I would like to study the enzyme substrate interactions. But I could not find the protein structure of almond ß-glucosidase in the literature. If anbody have any idea concerning its structure please share with me.
To find out whether there is a structure of your protein or at least a protein sufficiently closely related to your protein to generate a reliable homology model, go to the PDB website (http://www.rcsb.org), choose "advanced search" and under query type, choose "sequence features"/"Blast/FastA/PsiBlast". Enter the sequence of your protein to look for any structure that shows significant sequence homology
Searching one of the other PDB websites (There are four sites which serve PDB data to the world) at PDBe shows there are only 5 almond proteins solved, none glucosidase
http://www.ebi.ac.uk/pdbe/entry/search/index?organism_synonyms:Almond
You can BLAST your sequence against the PDB archive at the following link:
http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/
Thank you for your suggestions. But really I don't know the sequence, since I purchased almond ß-glucosidase from TCI, Japan. They mentioned only the molecular weight of the protein rest is unknown. Please refer me some publications on the structure elucidation of almond beta-glucosidase or the similar analog.
If you don't know the sequence, first search a sequence database for the sequence, e.g. uniprot at http://www.expasy.org or ncbi at http://www.ncbi.nlm.nih.gov.
Searching for "glycosidase almond" i found http://www.uniprot.org/uniprot/H9ZGD9 (and some others). Using this sequence for a blast search, I found the beta-glycosidase of clover as the closest homolog, as well as the one from rice with some substrate analogs in the active site. These seem to be close enough to the almond enzyme in sequence for a homology model. Of course, you have to redo the searches as there are some other hits in the sequence database that may be isoenzymes. You can use the modelling server at expose to create a homology model for the almond sequence.
Dear Annemarie Honegger
Thank you very much for your kind suggestions. It helps me a lot.
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