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SBSPKS: structure based sequence analysis of polyketide synthases

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Title SBSPKS: structure based sequence analysis of polyketide synthases
 
Creator Anand, Swadha
Prasad, M.V.R.
Yadav, Gitanjali
Kumar, Narendra
Shehara, Jyoti
Ansari, Md. Zeeshan
Mohanty, Debasisa
 
Subject polyketide synthases
SBSPKS
sequence analysis
 
Description Polyketide synthases (PKSs) catalyze biosynthesis of a diverse family of pharmaceutically important secondary metabolites. Bioinformatics analysis of sequence and structural features of PKS proteins plays a crucial role in discovery of new natural products by genome mining, as well as in design of novel secondary metabolites by biosynthetic engineering. The availability of the crystal structures of various PKS catalytic and docking domains, and mammalian fatty acid synthase module prompted us to develop SBSPKS software which consists of three major components. Model_3D_PKS can be used for modeling, visualization and analysis of 3D structure of individual PKS catalytic domains, dimeric structures for complete PKS modules and prediction of substrate specificity. Dock_Dom_Anal identifies the key interacting residue pairs in inter-subunit interfaces based on alignment of inter-polypeptide linker sequences to the docking domain structure. In case of modular PKS with multiple open reading frames (ORFs), it can predict the cognate order of substrate channeling based on combinatorial evaluation of all possible interface contacts. NRPS-PKS provides user friendly tools for identifying various catalytic domains in the sequence of a Type I PKS protein and comparing them with experimentally characterized PKS/NRPS clusters cataloged in the backend databases of SBSPKS. SBSPKS is available at http://www.nii.ac.in/sbspks.html.
Authors thank Director, NII for support and Rajesh S. Gokhale for valuable inputs and discussions. S.A. thanks CSIR, India for award of senior research fellowship. The authors are thankful to Prof. R.L. Dunbrack Jr for allowing the use of SCWRL program for modeling of side chains.
 
Date 2014-02-20T04:58:51Z
2014-02-20T04:58:51Z
2010
19 April 2010
 
Type Article
 
Identifier Nucl. Acids Res., 38: W487-W496
http://hdl.handle.net/123456789/137
 
Language en
 
Publisher Oxford University Press