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J Biol Chem. 2016 Sep 9;291(37):19387-400. doi: 10.1074/jbc.M116.736074. Epub 2016 Jul 20.

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

Author information

1
From the Departments of Molecular Biology and Biochemistry and.
2
the Biomolecular Science and Engineering Program and.
3
Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106-9625, and.
4
the Physics Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545.
5
the Biomolecular Science and Engineering Program and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106-9625, and chayes@lifesci.ucsb.edu.
6
From the Departments of Molecular Biology and Biochemistry and Pharmaceutical Sciences, University of California at Irvine, Irvine, California 92697, celia.goulding@uci.edu.

Abstract

Contact-dependent growth inhibition (CDI) is a widespread mechanism of inter-bacterial competition. CDI(+) bacteria deploy large CdiA effector proteins, which carry variable C-terminal toxin domains (CdiA-CT). CDI(+) cells also produce CdiI immunity proteins that specifically neutralize cognate CdiA-CT toxins to prevent auto-inhibition. Here, we present the crystal structure of the CdiA-CT/CdiI(E479) toxin/immunity protein complex from Burkholderia pseudomallei isolate E479. The CdiA-CT(E479) tRNase domain contains a core α/β-fold that is characteristic of PD(D/E)XK superfamily nucleases. Unexpectedly, the closest structural homolog of CdiA-CT(E479) is another CDI toxin domain from B. pseudomallei 1026b. Although unrelated in sequence, the two B. pseudomallei nuclease domains share similar folds and active-site architectures. By contrast, the CdiI(E479) and CdiI(1026b) immunity proteins share no significant sequence or structural homology. CdiA-CT(E479) and 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.

KEYWORDS:

Burkholderia pseudomallei; crystal structure; protein complex; ribonuclease; small-angle x-ray scattering (SAXS); tRNase; toxin; toxin/immunity complexes

PMID:
27445337
PMCID:
PMC5016678
DOI:
10.1074/jbc.M116.736074
[Indexed for MEDLINE]
Free PMC Article

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