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Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family
Burkholderia pseudomallei is a highly versatile pathogen with ~25% of its genome annotated to encode hypothetical proteins. One such hypothetical protein, BPSL1038, is conserved across seven bacterial genera and 654 Burkholderia spp. Here, we present a 1.55 Å resolution crystal structure of BPSL1038...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10491678/ https://www.ncbi.nlm.nih.gov/pubmed/37684342 http://dx.doi.org/10.1038/s42003-023-05265-4 |
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author | Shaibullah, Sofiyah Shuhaimi, Nurshahirah Ker, De-Sheng Mohd-Sharif, Nurhikmah Ho, Kok Lian Teh, Aik-Hong Waterman, Jitka Tang, Thean-Hock Wong, Rui-Rui Nathan, Sheila Mohamed, Rahmah Ng, Min Jia Fung, Shin-Yee Jonet, Mohd Anuar Firdaus-Raih, Mohd Ng, Chyan Leong |
author_facet | Shaibullah, Sofiyah Shuhaimi, Nurshahirah Ker, De-Sheng Mohd-Sharif, Nurhikmah Ho, Kok Lian Teh, Aik-Hong Waterman, Jitka Tang, Thean-Hock Wong, Rui-Rui Nathan, Sheila Mohamed, Rahmah Ng, Min Jia Fung, Shin-Yee Jonet, Mohd Anuar Firdaus-Raih, Mohd Ng, Chyan Leong |
author_sort | Shaibullah, Sofiyah |
collection | PubMed |
description | Burkholderia pseudomallei is a highly versatile pathogen with ~25% of its genome annotated to encode hypothetical proteins. One such hypothetical protein, BPSL1038, is conserved across seven bacterial genera and 654 Burkholderia spp. Here, we present a 1.55 Å resolution crystal structure of BPSL1038. The overall structure folded into a modified βαββαβα ferredoxin fold similar to known Cas2 nucleases. The Cas2 equivalent catalytic aspartate (D11) pairs are conserved in BPSL1038 although B. pseudomallei has no known CRISPR associated system. Functional analysis revealed that BPSL1038 is a nuclease with endonuclease activity towards double-stranded DNA. The DNase activity is divalent ion independent and optimum at pH 6. The concentration of monovalent ions (Na(+) and K(+)) is crucial for nuclease activity. An active site with a unique D(11)(X20)SST motif was identified and proposed for BPSL1038 and its orthologs. Structure modelling indicates the catalytic role of the D(11)(X20)SST motif and that the arginine residues R10 and R30 may interact with the nucleic acid backbone. The structural similarity of BPSL1038 to Cas2 proteins suggests that BPSL1038 may represent a sub-family of nucleases that share a common ancestor with Cas2. |
format | Online Article Text |
id | pubmed-10491678 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-104916782023-09-10 Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family Shaibullah, Sofiyah Shuhaimi, Nurshahirah Ker, De-Sheng Mohd-Sharif, Nurhikmah Ho, Kok Lian Teh, Aik-Hong Waterman, Jitka Tang, Thean-Hock Wong, Rui-Rui Nathan, Sheila Mohamed, Rahmah Ng, Min Jia Fung, Shin-Yee Jonet, Mohd Anuar Firdaus-Raih, Mohd Ng, Chyan Leong Commun Biol Article Burkholderia pseudomallei is a highly versatile pathogen with ~25% of its genome annotated to encode hypothetical proteins. One such hypothetical protein, BPSL1038, is conserved across seven bacterial genera and 654 Burkholderia spp. Here, we present a 1.55 Å resolution crystal structure of BPSL1038. The overall structure folded into a modified βαββαβα ferredoxin fold similar to known Cas2 nucleases. The Cas2 equivalent catalytic aspartate (D11) pairs are conserved in BPSL1038 although B. pseudomallei has no known CRISPR associated system. Functional analysis revealed that BPSL1038 is a nuclease with endonuclease activity towards double-stranded DNA. The DNase activity is divalent ion independent and optimum at pH 6. The concentration of monovalent ions (Na(+) and K(+)) is crucial for nuclease activity. An active site with a unique D(11)(X20)SST motif was identified and proposed for BPSL1038 and its orthologs. Structure modelling indicates the catalytic role of the D(11)(X20)SST motif and that the arginine residues R10 and R30 may interact with the nucleic acid backbone. The structural similarity of BPSL1038 to Cas2 proteins suggests that BPSL1038 may represent a sub-family of nucleases that share a common ancestor with Cas2. Nature Publishing Group UK 2023-09-08 /pmc/articles/PMC10491678/ /pubmed/37684342 http://dx.doi.org/10.1038/s42003-023-05265-4 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Shaibullah, Sofiyah Shuhaimi, Nurshahirah Ker, De-Sheng Mohd-Sharif, Nurhikmah Ho, Kok Lian Teh, Aik-Hong Waterman, Jitka Tang, Thean-Hock Wong, Rui-Rui Nathan, Sheila Mohamed, Rahmah Ng, Min Jia Fung, Shin-Yee Jonet, Mohd Anuar Firdaus-Raih, Mohd Ng, Chyan Leong Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family |
title | Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family |
title_full | Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family |
title_fullStr | Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family |
title_full_unstemmed | Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family |
title_short | Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family |
title_sort | structural and functional analyses of burkholderia pseudomallei bpsl1038 reveal a cas-2/vapd nuclease sub-family |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10491678/ https://www.ncbi.nlm.nih.gov/pubmed/37684342 http://dx.doi.org/10.1038/s42003-023-05265-4 |
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