This website was constructed as a class project for Genetics 564, an undergraduate Genetics course at UW-Madison.
Protein Domains and Motifs
A protein domain is a protein structure in a that is shared among species. Domains can give a protein its specific properties, such as binding certain molecules, interacting with other proteins, etc. Proteins can be classified into families based on the domains they contain. Websites Pfam and SMART have tools that can be used to identify these domains, and other proteins that also contain these domains. Aldolase B contains the Glycolytic and PDB domains, as shown below. Both domains are essential for an active site that breaks down fructose [1,2].
The Glycolytic domain as shown in Pfam.
A protein motif is an amino acid sequence shared among species (as opposed to a tertiary structure, which does not necessarily have to arise from the same amino acid sequence in every species it is conserved in). The LCR (low complexity region, sequence: ASALAAWGGKAANKKA) is highly conserved in aldolase B. Though it does not contain any commonly mutated sites in cases of HFI, its high degree of conservation may indicate its importance in enzymatic folding. Enzymes like aldolase B must be able to fold properly to function, and doing so requires specific sites on the enzyme itself for folding [4].
References
1. EMBL-EBI. (2014). What are Protein Domains? Electronic Resource. Retrieved May 18, 2014, from http://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/protein-classification/what-are-protein-domains
2. Wellcome Trust Sanger Institute. (2014). Fructose-bisphosphate aldolase. Retrieved March 6, 2014 from http://pfam.sanger.ac.uk/family/PF00274
3. SMART Genomes. (2012). Sequence Analysis. Retrieved March 6, 2014 from http://smart.embl-heidelberg.de/smart/job_status.pl?jobid=128104153129112521393865716tHkrzipgKg
4. Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. Protein Folding and Processing. Electronic resource. Retrieved May 18, 2014, from http://www.ncbi.nlm.nih.gov/books/NBK9843/
2. Wellcome Trust Sanger Institute. (2014). Fructose-bisphosphate aldolase. Retrieved March 6, 2014 from http://pfam.sanger.ac.uk/family/PF00274
3. SMART Genomes. (2012). Sequence Analysis. Retrieved March 6, 2014 from http://smart.embl-heidelberg.de/smart/job_status.pl?jobid=128104153129112521393865716tHkrzipgKg
4. Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. Protein Folding and Processing. Electronic resource. Retrieved May 18, 2014, from http://www.ncbi.nlm.nih.gov/books/NBK9843/