The structure of mitogen-activated protein kinase p38 at 2.1-A resolution

Conformational diversity of catalytic cores of protein kinases

X-ray crystallography of the protein kinase family has provided an impressive array of crystal structures, setting the stage for rational design of specific inhibitors of these vitally important regulators of the signaling pathways of the cell. Initial work on the first crystal structure of a protein kinase, cyclic AMP-dependent protein kinase, has provided evidence of conformational changes suggested to be critical for the common catalytic event of transferring the gamma phosphate from ATP onto the targeted protein. This review updates the current status of the extent of conformational diversity of the protein kinase family and suggests that both the nature and the extent of those changes can provide a rationale for the increased occurrence of specific protein kinase inhibitors targeted at the ATP-binding site. It focuses on the fact that in addition to the sequence diversities in ATP binding clefts reported recently, there is conformational diversity in the beta sheets of the upper domains of the catalytic cores. This difference is directly related to the regulation of kinases by multiple mechanisms.

Peptide inhibitors of the mitogen-activated protein kinase pathway: a structure -mimetic peptide corresponding to the conserved inter-DFG-APE region in the kinase domain

The signal transduction pathway mediated by mitogen-activated protein kinases is an attractive target for the design of pharmacologically effective inhibitors. Two specific cell-permeant small molecule inhibitors of this pathway have been reported. However, under certain circumstances, nonpermeable inhibitors, such as neutralizing antibodies and peptide inhibitors, are also useful. We present here a novel approach for such peptide inhibitor design. The procedure is based on the synthesis of a structure-mimetic peptide corresponding to a short peptide segment in the target molecule. The results obtained so far show that a peptide designed in such a way is an effective inhibitor of the pathway. The possible application of such peptides and antipeptide antibodies as probes for protein kinase regulation mechanisms is also evaluated.

p38 mitogen-activated protein kinase inhibitors--mechanisms and therapeutic potentials

The pyridinylimidazole compounds, exemplified by SB 203580, originally were prepared as inflammatory cytokine synthesis inhibitors. Subsequently, the compounds were found to be selective inhibitors for p38 mitogen-activated protein kinase (MAPK), a member of the MAPK family. SB 203580 inhibits the catalytic activity of p38 MAPK by competitive binding in the ATP pocket. Four homologues of p38 MAPK have been identified to date, and interestingly, their biochemical properties and their respective sensitivities to the inhibitors are distinct. X-ray crystallographic analysis of p38-inhibitor complexes reinforces the observations made from site-directed mutagenesis studies, thereby providing a molecular basis for understanding the kinase selectivity of these inhibitors. The p38 MAPK inhibitors are efficacious in several disease models, including inflammation, arthritis and other joint diseases, septic shock, and myocardial injury.

Crystal structure of the potent natural product inhibitor balanol in complex with the catalytic subunit of cAMP-dependent protein kinase

Endogenous protein kinase inhibitors are essential for a wide range of physiological functions. These endogenous inhibitors may mimic peptide substrates as in the case of the heat-stable protein kinase inhibitor (PKI), or they may mimic nucleotide triphosphates. Natural product inhibitors, endogenous to the unique organisms producing them, can be potent exogenous inhibitors against foreign protein kinases. Balanol is a natural product inhibitor exhibiting low nanomolar Ki values against serine and threonine specific kinases, while being ineffective against protein tyrosine kinases. To elucidate balanol's specific inhibitory effects and provide a basis for understanding inhibition-regulated biological processes, a 2.1 A resolution crystal structure of balanol in complex with cAMP-dependent protein kinase (cAPK) was determined. The structure reveals conserved binding regions and displays extensive complementary interactions between balanol and conserved cAPK residues. This report describes the structure of a protein kinase crystallized with a natural ATP mimetic in the absence of metal ions and peptide inhibitor.

