This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
Protein Domains
The FASTA-formatter protein sequence for the KRAS protein was entered into the Pfam database and to look for protein domains. 1 significant Pfam match and 2 insignificant Pfam matches were found
Ras protein domain in Pfam database.
According to Pfam, the Ras family Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more
As regards Rab GTPases, these are important regulators of vesicle
formation, motility and fusion. All Ras GTPases have a six-stranded beta-sheet surrounded by five
alpha-helices [1]
Many members of the Ras superfamily of GTPases have been implicated in the regulation of hematopoietic cells, with roles in growth, survival, differentiation, cytokine production, chemotaxis, vesicle-trafficking, and phagocytosis. The Ras superfamily of proteins now includes over 150 small GTPases (distinguished from the large, heterotrimeric GTPases, the G-proteins). It comprises six subfamilies, the Ras, Rho, Ran, Rab, Arf, and Kir/Rem/Rad subfamilies. They exhibit remarkable overall amino acid identities, especially in the regions interacting with the guanine nucleotide exchange factors that catalyze their activation. [1]
Many members of the Ras superfamily of GTPases have been implicated in the regulation of hematopoietic cells, with roles in growth, survival, differentiation, cytokine production, chemotaxis, vesicle-trafficking, and phagocytosis. The Ras superfamily of proteins now includes over 150 small GTPases (distinguished from the large, heterotrimeric GTPases, the G-proteins). It comprises six subfamilies, the Ras, Rho, Ran, Rab, Arf, and Kir/Rem/Rad subfamilies. They exhibit remarkable overall amino acid identities, especially in the regions interacting with the guanine nucleotide exchange factors that catalyze their activation. [1]
Crystal structure of human rab4b in complex with gd.
Analysis
In addition to Pfam, I also used SMART (Simple Modular Architecture Research Tool) [2] to analyze the protein domains, with similar results.Only 1 domain is found in my protein, therefore, it is likely that the protein size is small, given that the FASTA sequence is quite short as well, The existence of a single domain and apparent lack of complexity of the protein can be explained by the fact that the functions of the Ras family of proteins is mainly regulatory in the GTPase pathway.
References
1) Pfam
http://pfam.sanger.ac.uk/
2) SMART
http://smart.embl-heidelberg.de/
http://pfam.sanger.ac.uk/
2) SMART
http://smart.embl-heidelberg.de/
