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Detailed Three-dimensional Structure (detailed + three-dimensional_structure)
Selected AbstractsMicro-focus X-ray computed tomography images of the 3D structure of the cranium of a fetus with asymmetric double malformationCONGENITAL ANOMALIES, Issue 1 2006Takashi Shibata ABSTRACT,, Reconstructed micro computed tomography (Micro-CT, µ-CT) images have revealed the detailed three-dimensional structure of the cranium of human fetal congenital anomalies for the first time. The objects were a head and a cervix of female autosite and a parasite consisting of only a head conjoined to the scapular region of the autosite of an asymmetric double malformation (asymmetric conjoined twins, heteropagus twinning) at a gestational age of 8 months. The cranium of the autosite was normal, but that of the parasite was characterized by otocephaly (agnathia, synotia, and monorhina) and almost all the cranial bones were of an abnormal shape. It is suggested that a part of occipital bone (the basioccipital and exoccipital bones), the vomer and cribriform plate were absent and this resulted in the fusion and overlapping of bilateral temporal and craniofacial bones that should have been adjacent to them. This resulted in a reformation and relocation of most of the cranial bones. Micro-CT is a useful tool to visualize the detailed bone structure which has not been clarified by the conventional dissection methods and other imaging technologies and is a powerful instrument for studying congenital anomalies. [source] Structure,specificity relationships of an intracellular xylanase from Geobacillus stearothermophilusACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2007V. Solomon Geobacillus stearothermophilus T-6 is a thermophilic Gram-positive bacterium that produces two selective family 10 xylanases which both take part in the complete degradation and utilization of the xylan polymer. The two xylanases exhibit significantly different substrate specificities. While the extracellular xylanase (XT6; MW 43.8,kDa) hydrolyzes the long and branched native xylan polymer, the intracellular xylanase (IXT6; MW 38.6,kDa) preferentially hydrolyzes only short xylo-oligosaccharides. In this study, the detailed three-dimensional structure of IXT6 is reported, as determined by X-ray crystallography. It was initially solved by molecular replacement and then refined at 1.45,Å resolution to a final R factor of 15.0% and an Rfree of 19.0%. As expected, the structure forms the classical (,/,)8 fold, in which the two catalytic residues (Glu134 and Glu241) are located on the inner surface of the central cavity. The structure of IXT6 was compared with the highly homologous extracellular xylanase XT6, revealing a number of structural differences between the active sites of the two enzymes. In particular, structural differences derived from the unique subdomain in the carboxy-terminal region of XT6, which is completely absent in IXT6. These structural modifications may account for the significant differences in the substrate specificities of these otherwise very similar enzymes. [source] Structure of a bovine secretory signalling glycoprotein (SPC-40) at 2.1,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2006Janesh Kumar A recently discovered new class of 40,kDa glycoproteins forms a major component of the secretory proteins in the dry secretions of non-lactating animals. These proteins are implicated as protective signalling factors that determine which cells are to survive during the processes of drastic tissue remodelling. In order to understand its role in the remodelling of mammary glands, the detailed three-dimensional structure of the bovine signalling glycoprotein (SPC-40) has been determined using X-ray crystallography. SPC-40 was purified from bovine dry secretions and crystallized using the hanging-drop vapour-diffusion method. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 62.6, b = 67.4, c = 106.9,Å. The protein was also cloned in order to determine its complete amino-acid sequence. Its three-dimensional structure has been determined using data to 2.1,Å resolution. The amino-acid sequence determination of SPC-40 reveals two potential N-glycosylation sites at Asn39 and Asn345, but electron density for a glycan chain was only present at Asn39. The protein adopts a conformation with the classical (,/,)8 -barrel fold of triosephosphate isomerase (TIM barrel; residues 1,237 and 310,360) with the insertion of a small ,+, domain (residues 240,307) similar to that observed in chitinases. However, the substitution of Leu for Glu in the consensus catalytic sequence in SPC-40 caused a loss of chitinase activity. Furthermore, the chitin-binding groove in SPC-40 is considerably distorted owing to unfavourable conformations of several residues, including Trp78, Tyr120, Asp186 and Arg242. Three surface loops, His188,His197, Phe202,Arg212 and Tyr244,Pro260, have exceptionally high B factors, suggesting large-scale flexibility. Fluorescence studies indicate that various sugars bind to SPC-40 with low affinities. [source] Aspergillus niger lipase: Heterologous expression in Pichia pastoris, molecular modeling prediction and the importance of the hinge domains at both sides of the lid domain to interfacial activationBIOTECHNOLOGY PROGRESS, Issue 2 2009Zhengyu Shu Abstract Aspergillus niger lipase (ANL) is an important biocatalyst in the food processing industry. However, there is no report of its detailed three-dimensional structure because of difficulties in crystallization. In this article, based on experimental data and bioinformational analysis results, the structural features of ANL were simulated. Firstly, two recombinant ANLs expressed in Pichia pastoris were purified to homogeneity and their corresponding secondary structure compositions were determined by circular dichroism spectra. Secondly, the primary structure, the secondary structure and the three-dimensional structure of ANL were modeled by comparison with homologous lipases with known three-dimensional structures using the BioEdit software, lipase engineering database (http://www.led.uni-stuttgart.de/), PSIPRED server and SwissModel server. The predicted molecular structure of ANL presented typical features of the ,/, hydrolase fold including positioning of the putative catalytic triad residues and the GXSXG signature motif. Comparison of the predicted three-dimensional structure of ANL with the X-ray three-dimensional structure of A. niger feruloyl esterase showed that the functional difference of interfacial activation between lipase and esterase was concerned with the difference in position of the lid. Our three-dimensional model of ANL helps to modify lipase structure by protein engineering, which will further expand the scope of application of ANL. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] | ||||||||||