Modulation of the acetylation state of histones plays a pivotal role in the regulation of gene expression. Histone deacetylases (HDACs) catalyze the removal of acetyl groups from lysines near the N termini of histones. This reaction promotes the condensation of chromatin, leading to repression of transcription. HDAC deregulation has been linked to several types of cancer, suggesting a potential use for HDAC inhibitors in oncology. Here we describe the first crystal structures of a human HDAC: the structures of human HDAC8 complexed with four structurally diverse hydroxamate inhibitors. This work sheds light on the catalytic mechanism of the HDACs, and on differences in substrate specificity across the HDAC family. The structure also suggests how phosphorylation of Ser39 affects HDAC8 activity.

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...

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Aberrant signaling of ErbB family members human epidermal growth factor 2 (HER2) and epidermal growth factor receptor (EGFR) is implicated in many human cancers, and HER2 expression is predictive of human disease recurrence and prognosis. Small molecule kinase inhibitors of EGFR and of both HER2 and EGFR have received approval for the treatment of cancer. We present the first high resolution crystal structure of the kinase domain of HER2 in complex with a selective inhibitor to understand protein activation, inhibition, and function at the molecular level. HER2 kinase domain crystallizes as a dimer and suggests evidence for an allosteric mechanism of activation comparable with previously reported activation mechanisms for EGFR and HER4. A unique Gly-rich region in HER2 following the ␣-helix C is responsible for increased conformational flexibility within the active site and could explain the low intrinsic catalytic activity previously reported for HER2. In addition, we solved the crystal structure of the kinase domain of EGFR in complex with a HER2/EGFR dual inhibitor (TAK-285). Comparison with previously reported inactive and active EGFR kinase domain structures gave insight into the mechanism of HER2 and EGFR inhibition and may help guide the design and development of new cancer drugs with improved potency and selectivity.

Human 11␤-hydroxysteroid dehydrogenase type I (11␤-HSD1) is an ER-localized membrane protein that catalyzes the interconversion of cortisone and cortisol. In adipose tissue, excessive cortisol production through 11␤-HSD1 activity has been implicated in the pathogenesis of type II diabetes and obesity. We report here biophysical, kinetic, mutagenesis, and structural data on two ternary complexes of 11␤-HSD1. The combined results reveal flexible active site interactions relevant to glucocorticoid recognition and demonstrate how four 11␤-HSD1 C termini converge to form an as yet uncharacterized tetramerization motif. A C-terminal Pro-Cys motif is localized at the center of the tetramer and forms reversible enzyme disulfides that alter enzyme activity. Conformational flexibility at the tetramerization interface is coupled to structural changes at the enzyme active site suggesting how the central Pro-Cys motif may regulate enzyme activity. Together, the crystallographic and biophysical data provide a structural framework for understanding 11␤-HSD1 activities and will ultimately facilitate the development of specific inhibitors.

Alogliptin is a potent, selective inhibitor of the serine protease dipeptidyl peptidase IV (DPP-4). Herein, we describe the structure-based design and optimization of alogliptin and related quinazolinone-based DPP-4 inhibitors. Following an oral dose, these noncovalent inhibitors provide sustained reduction of plasma DPP-4 activity and a lowering of blood glucose in animal models of diabetes. Alogliptin is currently undergoing phase III trials in patients with type 2 diabetes.

Early forms of the genetic code likely generated ''statistical'' proteins, with similar side chains occupying the same sequence positions at different ratios. In this scenario, groups of related side chains were treated by aminoacyl-tRNA synthetases as a single molecular species until a discrimination mechanism developed that could separate them. The aromatic amino acids tryptophan, tyrosine, and phenylalanine likely constituted one of these groups. A crystal structure of human tryptophanyl-tRNA synthetase was solved at 2.1 Å with a tryptophanyl-adenylate bound at the active site. A cocrystal structure of an active fragment of human tyrosyltRNA synthetase with its cognate amino acid analog was also solved at 1.6 Å. The two structures enabled active site identifications and provided the information for structure-based sequence alignments of Ϸ45 orthologs of each enzyme. Two critical positions shared by all tyrosyl-tRNA synthetases and tryptophanyl-tRNA synthetases for amino acid discrimination were identified. The variations at these two positions and phylogenetic analyses based on the structural information suggest that, in contrast to many other amino acids, discrimination of tyrosine from tryptophan occurred late in the development of the genetic code.

018. Figure 4 depicts a recently obtained cocrystal structure (PDB code 2ONC).