The three-dimensional structure of MAP kinase p38β: different features of the ATP-binding site in p38β compared with p38α

Abstract

The p38 mitogen-activated protein kinases are activated in response to environmental stress and cytokines and play a significant role in transcriptional regulation and inflammatory responses. Of the four p38 isoforms known to date, two (p38alpha and p38beta) have been identified as targets for cytokine-suppressive anti-inflammatory drugs. Recently, it was reported that specific inhibition of the p38alpha isoform is necessary and sufficient for anti-inflammatory efficacy in vivo, while further inhibition of p38beta may not provide any additional benefit. In order to aid the development of p38alpha-selective compounds, the three-dimensional structure of p38beta was determined. To do so, the C162S and C119S,C162S mutants of human MAP kinase p38beta were cloned, expressed in Escherichia coli and purified. Initial screening hits in crystallization trials in the presence of an inhibitor led upon optimization to crystals that diffracted to 2.05 A resolution and allowed structure determination (PDB codes 3gc8 and 3gc9 for the single and double mutant, respectively). The structure of the p38alpha C162S mutant in complex with the same inhibitor is also reported (PDB code 3gc7). A comparison between the structures of the two kinases showed that they are highly similar overall but that there are differences in the relative orientation of the N- and C-terminal domains that causes a reduction in the size of the ATP-binding pocket in p38beta. This difference in size between the two pockets could be exploited in order to achieve selectivity.

X-ray Crystal Structure of ERK5 (MAPK7) in Complex with a Specific Inhibitor

“…38 The structure was solved by molecular replacement using Phaser 39 and the structure of p38β (PDB code 3GC9) 40 as a search model. There was one molecule in the asymmetric unit.…”

Discovering and validating unknown phospho-sites from p38 and HuR protein kinases in vitro by Phosphoproteomic and Bioinformatic tools

“…As shown in figure 4, phosphorylated Ser-279 of p38B is located in a loop placed on the external surface of the protein structure, far away from the active site of the kinase. It is conceivable that the phosphorylation of this residue does not affect p38B structure stability or folding, but external contacts to accompanying proteins, modulate the nature of the putative interaction (see reference previously mentioned [39]).…”

“…Crystal structure of MAP kinase p38beta protein and 3D coordinates of the quaternary structure of the first RNA recognition motif of human HuR protein were obtained from the Protein Data Bank (PDB <http://www.pdb.org> codes: 3GC8 - and 3HI9 -[39]- [40]-, respectively). As the published structure of HuR dimmer (dimmer) [40] showed a gap between residues 53 and 60 of the first monomer (chain B in 3HI9 structure), the coordinates for this external loop were completed by standard homology modelling procedures using the second monomer (chain D of 3HI9) as template.…”

p38α MAP Kinase Dimers with Swapped Activation Segments and a Novel Catalytic Loop Conformation

“…13 Such a singly phosphorylated p38 exhibits a substrate selectivity pattern distinct from the MKK dual phosphorylated form. 14 Although many structures of p38 are known, 19,20 including heterocomplexes with the downstream target MK2, 21,22 none show a homodimerized form.…”