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Binding asymmetry and conformational studies of the AtGSDA dimer
Guanosine deaminase (GSDA) is an important deaminase that converts guanosine to xanthosine, a key intermediate in nitrogen recycling in plants. We previously solved complex structures of Arabidopsis thaliana GSDA bound by various ligands and examined its catalytic mechanism. Here, we report cocrysta...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Research Network of Computational and Structural Biotechnology
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10663702/ https://www.ncbi.nlm.nih.gov/pubmed/38022696 http://dx.doi.org/10.1016/j.csbj.2023.11.004 |
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author | Jia, Qian Zeng, Hui Li, Mingwei Tang, Jing Xiao, Nan Gao, Shangfang Li, Huanxi Zhang, Jinbing Zhang, Zhiyong Xie, Wei |
author_facet | Jia, Qian Zeng, Hui Li, Mingwei Tang, Jing Xiao, Nan Gao, Shangfang Li, Huanxi Zhang, Jinbing Zhang, Zhiyong Xie, Wei |
author_sort | Jia, Qian |
collection | PubMed |
description | Guanosine deaminase (GSDA) is an important deaminase that converts guanosine to xanthosine, a key intermediate in nitrogen recycling in plants. We previously solved complex structures of Arabidopsis thaliana GSDA bound by various ligands and examined its catalytic mechanism. Here, we report cocrystal structures of AtGSDA bound by inactive guanosine derivatives, which bind relatively weakly to the enzyme and mostly have poor binding geometries. The two protomers display unequal binding performances, and molecular dynamics simulation identified diverse conformations during the enzyme-ligand interactions. Moreover, intersubunit, tripartite salt bridges show conformational differences between the two protomers, possibly acting as “gating” systems for substrate binding and product release. Our structural and biochemical studies provide a comprehensive understanding of the enzymatic behavior of this intriguing enzyme. |
format | Online Article Text |
id | pubmed-10663702 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Research Network of Computational and Structural Biotechnology |
record_format | MEDLINE/PubMed |
spelling | pubmed-106637022023-11-04 Binding asymmetry and conformational studies of the AtGSDA dimer Jia, Qian Zeng, Hui Li, Mingwei Tang, Jing Xiao, Nan Gao, Shangfang Li, Huanxi Zhang, Jinbing Zhang, Zhiyong Xie, Wei Comput Struct Biotechnol J Research Article Guanosine deaminase (GSDA) is an important deaminase that converts guanosine to xanthosine, a key intermediate in nitrogen recycling in plants. We previously solved complex structures of Arabidopsis thaliana GSDA bound by various ligands and examined its catalytic mechanism. Here, we report cocrystal structures of AtGSDA bound by inactive guanosine derivatives, which bind relatively weakly to the enzyme and mostly have poor binding geometries. The two protomers display unequal binding performances, and molecular dynamics simulation identified diverse conformations during the enzyme-ligand interactions. Moreover, intersubunit, tripartite salt bridges show conformational differences between the two protomers, possibly acting as “gating” systems for substrate binding and product release. Our structural and biochemical studies provide a comprehensive understanding of the enzymatic behavior of this intriguing enzyme. Research Network of Computational and Structural Biotechnology 2023-11-04 /pmc/articles/PMC10663702/ /pubmed/38022696 http://dx.doi.org/10.1016/j.csbj.2023.11.004 Text en © 2023 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Research Article Jia, Qian Zeng, Hui Li, Mingwei Tang, Jing Xiao, Nan Gao, Shangfang Li, Huanxi Zhang, Jinbing Zhang, Zhiyong Xie, Wei Binding asymmetry and conformational studies of the AtGSDA dimer |
title | Binding asymmetry and conformational studies of the AtGSDA dimer |
title_full | Binding asymmetry and conformational studies of the AtGSDA dimer |
title_fullStr | Binding asymmetry and conformational studies of the AtGSDA dimer |
title_full_unstemmed | Binding asymmetry and conformational studies of the AtGSDA dimer |
title_short | Binding asymmetry and conformational studies of the AtGSDA dimer |
title_sort | binding asymmetry and conformational studies of the atgsda dimer |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10663702/ https://www.ncbi.nlm.nih.gov/pubmed/38022696 http://dx.doi.org/10.1016/j.csbj.2023.11.004 |
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