SBSPKS: structure based sequence analysis of polyketide synthases.
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.
Anand
Swadha
S
National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
Prasad
M V R
MV
Yadav
Gitanjali
G
Kumar
Narendra
N
Shehara
Jyoti
J
Ansari
Md Zeeshan
MZ
Mohanty
Debasisa
D
D020134:Catalytic Domain; D020407:Internet; D008958:Models, Molecular; D048630:Polyketide Synthases / Q000737:chemistry* / Q000378:metabolism; D020539:Sequence Analysis, Protein; D012984:Software; D013379:Substrate Specificity
D048630:Polyketide Synthases
PLoS Comput Biol. 2007 Sep;3(9):1827-35
17907798
J Biol Chem. 1995 Jun 2;270(22):12961-4
7768883
Curr Opin Drug Discov Devel. 2008 Mar;11(2):186-95
18283606
Curr Opin Struct Biol. 2007 Dec;17(6):736-43
17935970
J Biotechnol. 2009 Mar 10;140(1-2):13-7
19297688
Chembiochem. 2008 Apr 14;9(6):826-48
18357594
Chem Biol. 2006 Mar;13(3):277-85
16638533
Chem Biol. 2000 Mar;7(3):211-24
10712928
Curr Opin Chem Biol. 2009 Apr;13(2):135-43
19217343
Chembiochem. 2006 Mar;7(3):485-94
16470766
Nat Prod Rep. 2007 Oct;24(5):1041-72
17898897
BMC Bioinformatics. 2007 Sep 03;8:327
17764579
J Nat Prod. 2005 Apr;68(4):493-6
15844935
Annu Rev Biochem. 2007;76:195-221
17328673
Chem Biol. 2007 Aug;14(8):898-908
17719489
J Mol Biol. 2007 May 18;368(5):1500-17
17400247
Nucleic Acids Res. 2008 Dec;36(21):6882-92
18978015
Nucleic Acids Res. 2005 Oct 12;33(18):5799-808
16221976
Chem Biol. 1999 Aug;6(8):493-505
10421756
Nat Prod Rep. 2007 Oct;24(5):1073-109
17898898
Protein Sci. 2003 Sep;12(9):2001-14
12930999
Structure. 2006 Apr;14(4):737-48
16564177
PLoS Comput Biol. 2009 Apr;5(4):e1000351
19360130
J Nat Prod. 2007 Jan;70(1):67-74
17253852
J Am Chem Soc. 2009 Dec 30;131(51):18501-11
19928853
Angew Chem Int Ed Engl. 2009;48(26):4688-716
19514004
Science. 2008 Sep 5;321(5894):1315-22
18772430
Chem Biol. 2003 Aug;10(8):723-31
12954331
PLoS One. 2008;3(10):e3515
18953415
Chembiochem. 2006 Sep;7(9):1334-42
16871615
BMC Bioinformatics. 2009 Jun 16;10:185
19531248
Chem Biol. 2007 Aug;14(8):931-43
17719492
EMBO J. 1997 Jul 16;16(14):4174-83
9250661
Chembiochem. 2003 Jul 7;4(7):654-7
12851937
Nat Biotechnol. 2003 Feb;21(2):187-90
12536216
Methods Enzymol. 2009;458:181-217
19374984
J Mol Biol. 2003 Apr 25;328(2):335-63
12691745
Protein Sci. 2007 Oct;16(10):2093-107
17893358
Nat Prod Rep. 2009 Jul;26(7):874-83
19554239
J Bacteriol. 2007 Jul;189(13):4597-602
17468241
Curr Opin Biotechnol. 2006 Dec;17(6):597-605
17046237
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W405-13
15215420
ACS Chem Biol. 2009 Jan 16;4(1):41-52
19146481
Mol Cell. 2005 Mar 4;17(5):631-43
15749014
J Nat Prod. 2004 Aug;67(8):1356-67
15332855
Methods Enzymol. 2009;459:17-47
19362634
Nat Biotechnol. 2006 Dec;24(12):1533-40
17160059
J Org Chem. 2009 Sep 4;74(17):6416-20
19711990
PLoS Biol. 2008 Jul 8;6(7):e163
18613748
J Mol Biol. 2008 Dec 26;384(4):941-53
18952099
Curr Opin Chem Biol. 2005 Oct;9(5):447-58
16107321