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Toliusis P, Tamulaitiene G, Grigaitis R, Tuminauskaite D, Silanskas A, Manakova E, Venclovas C, Szczelkun MD, Siksnys V, Zaremba M. The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor. Nucleic Acids Res 2019; 46:2560-2572. [PMID: 29471489 PMCID: PMC5861437 DOI: 10.1093/nar/gky107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/08/2018] [Indexed: 11/13/2022] Open
Abstract
CglI is a restriction endonuclease from Corynebacterium glutamicum that forms a complex between: two R-subunits that have site specific-recognition and nuclease domains; and two H-subunits, with Superfamily 2 helicase-like DEAD domains, and uncharacterized Z1 and C-terminal domains. ATP hydrolysis by the H-subunits catalyses dsDNA translocation that is necessary for long-range movement along DNA that activates nuclease activity. Here, we provide biochemical and molecular modelling evidence that shows that Z1 has a fold distantly-related to RecA, and that the DEAD-Z1 domains together form an ATP binding interface and are the prototype of a previously undescribed monomeric helicase-like motor. The DEAD-Z1 motor has unusual Walker A and Motif VI sequences those nonetheless have their expected functions. Additionally, it contains DEAD-Z1-specific features: an H/H motif and a loop (aa 163–aa 172), that both play a role in the coupling of ATP hydrolysis to DNA cleavage. We also solved the crystal structure of the C-terminal domain which has a unique fold, and demonstrate that the Z1-C domains are the principal DNA binding interface of the H-subunit. Finally, we use small angle X-ray scattering to provide a model for how the H-subunit domains are arranged in a dimeric complex.
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Affiliation(s)
- Paulius Toliusis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Rokas Grigaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Donata Tuminauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Ceslovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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An efficient tRNA cleaver without additional co-reactants at physiological condition. Biochem Biophys Res Commun 2019; 510:8-12. [PMID: 30661788 DOI: 10.1016/j.bbrc.2018.12.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/05/2018] [Indexed: 11/23/2022]
Abstract
A square-planar Cu(II) complex, [Cu(Me-Im)(gly-gly)]∙H2O 1 (Me-Im = 1-methyl-imidazole, gly-gly = glycylglycinato), has been prepared and structurally characterized by single crystal X-ray. The complex 1 was tested for its ability to the transfer RNA by UV-vis spectroscopy, cyclic voltammetry (CV), capillary electrophoresis (CE). Comparative spectroscopic analysis shows a maximum fluorescence-quenching ratio of 0.41 of 1 upon binding to RNA, which gives a binding constant (Kb) of 1.24 × 105 M-1. Cyclic voltammograms of complex 1 attached on the mercaptoethanol (-SH) linked Au electrodes in phosphate buffer solution give a well-defined and quasi-reversible redox couple, indicate complex 1 can efficiently degrade the high-order structure of RNA in physiological conditions (pH 7.0 phosphate buffer solution at 37 °C) without additional co-reactants, yielding a digestion coefficient more than 90% within 113 h. This study targeting the genetic biomacromolecule degradation based on the strong binding of chemical nucleases paves an important way to the novel materials in the decontamination of microorganisms (e.g., bacteria and viruses) at mild condition.
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