Cargando…
Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis
Metal ions at the active site of an enzyme act as cofactors, and their dynamic fluctuations can potentially influence enzyme activity. Here, we use λ-exonuclease as a model enzyme with two Mg(2+) binding sites and probe activity at various concentrations of magnesium by single-molecule-FRET. We find...
Autores principales: | , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6199318/ https://www.ncbi.nlm.nih.gov/pubmed/30353000 http://dx.doi.org/10.1038/s41467-018-06750-9 |
_version_ | 1783365119509528576 |
---|---|
author | Hwang, Wonseok Yoo, Jungmin Lee, Yuno Park, Suyeon Hoang, Phuong Lien Cho, HyeokJin Yu, Jeongmin Hoa Vo, Thi Minh Shin, Minsang Jin, Mi Sun Park, Daeho Hyeon, Changbong Lee, Gwangrog |
author_facet | Hwang, Wonseok Yoo, Jungmin Lee, Yuno Park, Suyeon Hoang, Phuong Lien Cho, HyeokJin Yu, Jeongmin Hoa Vo, Thi Minh Shin, Minsang Jin, Mi Sun Park, Daeho Hyeon, Changbong Lee, Gwangrog |
author_sort | Hwang, Wonseok |
collection | PubMed |
description | Metal ions at the active site of an enzyme act as cofactors, and their dynamic fluctuations can potentially influence enzyme activity. Here, we use λ-exonuclease as a model enzyme with two Mg(2+) binding sites and probe activity at various concentrations of magnesium by single-molecule-FRET. We find that while Mg(A)(2+) and Mg(B)(2+) have similar binding constants, the dissociation rate of Mg(A)(2+) is two order of magnitude lower than that of Mg(B)(2+) due to a kinetic-barrier-difference. At physiological Mg(2+) concentration, the Mg(B)(2+) ion near the 5’-terminal side of the scissile phosphate dissociates each-round of degradation, facilitating a series of DNA cleavages via fast product-release concomitant with enzyme-translocation. At a low magnesium concentration, occasional dissociation and slow re-coordination of Mg(A)(2+) result in pauses during processive degradation. Our study highlights the importance of metal-ion-coordination dynamics in correlation with the enzymatic reaction-steps, and offers insights into the origin of dynamic heterogeneity in enzymatic catalysis. |
format | Online Article Text |
id | pubmed-6199318 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-61993182018-10-25 Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis Hwang, Wonseok Yoo, Jungmin Lee, Yuno Park, Suyeon Hoang, Phuong Lien Cho, HyeokJin Yu, Jeongmin Hoa Vo, Thi Minh Shin, Minsang Jin, Mi Sun Park, Daeho Hyeon, Changbong Lee, Gwangrog Nat Commun Article Metal ions at the active site of an enzyme act as cofactors, and their dynamic fluctuations can potentially influence enzyme activity. Here, we use λ-exonuclease as a model enzyme with two Mg(2+) binding sites and probe activity at various concentrations of magnesium by single-molecule-FRET. We find that while Mg(A)(2+) and Mg(B)(2+) have similar binding constants, the dissociation rate of Mg(A)(2+) is two order of magnitude lower than that of Mg(B)(2+) due to a kinetic-barrier-difference. At physiological Mg(2+) concentration, the Mg(B)(2+) ion near the 5’-terminal side of the scissile phosphate dissociates each-round of degradation, facilitating a series of DNA cleavages via fast product-release concomitant with enzyme-translocation. At a low magnesium concentration, occasional dissociation and slow re-coordination of Mg(A)(2+) result in pauses during processive degradation. Our study highlights the importance of metal-ion-coordination dynamics in correlation with the enzymatic reaction-steps, and offers insights into the origin of dynamic heterogeneity in enzymatic catalysis. Nature Publishing Group UK 2018-10-23 /pmc/articles/PMC6199318/ /pubmed/30353000 http://dx.doi.org/10.1038/s41467-018-06750-9 Text en © The Author(s) 2018 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Hwang, Wonseok Yoo, Jungmin Lee, Yuno Park, Suyeon Hoang, Phuong Lien Cho, HyeokJin Yu, Jeongmin Hoa Vo, Thi Minh Shin, Minsang Jin, Mi Sun Park, Daeho Hyeon, Changbong Lee, Gwangrog Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis |
title | Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis |
title_full | Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis |
title_fullStr | Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis |
title_full_unstemmed | Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis |
title_short | Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis |
title_sort | dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6199318/ https://www.ncbi.nlm.nih.gov/pubmed/30353000 http://dx.doi.org/10.1038/s41467-018-06750-9 |
work_keys_str_mv | AT hwangwonseok dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT yoojungmin dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT leeyuno dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT parksuyeon dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT hoangphuonglien dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT chohyeokjin dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT yujeongmin dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT hoavothiminh dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT shinminsang dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT jinmisun dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT parkdaeho dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT hyeonchangbong dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis AT leegwangrog dynamiccoordinationoftwometalionsorchestrateslexonucleasecatalysis |