This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
Protein Domains
The tertiary structure of a protein is the three-dimensional structure formed by interactions between amino acids. Protein domains are the building blocks of tertiary structure; each domain is a smaller 3D structure, usually with a specific function (determined by its shape and biochemical properties) that can be performed independent of the rest of the protein.
Protein domains are conserved among different proteins, and learning what domains are present in a protein can give insight into its functions and evolutionary history.
Protein domains are conserved among different proteins, and learning what domains are present in a protein can give insight into its functions and evolutionary history.
Amino acid sequence analysis results: SMART and PROSITE
SMART
Click the image to go to the SMART [2] homepage
SMART (Simple Modular Architecture Research Tool) is a protein domain database that returns predicted protein functional domains for a protein sequence or accession number submitted by the user.
Below is the domain map of human ABCA1 protein generated by SMART:
Below is the domain map of human ABCA1 protein generated by SMART:
SMART protein domain predictions [2]. Click to view the full-sized image.
PROSITE
Click the image to go to the PROSITE [3] homepage
PROSITE is another protein domain database that allows users to access and visualize domain annotations for their protein sequence.
Below is the domain map of human ABCA1 protein generated by PROSITE:
Below is the domain map of human ABCA1 protein generated by PROSITE:
PROSITE domain predictions [3]. Click to view the full-sized image. O95477 is the UniProt ID for ABCA1.
Summary of SMART protein domain predictions:
Eleven transmembrane domains are represented as blue blocks:
Two AAA ATPase domains are represented as gray "AAA" rectangles:
Five low-complexity regions are represented by pink blocks, and four more overlapping regions are not displayed:
Eleven transmembrane domains are represented as blue blocks:
- Hydrophobic transmembrane domains anchor the protein in the cell membrane.
Two AAA ATPase domains are represented as gray "AAA" rectangles:
- The ATPase activity of ABC proteins is necessary to facilitate the transport of molecules against their chemical gradient.
Five low-complexity regions are represented by pink blocks, and four more overlapping regions are not displayed:
- These regions contain high proportions of repetitive, non-coding DNA
Summary of PROSITE protein domain predictions:
Two "ABC transporter" domains are represented as orange ovals:
Two "ABC transporter" domains are represented as orange ovals:
- The ATPase activity of ABC proteins is necessary to facilitate the transport of molecules against their chemical gradient.
- Two ATP-binding (nucleotide phosphate binding) sites are represented as green blocks above the ABC transporters
Analysis:
Although the results from SMART and PROSITE differ in terminology, they actually agree well.
Both detected two ATP-binding domains, which are referred to as "AAA ATPase" domains by SMART and "ABC transporter" domains by PROSITE. These are in fact the same; ATPase domains that bind and hydrolyze ATP to transport cholesterol across the cell membrane.
All other differences are simply a function of what the databases are configured to report.
Both detected two ATP-binding domains, which are referred to as "AAA ATPase" domains by SMART and "ABC transporter" domains by PROSITE. These are in fact the same; ATPase domains that bind and hydrolyze ATP to transport cholesterol across the cell membrane.
All other differences are simply a function of what the databases are configured to report.
Sources:
1. M.H. Kang, R. Singaraja, M.R. Hayden. Adenosine-Triphosphate-Binding Cassette Transporter-1 Trafficking and Function. Trends in Cardiovascular Medicine. 20:2 (2010) 41-49. doi:10.1016/j.tcm.2010.03.006.
2. http://smart.embl-heidelberg.de/smart/show_motifs.pl?ID=Q5VX33_HUMAN
3. http://ca.expasy.org/prosite/
1. M.H. Kang, R. Singaraja, M.R. Hayden. Adenosine-Triphosphate-Binding Cassette Transporter-1 Trafficking and Function. Trends in Cardiovascular Medicine. 20:2 (2010) 41-49. doi:10.1016/j.tcm.2010.03.006.
2. http://smart.embl-heidelberg.de/smart/show_motifs.pl?ID=Q5VX33_HUMAN
3. http://ca.expasy.org/prosite/
