protein domains is useful for characterizing protein functions and classification.
What domains are present in LXRA?
Using the SMART provides us the protein domains for LXRA (Figure 1). The small pink regions represent low complexity regions. These regions represent possible identifiable domains yet to be characterized. The blue region represents a zinc finger domain that play a role in DNA binding. The green region represents a ligand binding domain.
How conserved are the LXRA protein domains?
In the majority of the above organisms the domains and size of the protein is conserved. All of the organisms have both the zinc finger and ligand binding domains. The major difference between the species is the size of the protein.
Discussion
The LXRA protein is only 447 amino acids in humans and this number is mostly conserved especially with the more closely related organisms. The protein only has two domains and this is conserved across organisms. This shows that the protein likely functions in very similar manners across species. Regions of low complexity were also conserved with more distant organisms having an additional in some species. The regions of low complexity should be further explored to identify the significance of them.
References
[Header Image] https://upload.wikimedia.org/wikipedia/commons/e/e6/Spombe_Pop2p_protein_structure_rainbow.png
[1] What are protein domains? (2016, July 20). Retrieved March 16, 2018, from https://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/protein-classification/what-are-protein-domains
[1] What are protein domains? (2016, July 20). Retrieved March 16, 2018, from https://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/protein-classification/what-are-protein-domains