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Catalytic pathway, substrate binding and stability in SAICAR synthetase: A structure and molecular dynamics study

Manjunath, Kavyashree and Jeyakanthan, Jeyaraman and Sekar, Kanagaraj (2015) Catalytic pathway, substrate binding and stability in SAICAR synthetase: A structure and molecular dynamics study. In: JOURNAL OF STRUCTURAL BIOLOGY, 191 (1). pp. 22-31.

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Official URL: http://dx.doi.org/10.1016/j.jsb.2015.06.006

Abstract

The de novo purine biosynthesis is one of the highly conserved pathways among all organisms and is essential for the cell viability. A clear understanding of the enzymes in this pathway would pave way for the development of antimicrobial and anticancer drugs. Phosphoribosylaminoimidazole-succinocar boxamide (SAICAR) synthetase is one of the enzymes in this pathway that catalyzes ATP dependent ligation of carboxyaminoimidazole ribotide (CAIR) with L-aspartate (ASP). Here, we describe eight crystal structures of this enzyme, in C222(1) and H3 space groups, bound to various substrates and substrate mimics from a hyperthermophilic archaea Pyrococcus horikoshii along with molecular dynamics simulations of the structures with substrates. Complexes exhibit minimal deviation from its apo structure. The CAIR binding site displays a preference for pyrimidine nucleotides. In the ADP.TMP-ASP complex, the ASP binds at a position equivalent to that found in Saccharomyces cerevisiae structure (PDB: 2CNU) and thus, clears the ambiguity regarding ASP's position. A possible mode for the inhibition of the enzyme by CTP and UTP, observed earlier in the yeast enzyme, is clearly illustrated in the structures bound to CMP and UMP. The ADP.Mg2+.PO4.CD/MP complex having a phosphate ion between the ATP and CAIR sites strengthens one of the two probable pathways (proposed in Escherichia coli study) of catalytic mechanism and suggests the possibility of a phosphorylation taking place before the ASP's attack on CAIR. Molecular dynamic simulations of this enzyme along with its substrates at 90 degrees C reveal the relative strengths of substrate binding, possible antagonism and the role of Mg2+ ions. (C) 2015 Elsevier Inc. All rights reserved.

Item Type: Journal Article
Additional Information: Copy right for this article belongs to the ACADEMIC PRESS INC ELSEVIER SCIENCE, 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA
Keywords: Purine de novo biosynthesis; Pyrococcus horikoshii OT3; SAICAR synthetase; ATP binding; Molecular dynamics; Enzyme mechanism
Department/Centre: Division of Interdisciplinary Research > Supercomputer Education & Research Centre
Depositing User: Id for Latest eprints
Date Deposited: 11 Aug 2015 07:34
Last Modified: 11 Aug 2015 07:34
URI: http://eprints.iisc.ac.in/id/eprint/52075

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