Crystal structure of the cytoplasmic domain of the type I TGF beta receptor in complex with FKBP12

Activation of the type I TGFbeta receptor (TbetaR-I) requires phosphorylation of a regulatory segment known as the GS region, located upstream of the serine/threonine kinase domain in the cytoplasmic portion of the receptor. The crystal structure of a fragment of unphosphorylated TbetaR-I, containing both the GS region and the catalytic domain, has been determined in complex with the FK506-binding protein FKBP12. TbetaR-I adopts an inactive conformation that is maintained by the unphosphorylated GS region. FKBP12 binds to the GS region of the receptor, capping the TbetaR-II phosphorylation sites and further stabilizing the inactive conformation of TbetaR-I. Certain structural features at the catalytic center of TbetaR-I are characteristic of tyrosine kinases rather than Ser/Thr kinases.

Inhibition of MAPK pathway by a synthetic peptide corresponding to the activation segment of MAPK

Mitogen-activated protein kinase (MAPK) is activated by phosphorylation within its activation segment. Upon phosphorylation, the activation segment refolds to provide the active conformation of the enzyme. We reported previously that a phosphorylation-sensitive secondary structure could be formed in a 26-amino-acid long synthetic peptide corresponding to the activation segment of Xenopus MAPK, termed IDA (Inter-DFG-APE) MAPK peptide (Tokmakov, A. A., et al. 1997, Biochem. Biophys. Res. Commun. 236, 243-247). Here, we show that unphosphorylated IDA MAPK peptide can inhibit in vitro both MAPK and MAPK kinase activities with the inhibition constants of 82 and 18 microM, respectively. Phosphorylated forms of the peptide were of little effect. IDA MAPK peptide did not inhibit significantly the activity of some other protein kinases, including MAPK homologue p38 kinase, suggesting the specificity for MAPK and MAPK kinase. Microinjection of unphosphorylated IDA MAPK peptide into immature Xenopus oocytes significantly suppressed progesterone-induced oocyte maturation by inhibiting activation of both MAPK and maturation promoting factor. Similar inhibition of maturation was registered upon oocyte treatment with another specific inhibitor of MAPK pathway, PD098059. These results depict IDA MAPK peptide as a selective inhibitor of the MAPK pathway that can be used for the investigations of MAPK-mediated signaling.

A single amino acid substitution makes ERK2 susceptible to pyridinyl imidazole inhibitors of p38 MAP kinase

Mitogen-activated protein (MAP) kinases are serine/threonine kinases that mediate intracellular signal transduction pathways. Pyridinyl imidazole compounds block pro-inflammatory cytokine production and are specific p38 kinase inhibitors. ERK2 is related to p38 in sequence and structure, but is not inhibited by pyridinyl imidazole inhibitors. Crystal structures of two pyridinyl imidazoles complexed with p38 revealed these compounds bind in the ATP site. Mutagenesis data suggested a single residue difference at threonine 106 between p38 and other MAP kinases is sufficient to confer selectivity of pyridinyl imidazoles. We have changed the equivalent residue in human ERK2, Q105, into threonine and alanine, and substituted four additional ATP binding site residues. The single residue change Q105A in ERK2 enhances the binding of SB202190 at least 25,000-fold compared to wild-type ERK2. We report enzymatic analyses of wild-type ERK2 and the mutant proteins, and the crystal structure of a pyridinyl imidazole, SB203580, bound to an ERK2 pentamutant, I103L, Q105T, D106H, E109G. T110A. These ATP binding site substitutions induce low nanomolar sensitivity to pyridinyl imidazoles. Furthermore, we identified 5-iodotubercidin as a potent ERK2 inhibitor, which may help reveal the role of ERK2 in cell proliferation.

