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Nat Commun. 2018 Oct 23;9(1):4404. doi: 10.1038/s41467-018-06750-9.

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

Author information

1
Korea Institute for Advanced Study, Seoul, 02455, Republic of Korea.
2
Clova AI Research, NAVER Corp, Seongnam, 13561, Republic of Korea.
3
School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.
4
Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.
5
Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-Ro, Jung-gu, Daegu, 41944, Republic of Korea.
6
Korea Institute for Advanced Study, Seoul, 02455, Republic of Korea. hyeoncb@kias.re.kr.
7
School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea. glee@gist.ac.kr.

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.

PMID:
30353000
PMCID:
PMC6199318
DOI:
10.1038/s41467-018-06750-9
[Indexed for MEDLINE]
Free PMC Article

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