Crystal structures of an archaeal thymidylate kinase from Sulfolobus tokodaii provide insights into the role of a conserved active site Arginine residue

Biswas, Ansuman and Shukla, Arpit and Vijayan, R S K and Jeyakanthan, Jeyaraman and Sekar, Kanagaraj (2017) Crystal structures of an archaeal thymidylate kinase from Sulfolobus tokodaii provide insights into the role of a conserved active site Arginine residue. In: JOURNAL OF STRUCTURAL BIOLOGY, 197 (3). pp. 236-249.

PDF Jou_Srt_Bio_197_236_2017.pdf - Published Version Restricted to Registered users only Download (3MB) | Request a copy

Abstract

Thymidylate kinase (TMK) is a key enzyme that plays an important role in DNA synthesis. Therefore, it serves as an attractive therapeutic target for the development of antibacterial, antiparasitic and anticancer drugs. Herein, we report the biochemical characterization and crystal structure determination of thymidylate kinase from a hyperthermophilic organism Sulfolobus tokodaii (StTMK) in its apo and ADP-bound forms. Our study describes the first three-dimensional structure of an archaeal TMK. StTMK is a thermostable enzyme with optimum activity at 80 degrees C. Despite the overall similarity to homologous TMKs, StTMK structures revealed several residue substitutions at the active site. However, enzyme assays demonstrated specificity to its natural substrates ATP and dTMP. Analysis of the structures also revealed multiple conformational states of Arg93 which is located at the reaction centre and is a part of the highly conserved DRX motif. Only one of these states was found to be suitable for the proper positioning of the alpha-phosphate group of dTMP at the active site. Computational alanine scanning and MM/PBSA binding energy calculation revealed the importance of Arg93 side chain in substrate binding. Subsequent site directed mutagenesis at this position to an Ala resulted in the loss of activity. Thus, the computational and biochemical studies reveal the importance of Arg93 for enzyme function, while the different conformational states of Arg93 observed in the structural studies imply its regulatory role in the catalytically competent placement of dTMP. (C) 2016 Elsevier Inc. All rights reserved.

Item Type:	Journal Article
Publication:	JOURNAL OF STRUCTURAL BIOLOGY
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
Department/Centre:	Division of Interdisciplinary Sciences > Computational and Data Sciences Division of Physical & Mathematical Sciences > Physics
Date Deposited:	20 May 2017 03:41
Last Modified:	11 Oct 2018 15:16
URI:	http://eprints.iisc.ac.in/id/eprint/56687

Actions (login required)

View Item