Novel families of putative protein kinases in bacteria and archaea: evolution of the "eukaryotic" protein kinase superfamily

The central role of serine/threonine and tyrosine protein kinases in signal transduction and cellular regulation in eukaryotes is well established and widely documented. Considerably less is known about the prevalence and role of these protein kinases in bacteria and archaea. In order to examine the evolutionary origins of the eukaryotic-type protein kinase (ePK) superfamily, we conducted an extensive analysis of the proteins encoded by the completely sequenced bacterial and archaeal genomes. We detected five distinct families of known and predicted putative protein kinases with representatives in bacteria and archaea that share a common ancestry with the eukaryotic protein kinases. Four of these protein families have not been identified previously as protein kinases. From the phylogenetic distribution of these families, we infer the existence of an ancestral protein kinase(s) prior to the divergence of eukaryotes, bacteria, and archaea.

Structural basis of inhibitor selectivity in MAP kinases

BACKGROUND

The mitogen-activated protein (MAP) kinases are important signaling molecules that participate in diverse cellular events and are potential targets for intervention in inflammation, cancer, and other diseases. The MAP kinase p38 is responsive to environmental stresses and is involved in the production of cytokines during inflammation. In contrast, the activation of the MAP kinase ERK2 (extracellular-signal-regulated kinase 2) leads to cellular differentiation or proliferation. The anti-inflammatory agent pyridinylimidazole and its analogs (SB [SmithKline Beecham] compounds) are highly potent and selective inhibitors of p38, but not of the closely-related ERK2, or other serine/threonine kinases. Although these compounds are known to bind to the ATP-binding site, the origin of the inhibitory specificity toward p38 is not clear.

RESULTS

We report the structural basis for the exceptional selectivity of these SB compounds for p38 over ERK2, as determined by comparative crystallography. In addition, structural data on the origin of olomoucine (a better inhibitor of ERK2) selectivity are presented. The crystal structures of four SB compounds in complex with p38 and of one SB compound and olomoucine in complex with ERK2 are presented here. The SB inhibitors bind in an extended pocket in the active site and are complementary to the open domain structure of the low-activity form of p38. The relatively closed domain structure of ERK2 is able to accommodate the smaller olomoucine.

CONCLUSIONS

The unique kinase-inhibitor interactions observed in these complexes originate from amino-acid replacements in the active site and replacements distant from the active site that affect the size of the domain interface. This structural information should facilitate the design of better MAP-kinase inhibitors for the treatment of inflammation and other diseases.

The Eleventh Datta Lecture. The structural basis for substrate recognition and control by protein kinases

Protein kinases catalyse phospho transfer reactions from ATP to serine, threonine or tyrosine residues in target substrates and provide key mechanisms for control of cellular signalling processes. The crystal structures of 12 protein kinases are now known. These include structures of kinases in the active state in ternary complexes with ATP (or analogues) and inhibitor or peptide substrates (e.g. cyclic AMP dependent protein kinase, phosphorylase kinase and insulin receptor tyrosine kinase); kinases in both active and inactive states (e.g. CDK2/cyclin A, insulin receptor tyrosine kinase and MAPK); kinases in the active state (e.g. casein kinase 1, Lck); and kinases in inactive states (e.g. twitchin kinase, calcium calmodulin kinase 1, FGF receptor kinase, c-Src and Hck). This paper summarises the detailed information obtained with active phosphorylase kinase ternary complex and reviews the results with reference to other kinase structures for insights into mechanisms for substrate recognition and control.

Signalling in the yeasts: an informational cascade with links to the filamentous fungi

All cells, from bacteria and yeasts to mammalian cells, respond to cues from their environment. A variety of mechanisms exist for the transduction of these external signals to the interior of the cell, resulting in altered patterns of protein activity. Eukaryotic cells commonly transduce external cues via a conserved module composed of three protein kinases, the mitogen-activated protein kinase (MAPK) cascade. This module can then activate substrates, some of which include transcriptional activators. Multiple MAPK signalling pathways coexist in a cell. This review considers different MAPK cascade signalling pathways that govern several aspects of the life cycle of budding and fission yeasts: conjugation and meiosis by the pheromone response pathway, stress response by the high-osmolarity sensing pathway, cell wall biosynthesis in response to activation of the low-osmolarity and heat-sensing pathway, and pseudohyphal growth in response to activation of a subset of the components of the pheromone response pathway. Because the MAPK cascade components are highly conserved, a key question in studies of these pathways is the mechanism by which specificity of response is achieved. Several other issues to be addressed in this review concern the nature of the receptors used to sense the external signals and the mechanism by which the receptors communicate with other components leading to activation of the MAPK cascade. Recently, it has become apparent that MAPK cascades are important in governing the pathogenicity of filamentous fungi.

