University of Oulu

Myllykoski M, Kursula P (2017) Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase. PLoS ONE 12(1): e0170355. doi:10.1371/journal.pone.0170355

Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase

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Author: Myllykoski, Matti1; Kursula, Petri1,2
Organizations: 1Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
2Department of Biomedicine, University of Bergen, Bergen, Norway
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 2.2 MB)
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Language: English
Published: Public Library of Science, 2017
Publish Date: 2017-04-06


The 2H phosphoesterase family contains enzymes with two His-X-Ser/Thr motifs in the active site. 2H enzymes are found in all kingdoms of life, sharing little sequence identity despite the conserved overall fold and active site. For many 2H enzymes, the physiological function is unknown. Here, we studied the structure of the 2H family member LigT from Escherichia coli both in the apo form and complexed with different active-site ligands, including ATP, 20-AMP, 30-AMP, phosphate, and NADP⁺. Comparisons to the well-characterized vertebrate myelin enzyme 20,30-cyclic nucleotide 30-phosphodiesterase (CNPase) highlight specific features of the catalytic cycle and substrate recognition in both enzymes. The role played by the helix α7, unique to CNPases within the 2H family, is apparently taken over by Arg130 in the bacterial enzyme. Other residues and loops lining the active site groove are likely to be important for RNA substrate binding. We visualized conformational changes related to ligand binding, as well as the position of the nucleophilic water molecule. We also present a low-resolution model of E. coli LigT bound to tRNA in solution, and provide a model for RNA binding by LigT, involving flexible loops lining the active site cavity. Taken together, our results both aid in understanding the common features of 2H family enzymes and help highlight the distinct features in the 2H family members, which must result in different reaction mechanisms. Unique aspects in different 2H family members can be observed in ligand recognition and binding, and in the coordination of the nucleophilic water molecule and the reactive phosphate moiety.

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Series: PLoS one
ISSN: 1932-6203
ISSN-E: 1932-6203
ISSN-L: 1932-6203
Volume: 12
Issue: 1
Article number: e0170355
DOI: 10.1371/journal.pone.0170355
Type of Publication: A1 Journal article – refereed
Field of Science: 3111 Biomedicine
Funding: The study was funded by the Emil Aaltonen Foundation and the Sigrid Jusélius Foundation.
Dataset Reference: Structural data are available at the PDB under accession codes 5LDI (apo), 5LDJ (phosphate complex), 5LDK (ATP complex), 5LDM (2'-AMP complex), 5LDO (3'-AMP complex), 5LDP (ATP complex 2), and 5LDQ (NADP+ complex).
Copyright information: © 2017 Myllykoski, Kursula. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.