The Life of a Dead Enzyme: Structure of the Pseudokinase VRK3

About 10% of proteins in the human kinome are predicted to be catalytically dead, due to sequence changes in essential motifs. These pseudokinases are thought to retain other (non-catalytic) roles that render them essential to cellular function, but many questions remain: are they really inactive? how has the loss of activity affected the structure an function of the catalytic domain? what else are they doing, and how do they do it? Remarkably, however, there has been no structural information available for a genuine pseudokinase.

In collaboration with Stefan Knapp's group at Oxford, we present an extensive analysis of the structure of the pseudokinase VRK3. We also present the structure of the closest paralog of VRK3, the active kinase VRK2. Comparison of the these two close relatives, one inactive and one active, allows for a high-resolution accounting of the determinants of inactivity in VRK3. In addition, we use sequence constraint analysis to place the changes seen in VRK3 structure into evolutionary context. The results have implications for other pseudokinases, which currently lack structural data.

Structure of the Pseudokinase VRK3 Reveals a Degraded Catalytic Site, a Highly Conserved Kinase Fold, and a Putative Regulatory Binding Site
Scheeff, ED, Eswaran, J, Bunkoczi, G, Knapp, S, Manning, G (2009) Structure 17:128-38 (Medline , Full Text , PDF, Perspective by Kornev and Taylor).

Resources

We built a curated set of sequences of VRKs and CK1s for the paper, and used them in the evolutionary constraint analysis. They are available here:

Aligned, this is the alignment that was used in the paper for evolutionary constraint analysis, and presented in the supplementary material in a marked up form: aligned FASTA or ClustalW.
As an unaligned FASTA file.

We also provide a spreadsheet on pseudokinases in the human kinome. The spreadsheet is available in the supplementary material of the paper, but is also provided here so that we can update it as new information becomes available.