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Structure. 2018 Jan 2;26(1):40-50.e2. doi: 10.1016/j.str.2017.11.008. Epub 2017 Dec 7.

Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes.

Author information

1
Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy.
2
European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, Grenoble 38042, France.
3
Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy; IAS-5/INM-9 Computational Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany. Electronic address: marco.devivo@iit.it.
4
European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, Grenoble 38042, France. Electronic address: mmarcia@embl.fr.

Abstract

Synthesis and scission of phosphodiester bonds in DNA and RNA regulate vital processes within the cell. Enzymes that catalyze these reactions operate mostly via the recognized two-metal-ion mechanism. Our analysis reveals that basic amino acids and monovalent cations occupy structurally conserved positions nearby the active site of many two-metal-ion enzymes for which high-resolution (<3 Å) structures are known, including DNA and RNA polymerases, nucleases such as Cas9, and splicing ribozymes. Integrating multiple-sequence and structural alignments with molecular dynamics simulations, electrostatic potential maps, and mutational data, we found that these elements always interact with the substrates, suggesting that they may play an active role for catalysis, in addition to their electrostatic contribution. We discuss possible mechanistic implications of this expanded two-metal-ion architecture, including inferences on medium-resolution cryoelectron microscopy structures. Ultimately, our analysis may inspire future experiments and strategies for enzyme engineering or drug design to modulate nucleic acid processing.

KEYWORDS:

DNA/RNA polymerases; enzyme engineering; gene editing; metalloenzyme; molecular dynamics; molecular simulations; ribozymes; splicing

PMID:
29225080
PMCID:
PMC5758106
DOI:
10.1016/j.str.2017.11.008
[Indexed for MEDLINE]
Free PMC Article

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