Structural basis for the toxic activity of MafB2 from maf genomic island 2 (MGI-2) in N. meningitidis B16B6

The Maf polymorphic toxin system is involved in conflict between strains found in pathogenic Neisseria species such as Neisseria meningitidis and Neisseria gonorrhoeae. The genes encoding the Maf polymorphic toxin system are found in specific genomic islands called maf genomic islands (MGIs). In the MGIs, the MafB and MafI encode toxin and immunity proteins, respectively. Although the C-terminal region of MafB (MafB-CT) is specific for toxic activity, the underlying enzymatic activity that renders MafB-CT toxic is unknown in many MafB proteins due to lack of homology with domain of known function. Here we present the crystal structure of the MafB2-CT(MGI-2B16B6)/MafI2(MGI-2B16B6) complex from N. meningitidis B16B6. MafB2-CT(MGI-2B16B6) displays an RNase A fold similar to mouse RNase 1, although the sequence identity is only ~ 14.0%. MafB2-CT(MGI-2B16B6) forms a 1:1 complex with MafI2(MGI-2B16B6) with a Kd value of ~ 40 nM. The complementary charge interaction of MafI2(MGI-2B16B6) with the substrate binding surface of MafB2-CT(MGI-2B16B6) suggests that MafI2(MGI-2B16B6) inhibits MafB2-CT(MGI-2B16B6) by blocking access of RNA to the catalytic site. An in vitro enzymatic assay showed that MafB2-CT(MGI-2B16B6) has ribonuclease activity. Mutagenesis and cell toxicity assays demonstrated that His335, His402 and His409 are important for the toxic activity of MafB2-CT(MGI-2B16B6), suggesting that these residues are critical for its ribonuclease activity. These data provide structural and biochemical evidence that the origin of the toxic activity of MafB2(MGI-2B16B6) is the enzymatic activity degrading ribonucleotides.