Phosphorylation and association with the transcription factor Atf1 regulate localization of Spc1/Sty1 stress-activated kinase in fission yeast

Control of gene expression by stress-activated protein kinase (SAPK) cascades is crucial for combating cytotoxic stress. Elements of these cascades have been investigated in detail, but regulation of stress signal transduction from the cytoplasm to the nucleus is poorly understood. Herein are reported subcellular localization studies of fission yeast Spc1, a homolog of human p38 and budding yeast Hog1p SAPKs. Stress induces transient nuclear localization of Spc1. Nuclear translocation of Spc1 is coupled with disassociation from its activator kinase Wis1. However, Spc1 does not concentrate in the nucleus of Deltawis1 cells; therefore Wis1 does not tether Spc1 in the cytoplasm. Unphosphorylatable forms of Spc1 are dispersed in the cytoplasm and nucleus, even in cells that also produce wild-type Spc1. Thus, Spc1 must be phosphorylated by Wis1 to localize in the nucleus. Nuclear retention of Spc1 requires Atf1, a transcription factor that is the key nuclear substrate of Spc1. Nuclear localization of Atf1 requires Pcr1, a heterodimerization partner of Atf1. These studies show that phosphorylation and association with Atf1 are required for nuclear localization of Spc1.

Phosphorylation of the MAP kinase ERK2 promotes its homodimerization and nuclear translocation

The MAP kinase ERK2 is widely involved in eukaryotic signal transduction. Upon activation it translocates to the nucleus of the stimulated cell, where it phosphorylates nuclear targets. We find that nuclear accumulation of microinjected ERK2 depends on its phosphorylation state rather than on its activity or on upstream components of its signaling pathway. Phosphorylated ERK2 forms dimers with phosphorylated and unphosphorylated ERK2 partners. Disruption of dimerization by mutagenesis of ERK2 reduces its ability to accumulate in the nucleus, suggesting that dimerization is essential for its normal ligand-dependent relocalization. The crystal structure of phosphorylated ERK2 reveals the basis for dimerization. Other MAP kinase family members also form dimers. The generality of this behavior suggests that dimerization is part of the mechanism of action of the MAP kinase family.

A mitogen-activated protein (MAP) kinase homologue of Leishmania mexicana is essential for parasite survival in the infected host

The parasitic protozoon Leishmania mexicana undergoes two major developmental stages in its life cycle exhibiting profound physiological and morphological differences, the promastigotes in the insect vector and the amastigotes in mammalian macrophages. A deletion mutant, Deltalmsap1/2, for the secreted acid phosphatase (SAP) gene locus, comprising the two SAP genes separated by an intergenic region of approximately 11.5 kb, lost its ability to cause a progressive disease in Balb/c mice. While in vitro growth of promastigotes, invasion of host cells and differentiation from promastigotes to amastigotes was indistinguishable from the wild-type, the mutant parasites ceased to proliferate when transformed to amastigotes in infected macrophages or in a macrophage-free in vitro differentiation system, suggesting a stage-specific growth arrest. This phenotype could be reverted by complementation with 6 kb of the intergenic region of the SAP gene locus. Sequence analysis identified two open reading frames, both encoding single copy genes; one gene product shows high homology to mitogen-activated protein (MAP) kinases. Complementation experiments revealed that the MAP kinase homologue, designated LMPK, is required and is sufficient to restore the infectivity of the Deltalmsap1/2 mutant. Therefore, LMPK is a kinase that is essential for the survival of L.mexicana in the infected host by affecting the cell division of the amastigotes.

