4UD4

Structural Plasticity of Cid1 Provides a Basis for its RNA Terminal Uridylyl Transferase Activity

Summary for 4UD4

• Entry DOI: 10.2210/pdb4ud4/pdb
• Related: 4UD5
• Descriptor: POLY(A) RNA POLYMERASE PROTEIN CID1, GLYCEROL (3 entities in total)
• Functional Keywords: transferase, uridylyltransferase enzyme
• Biological source: SCHIZOSACCHAROMYCES POMBE (FISSION YEAST)
• Cellular location: Cytoplasm : O13833
• Total number of polymer chains: 2
• Total formula weight: 83511.08

Authors

Yates, L.A.,Durrant, B.P.,Fleurdepine, S.,Harlos, K.,Norbury, C.J.,Gilbert, R.J.C. (deposition date: 2014-12-07, release date: 2015-03-18, Last modification date: 2023-12-20)

Primary citation

Yates, L.A.,Durrant, B.P.,Fleurdepine, S.,Harlos, K.,Norbury, C.J.,Gilbert, R.J.
Structural plasticity of Cid1 provides a basis for its distributive RNA terminal uridylyl transferase activity.
Nucleic Acids Res., 43:2968-2979, 2015

PubMed Abstract: 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.

PubMed: 25712096
DOI: 10.1093/nar/gkv122

Experimental method

X-RAY DIFFRACTION (1.74 Å)