Protein structure

This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison

Protein Length: 294 Amino Acids
MAMSSGGSGGGVPEQEDSVLFRRGTGQSDDSDIWDDTALIKAYDKAVASFKH
ALKNGDICETSGKPKTTPKRKPAKKNKSQKKNTAASLQQWKVGDKCSAIWSE
DGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICEVANNIEQNAQEN
ENESQVSTDESENSRSPGNKSDNIKPKSAPWNSFLPPPPPMPGPRLGPGKPG
LKFNGPPPPPPPPPPHLLSCWLPPFPSGPPIIPPPPPICPDSLDDADALGSMLIS
WYMSGYHTGYYMGFRQNQKEGRCSHSLN(1)

Protein Localization

Using several subcellular localization programs I was able to find the location of my protein in the cell as predicted by its protein sequence. I used pTARGET, TargetP, and ESLpred to perform this test.
TargetP was unable to predict any location for SMN1.
pTARGET and ESLpred both predicted that SMN1 is located in the nucleus. pTARGET reported a 100% confidence level in its finding. ESLpred gave an expected accuracy of 53%. These sites were very easy to use, only requiring the FASTA format of a protein sequence. Given that SMN1 processes mRNA, it makes sense that it would be in the nucleus and these sites confirm this based on the protein sequence.

Protein Modifications

Certain mutations were found to reduce the ability of SMN to bind to sm-proteins.
These changes occur at AA95 a G-->R change and at AA111 an A-->G change(2)

All secondary structure forms were found to be in the Tudor domain.(2)

Secondary Structure AALocation

B-strand 97-101

Turn 103-105

B-strand 108-117

Turn 118-121

B-strand 122-127

Turn 128-131

B-strand 132-137

Helix 138-140

References:
1. NCBI (2009) Suvival of Motor Neuron retrived Feb 3, 2009 from: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_000335.1
2. Uniprot (2009) SMN. retrieved Apr 27, 2009 from: http://www.uniprot.org/uniprot/Q16637

William Baader
[email protected]
Feb 19 2009
www.gen677.weebly.com