Molecular cloning and characterization of a Drosophila p38 mitogen-activated protein kinase

A mitogen-activated protein kinase (MAPK) has been cloned and sequenced from a Drosophila neoplasmic l(2)mbn cell line. The cDNA sequence analysis showed that this Drosophila kinase is a homologue of mammalian p38 MAPK and the yeast HOG1 gene and thus was referred to as Dp38. A distinguishing feature of all MAPKs is the conserved sequence TGY in the activation domain. Dp38 was rapidly tyrosine 186-phosphorylated in response to osmotic stress, heat shock, serum starvation, and H2O2 in Drosophila l(2)mbn and Schneider cell lines. However, unlike mammalian p38 MAPK, the addition of lipopolysaccharide (LPS) did not significantly affect the phosphorylation of Dp38 in the LPS-responsive l(2)mbn cell line. Following osmotic stress, tyrosine 186-phosphorylated forms of Dp38 MAPK were detected exclusively in nuclear regions of Schneider cells. Yeast complementation studies demonstrated that the Saccharomyces cerevisiae HOG1 mutant strain JBY10 (hog1-Delta1) was functionally complemented by Dp38 cDNA in hyperosmolar medium. These findings demonstrate that similar osmotic stress-responsive signal transduction pathways are conserved in yeast, Drosophila, and mammalian cells, whereas LPS signal transduction pathways appear to be different.

Activation and signal transduction via mitogen-activated protein (MAP) kinases in T lymphocytes

The various mitogen-activated protein (MAP) kinases have central roles in the signalling pathways of T lymphocytes. Their activation is uniquely dependent on dual phosphorylation of a serine/threonine and a tyrosine residue and is regulated by several levels of kinases in parallel cascades. In addition, both the MAP kinases and their upstream, activating kinases are regulated by several phosphatases. Although each of the MAP kinases have many cytoplasmic substrates, their ability to translocate to the nucleus means that they can transmit signals from the cytoplasm directly to transcription factors, which are sometimes nuclear bound. The MAP kinase cascades are activated in T lymphocytes by a variety of different external stimuli. They play an important role in transducing both the signal from T cell receptor and costimulatory molecules, on the T cell surface, and are able to regulate several of the transcription factors controlling the expression of critical genes, including that for IL-2. This review examines how the activation of several MAP kinases is regulated, their role in signal transduction initiated by a variety of stimuli, and how this may lead to different cellular responses.

Activation mechanism of the MAP kinase ERK2 by dual phosphorylation

The structure of the active form of the MAP kinase ERK2 has been solved, phosphorylated on a threonine and a tyrosine residue within the phosphorylation lip. The lip is refolded, bringing the phosphothreonine and phosphotyrosine into alignment with surface arginine-rich binding sites. Conformational changes occur in the lip and neighboring structures, including the P+1 site, the MAP kinase insertion, the C-terminal extension, and helix C. Domain rotation and remodeling of the proline-directed P+1 specificity pocket account for the activation. The conformation of the P+1 pocket is similar to a second proline-directed kinase, CDK2-CyclinA, thus permitting the origin of this specificity to be defined. Conformational changes outside the lip provide loci at which the state of phosphorylation can be felt by other cellular components.

Protein kinase inhibition: natural and synthetic variations on a theme

How a protein kinase is turned off is as critical for its physiological function as is its catalytic activity. Examination of solved crystal structures representing different protein kinase subfamilies reveals a variety of strategies that are utilized by nature to lock protein kinases into inactive conformations. Pseudosubstrate and adenine mimetic mechanisms as well as complementarity to surfaces other than the active site are effective. Although most synthetic or natural product inhibitors target the active site, specifically the ATP binding site, a remarkably high degree of specificity can be achieved which is due to the extended surface of the protein that these inhibitors occupy. Although targeting of the ATP binding site is proving to be very successful, there is also wide latitude for designing inhibitors that target other surfaces of the kinases.