Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis

Wonseok Hwang, Jungmin Yoo, Yuno Lee, Suyeon Park, Phuong Lien Hoang, HyeokJin Cho, Jeongmin Yu, Thi Minh Hoa Vo, Minsang Shin, Mi Sun Jin, Daeho Park, Changbong Hyeon () and Gwangrog Lee ()
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Wonseok Hwang: Korea Institute for Advanced Study
Jungmin Yoo: Gwangju Institute of Science and Technology
Yuno Lee: Korea Institute for Advanced Study
Suyeon Park: Gwangju Institute of Science and Technology
Phuong Lien Hoang: Gwangju Institute of Science and Technology
HyeokJin Cho: Gwangju Institute of Science and Technology
Jeongmin Yu: Gwangju Institute of Science and Technology
Thi Minh Hoa Vo: Gwangju Institute of Science and Technology
Minsang Shin: Kyungpook National University
Mi Sun Jin: Gwangju Institute of Science and Technology
Daeho Park: Gwangju Institute of Science and Technology
Changbong Hyeon: Korea Institute for Advanced Study
Gwangrog Lee: Gwangju Institute of Science and Technology

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract 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 Mg2+ binding sites and probe activity at various concentrations of magnesium by single-molecule-FRET. We find that while MgA2+ and MgB2+ have similar binding constants, the dissociation rate of MgA2+ is two order of magnitude lower than that of MgB2+ due to a kinetic-barrier-difference. At physiological Mg2+ concentration, the MgB2+ 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 MgA2+ 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.

Date: 2018
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DOI: 10.1038/s41467-018-06750-9

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