Structural and Biochemical Studies of the Novel Hexameric Endoribonuclease YicC

The decay of mRNA is an essential process to bacteria.The newlyidentified E. coli protein YicC is a founding memberof the UPF0701 family, and biochemical studies indicated that it isan RNase involved in mRNA degradation. However, its biochemical propertiesand catalytic mechanism are poorly understood. Here, we report thecrystal structure of YicC, which shows an extended shape consistingof modular domains. While the backbone trace of the monomer formsa unique, nearly closed loop, the three monomers present in the asymmetricunit make a shoulder-by-shoulder trimer. In vitroRNA cleavage assays indicated that this endoribonuclease mainly recognizesthe consensus GUG motif, with a preference for an extended CGUG sequence.Additionally, the active enzyme exists as a hexamer in solution andassumes a funnel shape. Structural analysis indicated that the hexamerinterface is mainly formed by the hexamerization domain consistingof D71-D124 and that the disruption of the oligomeric formgreatly diminished the enzymatic activity. By studying the surfacecharge potential and the sequence conservation, we identified a seriesof residues that play critical functional roles, which helps to revealthe catalytic mechanism of this divalent metal-ion-dependent RNase.Last but not least, we discovered that the catalytic domain of YicCdid not share similarity with any known nuclease fold, suggestingthat the enzyme adopts a novel fold to perform its catalysis and invivo functions. In summary, our investigations into YicC provide anin-depth understanding of the functions of the UPF0701 protein familyand the DUF1732 domain in general.

Automated summary

Research found that the newly identified E. coli protein YicC is a founding member of the UPF0701 family and is involved in mRNA decay. The crystal structure of YicC was determined, showing an extended shape with modular domains. The enzyme mainly recognizes the consensus GUG motif in RNA cleavage, and it exists as a hexamer with a funnel shape. The catalytic domain of YicC has a novel fold and plays critical functional roles in catalysis and in vivo functions.