Crystal structure of the RNA 2'-phosphotransferase from Aeropyrum pernix K1

In the final step of tRNA splicing, the 2'-phosphotransferase catalyzes the transfer of the extra 2'-phosphate from the precursor-ligated tRNA to NAD. We have determined the crystal structure of the 2'-phosphotransferase protein from Aeropyrum pernix K1 at 2.8 Angstroms resolution. The structure of the 2'-phosphotransferase contains two globular domains (N and C-domains), which form a cleft in the center. The N-domain has the winged helix motif, a subfamily of the helix-turn-helix family, which is shared by many DNA-binding proteins. The C-domain of the 2'-phosphotransferase superimposes well on the NAD-binding fold of bacterial (diphtheria) toxins, which catalyze the transfer of ADP ribose from NAD to target proteins, indicating that the mode of NAD binding by the 2'-phosphotransferase could be similar to that of the bacterial toxins. The conserved basic residues are assembled at the periphery of the cleft and could participate in the enzyme contact with the sugar-phosphate backbones of tRNA. The modes by which the two functional domains recognize the two different substrates are clarified by the present crystal structure of the 2'-phosphotransferase.     

Pressure-jump NMR study of dissociation and association of amyloid protofibrils

The dissociation and reassociation processes of amyloid protofibrils initiated by pressure-jump have been monitored with real-time (1)H NMR spectroscopy using an intrinsically denatured disulfide-deficient variant of hen lysozyme. Upon pressure-jump up to 2 kbar, the matured protofibrils grown over several months become fully dissociated into monomers within a few days. Upon pressure-jump down to 30 bar, the dissociated monomers immediately start reassociating. The association and dissociation cycle can be repeated reproducibly by alternating pressure, establishing a notion that the protofibril formation is simply a slow kinetic process toward thermodynamic equilibrium. The outstanding simplicity and effectiveness of pressure in controlling the protofibril formation opens a new route for investigating mechanisms of amyloid fibril-forming reactions. The noted variation in the pressure-induced dissociation rate with the progress of the association reaction suggests multiple mechanisms for the elongation of the protofibril. The disulfide-deficient hen lysozyme offers a particularly simple model system for thermodynamic and kinetic studies of protofibril formation as well as for screening drugs for amyloidosis.     

Anti-thyroid hormonal activity of tetrabromobisphenol A, a flame retardant, and related compounds: Affinity to the mammalian thyroid hormone receptor, and effect on tadpole metamorphosis

The thyroid hormone-disrupting activity of tetrabromobisphenol A (TBBPA), a flame retardant, and related compounds was examined. TBBPA, tetrachlorobisphenol A (TCBPA), tetramethylbisphenol A (TMBPA) and 3,3'-dimethylbisphenol A (DMBPA) markedly inhibited the binding of triiodothyronine (T3; 1 x 10(-10) M) to thyroid hormone receptor in the concentration range of 1 x 10(-7)-1 x 10(-4) M, while bisphenol A and 2,2-diphenylpropane were inactive. TBBPA, TCBPA, TMBPA and DMBPA did not exhibit thyroid hormonal activity in a thyroid hormone-responsive reporter assay using a Chinese hamster ovary cell line (CHO-K1) transfected with thyroid hormone receptor alpha1 or beta1, but TBBPA and TCBPA showed significant anti-thyroid hormone effects on the activity of T3 (1 x 10(-8) M) in the concentration range of 3 x 10(-6) - 5 x 10(-5) M. The thyroid hormone-disrupting activity of TBBPA was also examined in terms of the effect on amphibian metamorphosis stimulated by thyroid hormone. TBBPA in the concentration range of 1 x 10(-8) to 1 x 10(-6) M showed suppressive action on T3 (5 x 10(-8) M)-enhancement of Rana rugosa tadpole tail shortening. These facts suggest that TBBPA, TCBPA, TMBPA and DMBPA can act as thyroid hormone-disrupting agents.     

