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Title: In Silico sequence analysis and molecular modeling of the three-dimensional structure of DAHP synthase from Pseudomonas fragi
Authors: Tapas S.
Kumar Patel G.
Dhindwal S.
Tomar, Shailly
Published in: Journal of Molecular Modeling
Abstract: The shikimate pathway is involved in production of aromatic amino acids in microorganisms and plants. The enzymes of this biosynthetic pathway are a potential target for the design of antimicrobial compounds and herbicides. 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHPS) catalyzes the first step of the pathway. The gene encoding DAHPS was cloned and sequenced from Pseudomonas fragi, the bacterium responsible for spoilage of milk, dairy products and meat. Amino acid sequence deduced from the nucleotide sequence revealed that P. fragi DAHPS (Pf-DAHPS) consists of 448 amino acids with calculated molecular weight of ?50 kDa and isoelectric point of 5.81. Primary sequence analysis of Pf-DAHPS shows that it has more than 84% identity with DAHPS of other Pseudomonas species, 46% identity with Mycobacterium tuberculosis DAHPS (Mt-DAHPS), the type II DAHPS and less than 11% sequence identity with the type I DAHPS. The three-dimensional structure of Pf-DAHPS was predicted by homology modeling based on the crystal structure of Mt-DAHPS. Pf-DAHPS model contains a (?/?)8 TIM barrel structure. Sequence alignment, phylogenetic analysis and 3D structure model classifies Pf-DAHPS as a type II DAHPS. Sequence analysis revealed the presence of DAHPS signature motif DxxHxN in Pf-DAHPS. Highly conserved sequence motif RxxxxxxKPRT(S/T) and xGxR present in type II DAHPS were also identified in Pf-DAHPS sequence. High sequence homology of DAHPS within Pseudomonas species points to the option of designing a broad spectrum drug for the genus. Pf-DAHPS 3D model provides molecular insights that may be beneficial in rationale inhibitor design for developing effective food preservative against P. fragi. © 2010 Springer-Verlag.
Citation: Journal of Molecular Modeling(2011), 17(4): 621-631
Issue Date: 2011
Keywords: 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
Homology modeling
Pseudomonas fragi
ISSN: 16102940
Author Scopus IDs: 35491918300
Author Affiliations: Tapas, S., Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
Kumar Patel, G., Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
Dhindwal, S., Department of Bio
Corresponding Author: Tomar, S.; Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India; email:
Appears in Collections:Journal Publications [BT]

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