Home About us Contact
|
Home About us Contact | ||
|
|
||
Second Structure (second + structure)
Selected AbstractsCrystal structures of thymidylate synthase mutant R166Q: Structural basis for the nearly complete loss of catalytic activity,JOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY, Issue 2 2006Rogerio R. Sotelo-Mundo Abstract Thymidylate synthase (TS) catalyzes the folate-dependent methylation of deoxyuridine monophosphate (dUMP) to form thymidine monophosphate (dTMP). We have investigated the role of invariant arginine 166, one of four arginines that contact the dUMP phosphate, using site-directed mutagenesis, X-ray crystallography, and TS from Escherichia coli. The R166Q mutant was crystallized in the presence of dUMP and a structure determined to 2.9 Å resolution, but neither the ligand nor the sulfate from the crystallization buffer was found in the active site. A second structure determined with crystals prepared in the presence of dUMP and the antifolate 10-propargyl-5,8-dideazafolate revealed that the inhibitor was bound in an extended, nonproductive conformation, partially occupying the nucleotide-binding site. A sulfate ion, rather than dUMP, was found in the nucleotide phosphate-binding site. Previous studies have shown that the substitution at three of the four arginines of the dUMP phosphate-binding site is permissive; however; for Arg166, all the mutations lead to a near-inactive mutant. The present structures of TS R166Q reveal that the phosphate-binding site is largely intact, but with a substantially reduced affinity for phosphate, despite the presence of the three remaining arginines. The position of Cys146, which initiates catalysis, is shifted in the mutant and resides in a position that interferes with the binding of the dUMP pyrimidine moiety. © 2006 Wiley Periodicals, Inc. J Biochem Mol Toxicol 20:88,92, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20122 [source] Structure of the B3 domain from Arabidopsis thaliana protein At1g16640PROTEIN SCIENCE, Issue 9 2005Jeanette K. Waltner Abstract A novel DNA binding motif, the B3 domain, has been identified in a number of transcription factors specific to higher plant species, and was recently found to define a new protein fold. Here we report the second structure of a B3 domain, that of the Arabidopsis thaliana protein, At1g16640. As part of an effort to ,rescue' structural genomics targets deemed unsuitable for structure determination as full-length proteins, we applied a combined bioinformatic and experimental strategy to identify an optimal construct containing a predicted conserved domain. By screening a series of N- and C-terminally truncated At1g16640 fragments, we isolated a stable folded domain that met our criteria for structural analysis by NMR spectroscopy. The structure of the B3 domain of At1g16640 consists of a seven-stranded ,-sheet arranged in an open barrel and two short ,-helices, one at each end of the barrel. While At1g16640 is quite distinct from previously characterized B3 domain proteins in terms of amino acid sequence similarity, it adopts the same novel fold that was recently revealed by the RAV1 B3 domain structure. However, putative DNA-binding elements conserved in B3 domains from the RAV, ARF, and ABI3/VP1 subfamilies are largely absent in At1g16640, perhaps suggesting that B3 domains could function in contexts other than transcriptional regulation. [source] Analysis of mitochondrial DNA protein-coding region in the Yeso Sika deer (Cervus nippon yesoensis)ANIMAL SCIENCE JOURNAL, Issue 4 2004Kenta WADA ABSTRACT In the present study, mitochondrial DNA sequences of the Yeso Sika deer (Cervus nippon yesoensis) were studied. Specifically, protein-coding genes as mitochondrial NADH dehydrogenase subunits (ND1, ND2, ND3, ND4L, ND4, ND5 and ND6), cytochrome c oxidase subunits (CO I and CO III), ATP synthase subunits (ATPase8 and ATPase6) and cytochrome b. Also, phylogenetic analyses on eight mammalian species were performed, including the Muntjac deer (Muntiacus reevesi). The rate of amino-acid substitution was lowest (3.74%) between Yeso Sika deer and Muntjac deer, and the values between Yeso Sika deer and other species (sheep, cattle, horse, pig, mouse, human and chimpanzee) were 6.63%, 7.30%, 12.55%, 13.03%, 23.59%, 24.82% and 25.04%, respectively. Among them, the highest value of divergence was recognized in ATPase8, and the second structure of ATPase8 showed a difference between the Yeso Sika deer and Muntjac deer as a result of the substitution of 34His,Tyr and 49Thr,Ile. In addition, we identified a substitution of an amino-acid sequence (19Thr,Ala) between the Yeso Sika deer and Yakushima Sika deer (C. n. yakushimae). From these results, ATPase8 was also a variable region in Cervidae. [source] Crystallization and crystallographic analysis of Bacillus subtilis xylanase CACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2009Franz J. St John The recent biochemical characterization of the xylanases of glycosyl hydrolase family 5 (GH 5) has identified a distinctive endo mode of action, hydrolyzing the ,-1,4 xylan chain at a specific site directed by the position of an ,-1,2-linked glucuronate moiety. Xylanase C (XynC), the GH 5 xylanase from Bacillus subtilis 168, has been cloned, overexpressed and crystallized. Initial data collection was performed and a preliminary model has been built into a low-quality 2.7,Å resolution density map. The crystals belonged to the primitive monoclinic space group P21. Further screening identified an additive that resulted in large reproducible crystals. This larger more robust crystal form belonged to space group P21212 and a resulting data set has been processed to 1.64,Å resolution. This will be the second structure to be solved from this unique xylanase family and the first from a Gram-positive bacterium. This work may help to identify the structural determinants that allow the exceptional specificity of this enzyme and the role it plays in the biological depolymerization and processing of glucuronoxylan. [source] | ||||||||||