Differential expression pattern of C4 bundle sheath expression genes in rice, a C3 plant

NADP-malic enzyme (NADP-ME) and phosphoenolpyruvate carboxykinase(PCK) are specifically expressed in bundle sheath cells (BSCs)in NADP-ME-type and PCK-type C₄ plants, respectively. Unlikethe high activities of these enzymes in the green leaves ofC₄ plants, their low activities have been detected in the leavesof C₃ plants. In order to elucidate the differences in the geneexpression system between C₃ and C₄ plants, we have producedchimeric constructs with the ß-glucuronidase (GUS)reporter gene under the control of the maize NADP-Me (ZmMe)or Zoysia japonica Pck (ZjPck) promoter and introduced theseconstructs into rice. In leaves of transgenic rice, the ZmMepromoter directed GUS expression not only in mesophyll cells(MCs) but also in BSCs and vascular cells, whereas the ZjPckpromoter directed GUS expression only in BSCs and vascular cells.Neither the ZjPck nor ZmMe promoters induced GUS expressiondue to light. In rice leaves, the endogenous NADP-Me (OsMe1)was expressed in MCs, BSCs and vascular cells, whereas the ricePck (OsPck1) was expressed only in BSCs and vascular cells.Taken together, the results obtained from transgenic rice demonstratethat the expression pattern of ZmMe or ZjPck in transgenic ricewas reflected by that of its counterpart gene in rice. (Received August 8, 2004; Accepted February 20, 2005 )     

Structure-based functional identification of a novel heme-binding protein from <Emphasis Type="Italic">Thermus thermophilus</Emphasis> HB8

The TT1485 gene from Thermus thermophilus HB8 encodes a hypothetical protein of unknown function with about 20 sequence homologs of bacterial or archaeal origin. Together they form a family of uncharacterized proteins, the cluster of orthologous group COG3253. Using a combination of amino acid sequence analysis, three-dimensional structural studies and biochemical assays, we identified TT1485 as a novel heme-binding protein. The crystal structure reveals that this protein is a pentamer and each monomer exhibits a β-barrel fold. TT1485 is structurally similar to muconolactone isomerase, but this provided no functional clues. Amino acid sequence analysis revealed remote homology to a heme enzyme, chlorite dismutase. Strikingly, amino acid residues that are highly conserved in the homologous hypothetical proteins and chlorite dismutase cluster around a deep cavity on the surface of each monomer. Molecular modeling shows that the cavity can accommodate a heme group with a strictly conserved His as a heme ligand. TT1485 reconstituted with iron protoporphyrin IX chloride gave a low chlorite dismutase activity, indicating that TT1485 catalyzes a reaction other than chlorite degradation. The presence of a possible Fe–His–Asp triad in the heme proximal site suggests that TT1485 functions as a novel heme peroxidase to detoxify hydrogen peroxide within the cell.     

Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana

The three-dimensional structure of the rhodanese homology domain At4g01050(175-195) from Arabidopsis thaliana has been determined by solution nuclear magnetic resonance methods based on 3043 upper distance limits derived from NOE intensities measured in three-dimensional NOESY spectra. The structure shows a backbone root mean square deviation to the mean coordinates of 0.43 A for the structured residues 7-125. The fold consists of a central parallel beta-sheet with five strands in the order 1-5-4-2-3 and arranged in the conventional counterclockwise twist, and helices packing against each side of the beta-sheet. Comparison with the sequences of other proteins with a rhodanese homology domain in Arabidopsis thaliana indicated residues that could play an important role in the scaffold of the rhodanese homology domain. Finally, a three-dimensional structure comparison of the present noncatalytic rhodanese homology domain with the noncatalytic rhodanese domains of sulfurtransferases from other organisms discloses differences in the length and conformation of loops that could throw light on the role of the noncatalytic rhodanese domain in sulfurtransferases.     

13-Deoxytedanolide, a marine sponge-derived antitumor macrolide, binds to the 60S large ribosomal subunit

13-Deoxytedanolide is a potent antitumor macrolide isolated from the marine sponge Mycale adhaerens. In spite of its remarkable activity, the mode of action of 13-deoxytedanolide has not been elucidated. [11-3H]-(11S)-13-Deoxydihydrotedanolide derived from the macrolide was used for identifying the target molecule from the yeast cell lysate. Fractionation of the binding protein revealed that the labeled 13-deoxytedanolide derivative strongly bound to the 80S ribosome as well as to the 60S large subunit, but not to the 40S small subunit. In agreement with this observation, 13-deoxytedanolide efficiently inhibited the polypeptide elongation. Interestingly, competition studies demonstrated that 13-deoxytedanolide shared the binding site on the 60S large subunit with pederin and its marine-derived analogues. These results indicate that 13-deoxytedanolide is a potent protein synthesis inhibitor and is the first macrolide to inhibit the eukaryotic ribosome.