This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison, Spring 2012.
SOD1 Protein Domains
What is a protein domain?
A domain is a part of a protein sequence and structure that can function on its own apart from the entire protein. The study of protein domains can be useful in determining gene function.
SOD1 Protein Domains
SOD1 is composed of only one domain: the Copper/Zinc Superoxide Dismutase (SODC) domain. The domain spans from amino acid 5 - 150, essentially the entire length of the human protein. This is nearly identical for model organism homologs as well. Pfam and SMART can be useful tools to help find the domains within proteins. Below are the results for SOD1 from both databases.
For an explanation of the molecular function of Copper/Zinc Superoxide Dismutase domains, see gene ontology.
Genes and Species with SODC Domains
There are many other genes that contain SODC domains in different arrangements than seen in SOD1. Below are a few examples from Pfam:
Analysis
In general, protein function can be inferred based off of the functions of known domains. SOD1 is comprised almost entirely of one domain, the Copper/Zinc Superoxide Dismutase (SODC) domain. The function of the domain is well known - SODC converts dangerous reactive oxygen species into hydrogen peroxide. While the SODC domain makes up most of the SOD1 protein, it is seen in various domain combinations in other proteins in other species, helping us to better understand the functions of those proteins. The sunburst graph demonstrates the prevalence of SODC domains in both Eukaryota and Bacteria.
It is assumed that SOD1 mutations disrupt the ability of cells to process reactive oxygen species; however, this loss of the SODC function is not presumed to cause ALS. SOD1 mutations are likely toxic gain-of-function mutations, meaning that they are disturbing other biological processes not associated with SODC, making it difficult to discern the true cause of the disease.
It is assumed that SOD1 mutations disrupt the ability of cells to process reactive oxygen species; however, this loss of the SODC function is not presumed to cause ALS. SOD1 mutations are likely toxic gain-of-function mutations, meaning that they are disturbing other biological processes not associated with SODC, making it difficult to discern the true cause of the disease.