Interleukin-1 beta converting enzyme (ICE) processes an inactive precursor to the proinflammatory cytokine, interleukin-1 beta, and may regulate programmed cell death in neuronal cells. The high-resolution structure of human ICE in complex with an inhibitor has been determined by X-ray diffraction. The structure confirms the relationship between human ICE and cell-death proteins in other organisms. The active site spans both the 10 and 20K subunits, which associate to form a tetramer, suggesting a mechanism for ICE autoactivation.

The activity of the c-Kit receptor protein-tyrosine kinase is tightly regulated in normal cells, whereas deregulated c-Kit kinase activity is implicated in the pathogenesis of human cancers. The c-Kit juxtamembrane region is known to have an autoinhibitory function; however the precise mechanism by which c-Kit is maintained in an autoinhibited state is not known. We report the 1.9-Å resolution crystal structure of native c-Kit kinase in an autoinhibited conformation and compare it with active c-Kit kinase. Autoinhibited c-Kit is stabilized by the juxtamembrane domain, which inserts into the kinase-active site and disrupts formation of the activated structure. A 1.6-Å crystal structure of c-Kit in complex with STI-571 (Imatinib® or Gleevec®) demonstrates that inhibitor binding disrupts this natural mechanism for maintaining c-Kit in an autoinhibited state. Together, these results provide a structural basis for understanding c-Kit kinase autoinhibition and will facilitate the structure-guided design of specific inhibitors that target the activated and autoinhibited conformations of c-Kit kinase.The stem cell factor receptor c-Kit is a receptor proteintyrosine kinase (RPTK) 1 that initiates cell growth and proliferation signal transduction cascades in response to stem cell factor binding (1). c-Kit, named after its viral homolog v-Kit (2), is a member of the Type III transmembrane RPTK subfamily, which includes the colony-stimulating factor-1 receptor (3), also known as the FMS receptor, the related Flt-3 receptor (4), and the platelet-derived growth factor ␣-and ␤-receptors (5, 6), as well as c-Kit (7). The Type III RPTK family is characterized by five extracellular immunoglobulin (Ig) domains, a single transmembrane helix, an autoinhibitory juxtamembrane domain, and a cytoplasmic kinase domain that is split by a kinase insertion domain (KID) (see Fig. 1A) (6,8).The binding of a stem cell factor dimer to the extracellular Ig domains of c-Kit causes two c-Kit RPTKs to dimerize and permits the kinase domains to act in trans as a substrate and enzyme for one another. The result of stem cell factor binding is the phosphorylation of specific tyrosine residues located in c-Kit juxtamembrane regions (9 -12). Tyrosine residue 568 is the primary site of in vivo autophosphorylation (see Fig. 1B). Phosphorylation of the tyrosine initiates a cytoplasmic serine/ threonine phosphorylation cascade that promotes cell growth and proliferation (12). Mutations that cause constitutive activation of c-Kit kinase activity in the absence of stem cell factor binding are implicated in highly malignant human cancers, including gastrointestinal stromal tumors (13, 14), germ cell tumors (15), mast cell and myeloid leukemias (16), and in mastocytosis (17). Moreover, activating c-Kit mutations that occur in the kinase domain are resistant to many kinase inhibitors currently in use as chemotherapy treatments (18 -21).The kinase activity of c-Kit is tightly regulated throughout its signaling cycle. Binding of the protein-tyrosine phosphatase S...

The structure of inosine-5'-monophosphate dehydrogenase (IMPDH) in complex with IMP and mycophenolic acid (MPA) has been determined by X-ray diffraction. IMPDH plays a central role in B and T lymphocyte replication. MPA is a potent IMPDH inhibitor and the active metabolite of an immunosuppressive drug recently approved for the treatment of allograft rejection. IMPDH comprises two domains: a core domain, which is an alpha/beta barrel and contains the active site, and a flanking domain. The complex, in combination with mutagenesis and kinetic data, provides a structural basis for understanding the mechanism of IMPDH activity and indicates that MPA inhibits IMPDH by acting as a replacement for the nicotinamide portion of the nicotinamide adenine dinucleotide cofactor and a catalytic water molecule.

