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Structural and biochemical studies on the role of active site Thr166 and Asp236 in the catalytic function of D-Serine deaminase from Salmonella typhimurium

Deka, Geeta and Bharath, Sakshibeedu R and Savithri, Handanhal Subbarao and Murthy, Mathur Ramabhadrashastry Narasimha (2018) Structural and biochemical studies on the role of active site Thr166 and Asp236 in the catalytic function of D-Serine deaminase from Salmonella typhimurium. In: BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 504 (1). pp. 40-45.

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Official URL: http://dx.doi.org/10.1016/j.bbrc.2018.08.116

Abstract

D-Serine deaminase (DSD) degrades D-Ser to pyruvate and ammonia. Uropathogenic bacteria survive in the toxic D-Ser containing mammalian urine because of DSD activity. The crystal structure of the apo form of Salmonella typhimurium DSD (StDSD) has been reported earlier. In the present work, we have investigated the role of two active site residues, Thr166 and Asp236 by site directed mutagenesis (T166A and D236L). The enzyme activity is lost upon mutation of these residues. The 2.7 angstrom resolution crystal structure of T166A DSD with bound PLP reported here represents the first structure of the holo form of StDSD. PLP binding induces small changes in the relative dispositions of the minor and major domains of the protein and this inter-domain movement becomes substantial upon interaction with the substrate. The conformational changes bring Thr166 to a position at the active site favorable for the degradation of D-Ser. Examination of the different forms of the enzyme and comparison with structures of homologous enzymes suggests that Thr166 is the most probable base abstracting proton from the C alpha atom of the substrate and Asp236 is crucial for binding of the cofactor. (C) 2018 Elsevier Inc. All rights reserved.

Item Type: Journal Article
Additional Information: Copy right for this article belong to ACADEMIC PRESS INC ELSEVIER SCIENCE
Keywords: Salmonella typhimurium; PLP binding; X-ray crystal structure; D-ser; Active site
Department/Centre: Division of Biological Sciences > Biochemistry
Division of Biological Sciences > Molecular Biophysics Unit
Depositing User: Id for Latest eprints
Date Deposited: 31 Oct 2018 13:58
Last Modified: 31 Oct 2018 13:58
URI: http://eprints.iisc.ac.in/id/eprint/61001

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