Seiichiro Kishishita

Crystal Structure of the Interleukin-15·Interleukin-15 Receptor α Complex INSIGHTS INTO TRANS AND CIS PRESENTATION

Interleukin (IL)-15 is a pleiotropic cytokine that plays a pivotal role in both innate and adaptive immunity. IL-15 is unique among cytokines due to its participation in a trans signaling mechanism in which IL-15 receptorα (IL-15Rα) from one subset of cells presents IL-15 to neighboring IL-2Rβ/γc-expressing cells. Here we present the crystal structure of IL-15 in complex with the sushi domain of IL-15Rα. The structure reveals that theα receptor-binding epitope of IL-15 adopts a unique conformation, which, together with amino acid substitutions, permits specific interactions with IL-15Rα that account for the exceptionally high affinity of the IL-15·IL-15Rα complex. Interestingly, analysis of the topology of IL-15 and IL-15Rα at the IL-15·IL-15Rα interface suggests that IL-15 should be capable of participating in a cis signaling mechanism similar to that of the related cytokine IL-2. Indeed, we present biochemical data demonstrating that IL-15 is capable of efficiently signaling in cis through IL-15Rα and IL-2Rβ/γc expressed on the surface of a single cell. Based on our data we propose that cis presentation of IL-15 may be important in certain biological contexts and that flexibility of IL-15Rα permits IL-15 and its three receptor components to be assembled identically at the ligand-receptor interface whether IL-15 is presented in cis or trans. Finally, we have gained insights into IL-15·IL-15Rα·IL-2Rβ·γc quaternary complex assembly through the use of molecular modeling.

Crystal structure of the GAF-B domain from human phosphodiesterase 10A complexed with its ligand, cAMP.

Cyclic nucleotide phosphodiesterases (PDEs) catalyze the degradation of the cyclic nucleotides cAMP and cGMP, which are important second messengers. Five of the 11 mammalian PDE families have tandem GAF domains at their N termini. PDE10A may be the only mammalian PDE for which cAMP is the GAF domain ligand, and it may be allosterically stimulated by cAMP. PDE10A is highly expressed in striatal medium spiny neurons. Here we report the crystal structure of the C-terminal GAF domain (GAF-B) of human PDE10A complexed with cAMP at 2.1-Å resolution. The conformation of the PDE10A GAF-B domain monomer closely resembles those of the GAF domains of PDE2A and the cyanobacterium Anabaena cyaB2 adenylyl cyclase, except for the helical bundle consisting of α1, α2, and α5. The PDE10A GAF-B domain forms a dimer in the crystal and in solution. The dimerization is mainly mediated by hydrophobic interactions between the helical bundles in a parallel arrangement, with a large buried surface area. In the PDE10A GAF-B domain, cAMP tightly binds to a cNMP-binding pocket. The residues in the α3 and α4 helices, the β6 strand, the loop between 310 and α4, and the loop between α4 and β5 are involved in the recognition of the phosphate and ribose moieties. This recognition mode is similar to those of the GAF domains of PDE2A and cyaB2. In contrast, the adenine base is specifically recognized by the PDE10A GAF-B domain in a unique manner, through residues in the β1 and β2 strands.

Novel dimerization mode of the human Bcl-2 family protein Bak, a mitochondrial apoptosis regulator.

Interactions of Bcl-2 family proteins play a regulatory role in mitochondrial apoptosis. The pro-apoptotic protein Bak resides in the outer mitochondrial membrane, and the formation of Bak homo- or heterodimers is involved in the regulation of apoptosis. The previously reported structure of the human Bak protein (residues Glu16-Gly186) revealed that a zinc ion was coordinated with two pairs of Asp160 and His164 residues from the symmetry-related molecules. This zinc-dependent homodimer was regarded as an anti-apoptotic dimer. In the present study, we determined the crystal structure of the human Bak residues Ser23-Asn185 at 2.5A, and found a distinct type of homodimerization through Cys166 disulfide bridging between the symmetry-related molecules. In the two modes of homodimerization, the molecular interfaces are completely different. In the membrane-targeted model of the S-S bridged dimer, the BH3 motifs are too close to the membrane to interact directly with the anti-apoptotic relatives, such as Bcl-x(L). Therefore, the Bak dimer structure reported here may represent a pro-apoptotic mode under oxidized conditions.