The three-dimensional structure of BirA, the repressor of the Escherichia col biotin biosynthetic operon, has been determined by x-ray crystallography and refined to a crystallographic residual of 19.0% at 2.3-A resolution. BirA is a sequence-specific DNA-binding protein that also catalyzes the formation of biotinyl-5'-adenylate from biotin and ATP and transfers the biotin moiety to other proteins. The level of biotin biosynthetic enzymes in the cell is controlled by the amount of biotinyl-5'-adenylate, which is the BirA corepressor. The structure provides an example of a transcription factor that is also an enzyme. The structure ofBirA is highly asymmetric and consists of three domains. The N-terminal domain is mostly a-helical, contains a helix-turn-helix DNA-binding motif, and is loosely connected to the remainder of the molecule. The central domain consists of a seven-stranded mixed 13-sheet with a-helices covering one face. The other side of the sheet is largely solventexposed and contains the active site. The C-terminal domain comprises a six-stranded, antiparallel 13-sheet sandwich. The location of biotin binding is consistent with mutations that affect enzymatic activity. A nearby loop has a sequence that has been associated with phosphate binding in other proteins. It is inferred that ATP binds in this region, adjacent to the biotin. It is proposed that the binding of corepressor to monomeric BirA may promote DNA binding by facilitating the formation of a multimeric BirA-corepressor-DNA complex. The structural details of this complex remain an open question, however.The biotin operon repressor, BirA, is a 33.5-kDa protein that regulates transcription of the Escherichia coli biotin operon (1-3). BirA is bifunctional, serving both as the biotin (vitamin H)-activating enzyme and as a transcriptional regulator. It catalyzes the formation of biotinyl-5'-adenylate from biotin and ATP and transfers biotin to a specific lysine residue on the biotin carboxyl carrier protein, a subunit of acetyl-CoA carboxylase (4,5). If all the biotin-accepting proteins in the cell have been biotinylated, the BirA-biotinyl-5'-AMP complex accumulates and binds to the 40-base-pair bio operator, repressing transcription of the biotin biosynthetic genes (4, 6-8). Thus BirA synthesizes its own corepressor, a unique property among known DNA-binding proteins. BirA represses transcription when biotinyl-5'-AMP is bound to the enzyme, suggesting that binding of corepressor helps form the BirA-DNA complex. Structure DeterminationCrystals of BirA were grown as described (9) and equilibrated with 2.05 M phosphate, pH 6.5/5% (vol/vol) glycerol. Native and derivative data sets were collected by using film or a Xuong-Hamlin (10) area detector ( Table 1). Inclusion of anomalous data in cross-phased difference Fourier maps showed the space group to be P43212 rather than its enantiomorph.Refined heavy-atom parameters were employed to compute multiple isomorphous replacement phases to 3.0-A resolution. The mean figure of merit, including an...

Our results reveal how pyridinylimidazole compounds are potent and selective inhibitors of p38 MAP kinase but not other MAP kinases. It should now be possible to design other specific inhibitors of activated p38 MAP kinase using the structure of the nonphosphorylated enzyme.

These structures span all three caspase subgroups, and provide a basis for inferring substrate and inhibitor binding, as well as selectivity for the entire caspase family. This information will influence the design of selective caspase inhibitors to further elucidate the role of caspases in biology and hopefully lead to the design of therapeutic agents to treat caspase-mediated diseases, such as rheumatoid arthritis, certain neurogenerative diseases and stroke.

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Interleukin-1␤-converting enzyme (ICE) is a novel cysteine protease responsible for the cleavage of pre-interleukin-1␤ (pre-IL-1␤) to the mature cytokine and a member of a family of related proteases (the caspases) that includes the Caenorhabditis elegans cell death gene product, CED-3. In addition to their sequence homology, these cysteine proteases display an unusual substrate specificity for peptidyl sequences with a P 1 aspartate residue. We have examined the kinetics of processing pre-IL-1␤ to the mature form by ICE and three of its homologs, TX, CPP-32, and CMH-1. Of the ICE homologs, only TX processes pre-IL-1␤, albeit with a catalytic efficiency 250-fold less than ICE itself. We also investigated the ability of these four proteases to process poly(ADPribose) polymerase, a DNA repair enzyme that is cleaved within minutes of the onset of apoptosis. Every caspase examined cleaves PARP, with catalytic efficiencies ranging from 2.3 ؋ 10 ICE 1 is the prototypical member of a new family of mammalian cysteine proteases (the caspases) 2 that is distinct from cysteine proteases in the papain superfamily (1-3). The mutagenesis experiments and crystal structure reported by Wilson et al. (4) revealed a different active site geometry and catalytic mechanism for ICE than observed for papain. The structure of the ICE active site contains a Cys-His catalytic diad, and two Arg residues that confer high selectivity for peptidyl substrates with Asp residues at the P 1 position (Nterminal to the scissile bond) (4, 5). Although ICE has recently been reported to cleave other proteins in vitro (6, 7), it was identified from its essential role in processing the inactive 31-kDa precursor of interleukin-1␤ (pre-IL-1␤) to the mature 17-kDa cytokine (8).In 1993, Yuan et al. (9) reported the sequence of the Caenorhabditis elegans programmed cell death gene ced-3. This gene is 29% identical to human ICE. Due to the central role of the CED-3 protein in C. elegans apoptosis, Yuan and colleagues deduced that ICE or ICE homologs might play a similar role in mammalian apoptosis. Overexpression of ICE in rat fibroblast, mammalian COS cells, and neuronal cell lines demonstrated that this protease can indeed induce apoptosis (6, 10, 11). Subsequently, Kuida et al. (12) confirmed an in vivo role for ICE in Fas-mediated apoptosis by disruption of the murine ICE gene.A family of ICE-related proteases (the caspases) was discovered by searching human cDNA libraries for sequences homologous to 14). At present, at least 10 human homologs of ICE possessing cysteine protease activity have been identified. These homologs can be grouped by sequence similarity into three subfamilies. The most closely related homologs to ICE are TX (caspase-4, also denoted ICH-2 or ICErel II) (15-17) and TY (caspase-5, also denoted ICE rel III) (17, 18), which are 58 and 57% identical to ICE at the amino acid level. Another homolog, ICH-1 (caspase-2, corresponding to the murine Nedd-2 gene) (19,20), is 20% identical to ICE and belongs to a distinct subfamily. A third gr...