Structure and function prediction of arsenate reductase from Deinococcus indicus DR1

Abstract

Arsenic prevalence in the environment impelled many organisms to develop resistance over the course of evolution. Tolerance to arsenic, either as the pentavalent [As(V)] form or the trivalent form [As(III)], by bacteria has been well studied in prokaryotes, and the mechanism of action is well defined. However, in the rod-shaped arsenic tolerant Deinococcus indicus DR1, the key enzyme, arsenate reductase (ArsC) has not been well studied. ArsC of D. indicus belongs to the Grx-linked prokaryotic arsenate reductase family. While it shares homology with the well-studied ArsC of Escherichia coli having a catalytic cysteine (Cys 12) and arginine triad (Arg 60, 94, and 107), the active site of D.indicus ArsC contains four residues Glu 9, Asp 53, Arg 86, and Glu 100, and with complete absence of structurally equivalent residue for crucial Cys 12. Here, we report that the mechanism of action of ArsC of D. indicus is different as a result of convergent evolution and most likely able to detoxify As(V) using a mix of positively- and negatively-charged residues in its active site, unlike the residues of E. coli. This suggests toward the possibility of an alternative mechanism of As (V) degradation in bacteria.

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Data availability

The model used in this study has been deposited at ModelArchive (https://www.modelarchive.org/doi/10.5452/ma-abpir) and is available for public use. The trajectory snapshot from MD simulation has been uploaded as Supplementary material.

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Acknowledgments

PAS, VA, and RMY acknowledge Jaypee University of Information Technology for providing research facilities to conduct this study. RP acknowledges Shiv Nadar University for providing research facilities and DC is supported by a doctoral research fellowship from Shiv Nadar University.

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Correspondence to Ragothaman M. Yennamalli or Richa Priyadarshini.

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Electronic supplementary material

Supplementary Fig. S1
figure4

Ramachandran plot of model 1. (PNG 426 kb)

Supplementary Fig. S2
figure5

Root mean square deviation analysis of MD simulation. The least square fit of the entire protein from 0 ns was compared to snapshots of the entire protein at frequent intervals throughout the 100 ns simulation. The plot indicates equilibration of model 1 reached after 20 ns or so. (PNG 68 kb)

Supplementary Fig. S3
figure6

Root mean square fluctuation of residue of MD simulation. The fluctuation throughout the trajectory for each residue in model 1 is plotted, where the maximum fluctuation is observed in the C-terminal region of the protein. (PNG 194 kb)

Supplementary Fig. S4
figure7

Radius of gyration of model 1. The radius of gyration of the entire protein fluctuates between 1.4 nm to 1.52 nm throughout the trajectory indicating that the model is stable and does not denature during the simulation. (PNG 55 kb)

Supplementary Fig. S5
figure8

Molecular docking of As (III) with ArsC of D. indicus and residues that are within 5 Å radius. (PNG 2067 kb)

High resolution image (TIFF 33951 kb)

High resolution image (TIF 825 kb)

High resolution image (TIFF 20738 kb)

High resolution image (TIF 604 kb)

High resolution image (TIF 198 kb)

ESM 1

(DOCX 13 kb)

ESM 2

(DOCX 18 kb)

ESM 3

(PDB 14357 kb)

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Chauhan, D., Srivastava, P.A., Agnihotri, V. et al. Structure and function prediction of arsenate reductase from Deinococcus indicus DR1. J Mol Model 25, 15 (2019). https://doi.org/10.1007/s00894-018-3885-3

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Keywords

  • Arsenate reductase
  • Deinococcus indicus DR1
  • Mechanism of action
  • Arsenic tolerance
  • Molecular modeling