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Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5

Jeyakanthan, Jeyaraman and Kanaujia, Shankar Prasad and Nishida, Yuya and Nakagawa, Noriko and Praveen, Surendran and Shinkai, Akeo and Kuramitsu, Seiki and Yokoyama, Shigeyuki and Sekar, Kanagaraj (2010) Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5. In: Acta Crystallographica Section D Biological Crystallography, 66 (Part 2). pp. 116-124.

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Abstract

Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 angstrom resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alpha beta alpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.

Item Type: Journal Article
Additional Information: Copyright for this article belongs to Wiley.
Department/Centre: Division of Information Sciences > BioInformatics Centre
Date Deposited: 09 Feb 2010 11:29
Last Modified: 19 Sep 2010 05:55
URI: http://eprints.iisc.ernet.in/id/eprint/25531

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