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

Wonseok Hwang, Jungmin Yoo, Yuno Lee, Suyeon Park, Phuong Lien Hoang, Hyeok Jin Cho, Jeongmin Yu, Thi Minh Hoa Vo, Minsang Shin, Mi Sun Jin, Daeho Park, Changbong Hyeon, Gwangrog Lee

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


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 MgA 2+ and MgB 2+ have similar binding constants, the dissociation rate of MgA 2+ is two order of magnitude lower than that of MgB 2+ due to a kinetic-barrier-difference. At physiological Mg2+ concentration, the MgB 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 MgA 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.

Original languageEnglish
Article number4404
JournalNature Communications
Issue number1
StatePublished - 1 Dec 2018


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