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Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies

In plants, guanosine deaminase (GSDA) catalyzes the deamination of guanosine for nitrogen recycling and re-utilization. We previously solved crystal structures of GSDA from Arabidopsis thaliana (AtGSDA) and identified several novel substrates for this enzyme, but the structural basis of the enzyme a...

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Autores principales: Jia, Qian, Zhang, Jinbing, Zeng, Hui, Tang, Jing, Xiao, Nan, Gao, Shangfang, Li, Huanxi, Xie, Wei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9739398/
https://www.ncbi.nlm.nih.gov/pubmed/36499303
http://dx.doi.org/10.3390/ijms232314976
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author Jia, Qian
Zhang, Jinbing
Zeng, Hui
Tang, Jing
Xiao, Nan
Gao, Shangfang
Li, Huanxi
Xie, Wei
author_facet Jia, Qian
Zhang, Jinbing
Zeng, Hui
Tang, Jing
Xiao, Nan
Gao, Shangfang
Li, Huanxi
Xie, Wei
author_sort Jia, Qian
collection PubMed
description In plants, guanosine deaminase (GSDA) catalyzes the deamination of guanosine for nitrogen recycling and re-utilization. We previously solved crystal structures of GSDA from Arabidopsis thaliana (AtGSDA) and identified several novel substrates for this enzyme, but the structural basis of the enzyme activation/inhibition is poorly understood. Here, we continued to solve 8 medium-to-high resolution (1.85–2.60 Å) cocrystal structures, which involved AtGSDA and its variants bound by a few ligands, and investigated their binding modes through structural studies and thermal shift analysis. Besides the lack of a 2-amino group of these guanosine derivatives, we discovered that AtGSDA’s inactivity was due to the its inability to seclude its active site. Furthermore, the C-termini of the enzyme displayed conformational diversities under certain circumstances. The lack of functional amino groups or poor interactions/geometries of the ligands at the active sites to meet the precise binding and activation requirements for deamination both contributed to AtGSDA’s inactivity toward the ligands. Altogether, our combined structural and biochemical studies provide insight into GSDA.
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spelling pubmed-97393982022-12-11 Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies Jia, Qian Zhang, Jinbing Zeng, Hui Tang, Jing Xiao, Nan Gao, Shangfang Li, Huanxi Xie, Wei Int J Mol Sci Article In plants, guanosine deaminase (GSDA) catalyzes the deamination of guanosine for nitrogen recycling and re-utilization. We previously solved crystal structures of GSDA from Arabidopsis thaliana (AtGSDA) and identified several novel substrates for this enzyme, but the structural basis of the enzyme activation/inhibition is poorly understood. Here, we continued to solve 8 medium-to-high resolution (1.85–2.60 Å) cocrystal structures, which involved AtGSDA and its variants bound by a few ligands, and investigated their binding modes through structural studies and thermal shift analysis. Besides the lack of a 2-amino group of these guanosine derivatives, we discovered that AtGSDA’s inactivity was due to the its inability to seclude its active site. Furthermore, the C-termini of the enzyme displayed conformational diversities under certain circumstances. The lack of functional amino groups or poor interactions/geometries of the ligands at the active sites to meet the precise binding and activation requirements for deamination both contributed to AtGSDA’s inactivity toward the ligands. Altogether, our combined structural and biochemical studies provide insight into GSDA. MDPI 2022-11-29 /pmc/articles/PMC9739398/ /pubmed/36499303 http://dx.doi.org/10.3390/ijms232314976 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Jia, Qian
Zhang, Jinbing
Zeng, Hui
Tang, Jing
Xiao, Nan
Gao, Shangfang
Li, Huanxi
Xie, Wei
Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies
title Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies
title_full Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies
title_fullStr Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies
title_full_unstemmed Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies
title_short Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies
title_sort substrate specificity of gsda revealed by cocrystal structures and binding studies
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9739398/
https://www.ncbi.nlm.nih.gov/pubmed/36499303
http://dx.doi.org/10.3390/ijms232314976
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