Hi, I have a sequence of toxin genes of a bacteria. I would like to find out the motif that is toxic and if there is any bioinformatics approaches to it?
There are hundreds of types of bacterial toxins. Some, such as the neurotoxins of Clostridium botulinum, are proteases which cleave SNARE proteins as specific sites. Others, such as Diphtheria toxin and Pseudomonas exotoxin A, modify proteins. Others cause toxicity in other ways. The method of finding the catalytic or toxic sites in different classes of toxins can be different. For many classes of bacterial toxins, the 3D structures and exact mechanisms of toxicity are well known. For example, see:
Crystal structure of Clostridium botulinum neurotoxin protease in a product-bound state: Evidence for noncanonical zinc protease activity.
Segelke B, Knapp M, Kadkhodayan S, Balhorn R, Rupp B.
Proc Natl Acad Sci U S A. 2004 May 4;101(18):6888-93. Epub 2004 Apr 23.
PMID: 15107500
http://www.ncbi.nlm.nih.gov/pubmed/15107500
Hi Karthik
Do you any information of these genes..Whether they are Protease , Phosphatase deubiquitanase etc. Try to find the conserved sequences in your protein and its homologs....The conserved sequences among them might have structural or functional roles....Later you can try to find whether this sequences resemble any known motifs....For example if your protein is protease then try to do blast in merops database...from here you will come to know to which class your protease toxin belongs too and its probable catalytic site etc...For example if your protease belongs Zinc metalloprotease subfamily then your toxin is mostly likely to have a zinc binding motif... Hope this helps you...
Also, if you do not know what class of toxin your toxin belongs to, then finding a motif like a zinc binding motif (as Bassavraj mentioned) for exmaple, can lead you to discovering what type of toxin you are studying. So these methods can work from both directions.
Thank you Brain Thomas Foley and Basavraj Khanppnavar
My toxin gene is a beta-barrel pore forming toxins of the leucocidin superfamily,having cytotoxic and haemolytic
It is having 50% identical, 60% similar a.a. to Clostridium botulinum.
It is having around 310 amino acids. I would like to know the motif in this amino acid sequence responsible for cytotoxic and haemolytic activity of this gene.
What Clostridium toxin protein is it similar to? The BoNT toxin itself is huge and diverse (different serotypes of the same toxin are not very similar to each other), but Clostridia also produce dozens of other toxins besides the BoNT. I am not familiar with Costridium leucocidins.
My toxin gene is CctA of Clostridium chauvoei which is 50% identical, 60% similar to alpha hemolysin of Clostridium botulinum. As I said it is having cytotoxic and haemolytic activity. I would like to know is there any bio informatics tool to find out the motif responsible for these toxin property of this CctA before I go to invitro or invivo studies?
http://www.ncbi.nlm.nih.gov/pubmed/23805259 describes a crystal structure of a different Clostridial leukocydin. I BLASTed the CctA protein against the protein databases and it is indeed most similar to a protein annotated as alpha hemolysin from Clostridium botulinum. But this annotation seems to be from complete genome, by similarity to other alpha hemolysins from other bacteria. So, there is probably no structure/function information on the Clostridial proteins, but there is enough similarity to the other alpha hemolysins that I would trust that this is truly an alpha hemolysin, and if you dig through the dozens of other alpha hemolysins, there is probably one that has been studied for structure/function.
http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=TIGR01002&islf=1
is the link to the protein families database on the alpha hemolysins. From there you can see a sequence alignment and 3D structure. The next step would be to align your proteins to those already in this alignment, so you can see where your amino acids map onto the structure.
http://www.biomedcentral.com/1471-2164/12/88/
I made same investigation for sea anemone toxin using SRDA technique. Try to use software in supplimentary.
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