Structural Analysis of the Heterodimeric Type IIS Restriction Endonuclease R.BspD6I Acting as a Complex between a Monomeric Site-specific Nickase and a Catalytic Subunit

Качалова, Г.С.; Rogulin, E. A.; Yunusova, A. K.; Artyukh, R. I.; Perevyazova, T. A.; Matvienko, N. I.; Zheleznaya, L. A.; Bartunik, H.D.

doi:10.1016/j.jmb.2008.09.033

Cited by 38 publications

(42 citation statements)

References 56 publications

(66 reference statements)

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“…CdiA-CT o11 EC869 converted supercoiled plasmid DNA into an open-circular form in the presence of Mg 2+ (Fig. 5A), consistent with "nickase" activity in which only one strand of double-stranded DNA is cleaved (10). Because Zn 2+ is coordinated in the predicted CdiA-CT o11 EC869 active site, we also tested nuclease activity with this cation.…”

Section: Ec869supporting

confidence: 57%

Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems

Morse¹,

Nikolakakis²,

Willett

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

168

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Contact-dependent growth inhibition (CDI) systems encode polymorphic toxin/immunity proteins that mediate competition between neighboring bacterial cells. We present crystal structures of CDI toxin/ immunity complexes from Escherichia coli EC869 and Burkholderia pseudomallei 1026b. Despite sharing little sequence identity, the toxin domains are structurally similar and have homology to endonucleases. The EC869 toxin is a Zn 2+ -dependent DNase capable of completely degrading the genomes of target cells, whereas the Bp1026b toxin cleaves the aminoacyl acceptor stems of tRNA molecules. Each immunity protein binds and inactivates its cognate toxin in a unique manner. The EC869 toxin/immunity complex is stabilized through an unusual β-augmentation interaction. In contrast, the Bp1026b immunity protein exploits shape and charge complementarity to occlude the toxin active site. These structures represent the initial glimpse into the CDI toxin/immunity network, illustrating how sequence-diverse toxins adopt convergent folds yet retain distinct binding interactions with cognate immunity proteins. Moreover, we present visual demonstration of CDI toxin delivery into a target cell.structural biology | bacterial competition | β-complementation | tRNase activity

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Section: Ec869supporting

confidence: 57%

Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems

Morse¹,

Nikolakakis²,

Willett

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

168

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show abstract

“…For the CdiA-CT E479 nuclease domain, Asp-229 and Asp-243 occupy canonical positions within ␤2 and ␤3, but Glu-204 and His-275 are contributed by ␣1 and ␣2, respectively. This arrangement is very similar to the active site of CdiA-CT 1026b and the type IIS restriction endonuclease BspD6I (17,39). The DNase domains of CdiA-CT o11 EC869 and CdiA-CT YPIII have yet another configuration that was first described for EcoO109I (17,27,40,41).…”

Section: Discussionsupporting

confidence: 51%

Functional Diversity of Cytotoxic tRNase/Immunity Protein Complexes from Burkholderia pseudomallei

Johnson¹,

Gucinski²,

Garza-Sánchez

et al. 2016

Journal of Biological Chemistry

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Contact-dependent growth inhibition (CDI) is a widespread mechanism of inter-bacterial competition. CDIand CdiA-CT 1026b are both tRNases; however, each nuclease cleaves tRNA at a distinct position. We used a molecular docking approach to model each toxin bound to tRNA substrate. The resulting models fit into electron density envelopes generated by small-angle x-ray scattering analysis of catalytically inactive toxin domains bound stably to tRNA. CdiA-CT E479 is the third CDI toxin found to have structural homology to the PD(D/E)XK superfamily. We propose that CDI systems exploit the inherent sequence variability and active-site plasticity of PD(D/E)XK nucleases to generate toxin diversity. These findings raise the possibility that many other uncharacterized CDI toxins may belong to the PD(D/E)XK superfamily.

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“…1b). When we determined the structure of nickase N.BspD6I [24] and revealed amino acid residues forming the catalytic center, it became clear that the ORF contains the same motif that forms the catalytic center of nickase. Therefore, it could be expected that the ORF product will have endonuclease activity.…”

Section: Nicking Endonucleases -Subunits Of Heterodimeric Restrictionmentioning

confidence: 99%

“…We were able to obtain a crystal of nickase N.BspD6I and to determine the enzyme spatial structure at high resolution (1.8 Å) [23,24]. The full size molecule (604 a.a.) is a compact elongated globule of 50 × 60 × 80 Å.…”

Section: Spatial Structures Of Subunits Of Heterodimeric Restriction mentioning

confidence: 99%

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Nicking endonucleases

Zheleznaya

Качалова

Artyukh

et al. 2009

Biochemistry Moscow

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Structural Analysis of the Heterodimeric Type IIS Restriction Endonuclease R.BspD6I Acting as a Complex between a Monomeric Site-specific Nickase and a Catalytic Subunit

Cited by 38 publications

References 56 publications

Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems

Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems

Functional Diversity of Cytotoxic tRNase/Immunity Protein Complexes from Burkholderia pseudomallei

Nicking endonucleases

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