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Insight into the binding affinity of thiourea in the calcium binding pocket of proteinase K, through high resolution X-ray crystallography.

Authors
  • Ahmad, Malik Shoaib1
  • Akbar, Zeeshan2
  • Choudhary, M Iqbal3
  • 1 Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan. Electronic address: [email protected] , (Pakistan)
  • 2 H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan. , (Pakistan)
  • 3 Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21412, Saudi Arabia. , (Pakistan)
Type
Published Article
Journal
Bioorganic chemistry
Publication Date
Nov 15, 2019
Pages
103443–103443
Identifiers
DOI: 10.1016/j.bioorg.2019.103443
PMID: 31812259
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Proteinase K is a stable serine protease, crystallized and extensively used in the study of molecular interactions at the atomic level. During the current study, crystal structure of proteinase K with thiourea (TU) was solved at 1.45 Å (angstrom) resolution. Proteinase K showed its binding affinity with thiourea after soaking with 200 mM (millimolar) concentration of thiourea solution for 6 h. The binding affinity of proteinase K was evaluated with three different molecules i.e., thiourea, acetamide, and thiosemicarbazide. Interestingly, only the thiourea went into the calcium-binding region, and showed interactions with those amino acids which have also displayed interactions with calcium previously. Pro175 (proline 175), Ser197 (Serine 197), Val198 (valine 198), and Asp200 (aspartic acid 200) were the key amino acids involved in the binding of thiourea with proteinase K. Thiourea showed strong hydrogen bondings with Pro175 (2.85 Å), Ser197 (2.88 Å), and Asp200 (2.90 Å, and 3.30 Å), as the key interactions involved in the binding of thiourea with proteinase K. This study provides an insight into the binding mechanism of thiourea with calcium-binding pocket of proteinase K, and thus can be extrapolated to other calcium-binding proteins. Copyright © 2019 Elsevier Inc. All rights reserved.

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