Terminal uridylyl transferases (TUTs) are responsible for the post-transcriptional addition of uridyl residues to RNA 3' ends, leading in some cases to altered stability. The Schizosaccharomyces pombe TUT Cid1 is a model enzyme that has been characterized structurally at moderate resolution and provides insights into the larger and more complex mammalian TUTs, ZCCHC6 and ZCCHC11. Here, we report a higher resolution (1.74 Å) crystal structure of Cid1 that provides detailed evidence for uracil selection via the dynamic flipping of a single histidine residue. We also describe a novel closed conformation of the enzyme that may represent an intermediate stage in a proposed product ejection mechanism. The structural insights gained, combined with normal mode analysis and biochemical studies, demonstrate that the plasticity of Cid1, particularly about a hinge region (N164-N165), is essential for catalytic activity, and provide an explanation for its distributive uridylyl transferase activity. We propose a model clarifying observed differences between the in vitro apparently processive activity and in vivo distributive monouridylylation activity of Cid1. We suggest that modulating the flexibility of such enzymes-for example by the binding of protein co-factors-may allow them alternatively to add single or multiple uridyl residues to the 3' termini of RNA molecules.

Original publication

DOI

10.1093/nar/gkv122

Type

Journal article

Journal

Nucleic Acids Res

Publication Date

11/03/2015

Volume

43

Pages

2968 - 2979

Keywords

Biocatalysis, Catalytic Domain, Crystallography, X-Ray, Models, Molecular, Mutation, Nucleotidyltransferases, Protein Structure, Tertiary, RNA Nucleotidyltransferases, RNA, Fungal, Rotation, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Uridine Triphosphate