Structure of the human Tim44 C-terminal domain in complex with pentaethylene glycol: ligand-bound form.

Familial oncocytic thyroid carcinoma is associated with a missense mutation, P308Q, in the C-terminal domain of Tim44. Tim44 is the mitochondrial inner-membrane translocase subunit and it functions as a membrane anchor for the mitochondrial heat-shock protein 70 (mtHsp70). Here, the crystal structure of the human Tim44 C-terminal domain complexed with pentaethylene glycol has been determined at 1.9 A resolution. The overall structure resembles that of the nuclear transport factor 2-like domain. In the crystal structure, pentaethylene glycol molecules are associated at two potential membrane-binding sites: the large hydrophobic cavity and the highly conserved loop between the alpha1 and alpha2 helices near Pro308. A comparison with the yeast homolog revealed that lipid binding induces conformational changes around the alpha1-alpha2 loop, leading to slippage of the alpha1 helix along the large beta-sheet. These changes may play important roles in the translocation of polypeptides across the mitochondrial inner membrane.

Crystal structure of the single-domain rhodanese homologue TTHA0613 from Thermus thermophilus HB8

Motoyuki Hattori, Eiichi Mizohata, Ayako Tatsuguchi, Rie Shibata, Seiichiro Kishishita, Kazutaka Murayama, Takaho Terada, Seiki Kuramitsu, Mikako Shirouzu, and Shigeyuki Yokoyama* RIKEN Genomic Sciences Center, Yokohama, Japan Graduate School of Science, University of Tokyo, Tokyo, Japan RIKEN SPring-8 Center, Harima Institute, Hyogo, Japan Department of Biology, Graduate School of Science, Osaka University, Osaka, Japan

Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2

The target of diphtheria toxin is the diphthamide residue in translation elongation factor 2 (EF-2), which is generated by a three-step post-translational modification of a specific histidine residue in the EF-2 precursor. In the second modification step, an S-adenosylmethionine-dependent methyltransferase, diphthine synthase (DS), catalyzes the trimethylation of the EF-2 precursor. The homodimeric crystal structures of the archaeal diphthine synthases from Pyrococcus horikoshii OT3 and Aeropyrum pernix K1 have been determined. These structures share essentially the same overall fold as the cobalt-precorrin-4 methyltransferase CbiF, confirming that DS belongs to the dimeric class III family of methyltransferases. In the P. horikoshii DS dimer, only one of the two active sites binds the reaction product S-adenosyl-L-homocysteine (AdoHcy), while the other active site contains no ligand. This asymmetric AdoHcy binding may be a consequence of intra-domain and inter-domain movements upon binding of AdoHcy at one of the two sites. These movements disrupt the twofold dimeric symmetry of the DS dimer and probably cause lower AdoHcy affinity at the other binding site.

Structure of the minimized alpha/beta-hydrolase fold protein from Thermus thermophilus HB8.

The gene encoding TTHA1544 is a singleton found in the Thermus thermophilus HB8 genome and encodes a 131-amino-acid protein. The crystal structure of TTHA1544 has been determined at 2.0 A resolution by the single-wavelength anomalous dispersion method in order to elucidate its function. There are two molecules in the asymmetric unit. Each molecule consists of four alpha-helices and six beta-strands, with the beta-strands composing a central beta-sheet. A structural homology search revealed that the overall structure of TTHA1544 resembles the alpha/beta-hydrolase fold, although TTHA1544 lacks the catalytic residues of a hydrolase. These results suggest that TTHA1544 represents the minimized alpha/beta-hydrolase fold and that an additional component would be required for its activity.

Crystal structure of a conserved hypothetical protein TT1751 from Thermus thermophilus HB8

Seiichiro Kishishita, Ayako Tatsuguchi, Ryoko Ushikoshi-Nakayama, Takaho Terada, Seiki Kuramitsu, Sam-Yong Park, Jeremy R. H. Tame, Mikako Shirouzu, and Shigeyuki Yokoyama* RIKEN Genomic Sciences Center, Yokohama, Japan RIKEN Harima Institute at SPring-8, Hyogo, Japan Department of Biology, Graduate School of Science, Osaka University, Osaka, Japan Protein Design Laboratory, Yokohama City University, Yokohama, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan