Display options
Cite
Kamjula V, Kanneganti A, Metla R, et al. Decoding the vital segments in human ATP-dependent RNA helicase. Bioinformation. 2020;16(2):160-170doi: 10.6026/97320630016160.
Kamjula, V., Kanneganti, A., Metla, R., Nidamanuri, K., Idupulapati, S., & Runthala, A. (2020). Decoding the vital segments in human ATP-dependent RNA helicase. Bioinformation, 16(2), 160-170. https://doi.org/10.6026/97320630016160
Kamjula, Vandana, et al. "Decoding the vital segments in human ATP-dependent RNA helicase." Bioinformation vol. 16,2 (2020): 160-170. doi: https://doi.org/10.6026/97320630016160
Kamjula V, Kanneganti A, Metla R, Nidamanuri K, Idupulapati S, Runthala A. Decoding the vital segments in human ATP-dependent RNA helicase. Bioinformation. 2020 Feb 29;16(2):160-170. doi: 10.6026/97320630016160. eCollection 2020. PMID: 32405168; PMCID: PMC7196165.
Copy Download .nbib Format: NLM
Share it on

Bioinformation. 2020 Feb 29;16(2):160-170. doi: 10.6026/97320630016160. eCollection 2020.

Decoding the vital segments in human ATP-dependent RNA helicase.

Bioinformation

Vandana Kamjula, Ananya Kanneganti, Rohan Metla, Kusuma Nidamanuri, Sudarshan Idupulapati, Ashish Runthala

Affiliations

  1. Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India.

PMID: 32405168 PMCID: PMC7196165 DOI: 10.6026/97320630016160

Abstract

An analysis of the ATP-dependent RNA helicase using known functionally close analogs helps disclose the structural and functional information of the enzyme. The enzyme plays several interlinked biological functions and there is an urgent need to interpret its key active-site residues to infer function and establish role. The human protein q96c10.1 is annotated using tools such as interpro, go and cdd. The physicochemical properties are estimated using the tool protparam. We describe the enzyme protein model developed using modeller to identify active site residues. We used consurf to estimate the structural conservation and is evolutionary relationship is inferred using known close sequence homologs. The active site is predicted using castp and its topological flexibility is estimated through cabs-flex. The protein is annotated as a hydrolase using available data and ddx58 is found as its top-ranked interacting protein partner. We show that about 124 residues are found to be highly conserved among 259 homologs, clustered in 7 clades with the active-site showing low sequence conservation. It is further shown that only 9 loci among the 42 active-site residues are conserved with limited structural fluctuation from the wild type structure. Thus, we document various useful information linked to function, sequence similarity and phylogeny of the enzyme for annotation as potential helicase as designated by uniprot. Data shows limited degree of conserved sequence segments with topological flexibility unlike in other subfamily members of the protein.

© 2020 Biomedical Informatics.

Keywords: MODELLER; RNA helicase; flexibility; innate immunity; motif

References

  1. J Mol Biol. 2018 Jul 20;430(15):2237-2243 - PubMed
  2. Sci Rep. 2017 Nov 16;7(1):15710 - PubMed
  3. Biol Chem. 2009 Dec;390(12):1237-50 - PubMed
  4. Curr Opin Immunol. 2008 Feb;20(1):17-22 - PubMed
  5. PLoS Comput Biol. 2008 May 09;4(4):e1000071 - PubMed
  6. Biochim Biophys Acta. 2013 Aug;1829(8):750-5 - PubMed
  7. Mol Biol Evol. 2000 Apr;17(4):540-52 - PubMed
  8. Int Rev Cell Mol Biol. 2019;344:215-253 - PubMed
  9. Trends Biochem Sci. 2011 Jan;36(1):19-29 - PubMed
  10. Nucleic Acids Res. 2016 Jul 8;44(W1):W344-50 - PubMed
  11. Sci Rep. 2018 Sep 21;8(1):14189 - PubMed
  12. Mol Cell Endocrinol. 2017 Jan 5;439:175-186 - PubMed
  13. J Bioinform Comput Biol. 2019 Apr;17(2):1950006 - PubMed
  14. Curr Protoc Bioinformatics. 2016 Jun 20;54:5.6.1-5.6.37 - PubMed
  15. PLoS One. 2010 Sep 30;5(9): - PubMed
  16. J Biol Chem. 2019 Jul 26;294(30):11473-11485 - PubMed
  17. Curr Opin Immunol. 2014 Feb;26:49-55 - PubMed
  18. Trends Biochem Sci. 1999 May;24(5):192-8 - PubMed
  19. J Biol Chem. 2008 Jun 6;283(23):15825-33 - PubMed
  20. J Mol Biol. 1999 Sep 17;292(2):195-202 - PubMed
  21. Methods Enzymol. 2012;511:385-403 - PubMed
  22. FEBS J. 2006 Nov;273(22):5086-100 - PubMed
  23. Clin Chim Acta. 2014 Sep 25;436:45-58 - PubMed
  24. J Biomol Struct Dyn. 2012;30(5):607-15 - PubMed
  25. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37 - PubMed
  26. Nucleic Acids Res. 2016 Jul 8;44(W1):W406-9 - PubMed
  27. J Immunol. 2005 Sep 1;175(5):2851-8 - PubMed
  28. Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36 - PubMed
  29. Nucleic Acids Res. 2019 Jan 8;47(D1):D351-D360 - PubMed
  30. Crit Rev Biochem Mol Biol. 2014 Jul-Aug;49(4):343-60 - PubMed
  31. Bioinformatics. 2004 Oct 12;20(15):2460-2 - PubMed
  32. Nucleic Acids Res. 2006;34(15):4168-80 - PubMed
  33. Trends Cell Biol. 1994 Aug;4(8):271-4 - PubMed
  34. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W427-31 - PubMed
  35. Nucleic Acids Res. 2018 Jul 2;46(W1):W363-W367 - PubMed
  36. Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613 - PubMed
  37. Prog Biophys Mol Biol. 2018 Dec;140:79-89 - PubMed
  38. Curr Opin Struct Biol. 2007 Jun;17(3):316-24 - PubMed
  39. J Mol Biol. 2001 Jan 19;305(3):567-80 - PubMed
  40. Nat Rev Mol Cell Biol. 2011 Jul 22;12(8):505-16 - PubMed
  41. Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1512-7 - PubMed
  42. Nucleic Acids Res. 2017 Jan 4;45(D1):D200-D203 - PubMed
  43. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W89-93 - PubMed
  44. Nucleic Acids Res. 2002 Apr 1;30(7):1427-64 - PubMed
  45. J Interferon Cytokine Res. 2019 Nov;39(11):669-683 - PubMed
  46. J Interferon Cytokine Res. 2019 Jun;39(6):331-346 - PubMed
  47. Nat Rev Mol Cell Biol. 2018 May;19(5):327-341 - PubMed
  48. Science. 2006 Jul 7;313(5783):68-71 - PubMed
  49. J Neurochem. 1988 Jul;51(1):1-14 - PubMed
  50. Gene. 2006 Feb 15;367:17-37 - PubMed
  51. Wiley Interdiscip Rev RNA. 2013 Jul-Aug;4(4):369-85 - PubMed
  52. Biochem J. 2019 Sep 13;476(18):2521-2543 - PubMed
  53. Nucleic Acids Res. 2006;34(15):4206-15 - PubMed
  54. Hepatology. 2016 Oct;64(4):1033-48 - PubMed
  55. Syst Biol. 2010 May;59(3):307-21 - PubMed

Publication Types