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Online Journal of Bioinformatics ©
Volume 12(2):345-356, 2011
Model of a Zn2+ binding domain of peptidase M48 Ste24p from Cyanothece Sp. (Strain PCC 7822).
Patra MC, Rath SN*, Bhoi GK, Pradhan SK
Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, Orissa, India- 751003
Patra MC, Rath SN, Bhoi GK, Pradhan SK, Model of a Zn2+ Binding Domain of Peptidase M48 Ste24p from Cyanothece Sp. (Strain PCC 7822), Onl J Bioinform., 12(2):345-356, 2011. A three dimensional model for the catalytic domain of Peptidase M48 Ste24p from Cyanothece sp. (strain PCC 7822) was computed using homology modeling and molecular dynamics simulation. Modeling was performed for the 228 amino acids containing the HEXXH motif, which is implicated with metal binding in M48 family of metallopeptidases. The Zinc atom was found to coordinate tetrahedrally with His459, His463, Glu506 and His549 of the model that substantiates the existing experimental information on the active site of metallopeptidases. Consequently, the tertiary structure reported here might be able to justify the molecular function and catalytic properties of the novel metallopeptidases of cyanobacteria. The coordinates of the model can be downloaded at http://mi.caspur.it/PMDB using PMDB ID: PM0077456.
Key Words: Cyanobacteria, Cyanothece sp., HEXXH motif, Metallopeptidase, Homology modeling, Molecular dynamics simulation.