Structure of the small ribosomal subunit from T. Thermophilus

Die kleine ribosomale Untereinheit vollzieht die Dekodierung der genetischen Information in der Protein-Biosynthese. Die Struktur dieser Untereinheit von Thermus thermophilus zeigt, daß das Dekodierungszentrum, in dem die mRNA und die drei tRNA-Moleküle positioniert werden, ausschließlich aus RNA aufgebaut ist. Der Eingang zum mRNA-Kanal wird durch eine flexible, molekulare Klammer, die wesentlich an dem präzisen Transport der mRNA durch das Ribosom beteiligt ist, umschlossen. RNA-Helizes, die die ribosomale Untereinheit in ihrer ganzen Länge durchziehen, können periphere strukturelle Änderungen innheralb des Moleküls weiterleiten, und so mit dem Zyklus der mRNA-Translokation synchronisieren. 96% der Nukleotide und die Faltung aller Proteine konnten modelliert werden. Die ribosomalen Proteine sind zum Teil an der Peripherie des Moleküls und tragen als Linker zur Organisation der RNA bei. In gewissen Maße können manche der Proteine zur Translokation beitragen

Pulmonary Function in Persons Who are Professionally Exposed to Formaldehyde Fumes

The present study examines long-term effects of occupational exposure to formaldehyde fumes on lung function. Forced spirometry and diffusing lung capacity were measured in 16 health-service professionals (8 medical doctors and 8 laboratory technicians) working at the pathoanatomic laboratory for at least 4 years with daily exposure 8+1 hours. Control group employed 16 males, which were matched by age and stature to members of the exposed group. Only non-smokers were included in the study. Spirometric parameters in study participants exposed to formaldehyde fumes compared to control group were not significantly different indicating absence of restrictive and/or obstructive deterioration of lung function in exposed group. The only parameter differing in two groups was blood volume of pulmonary capillaries (Vc’) which was significantly larger in a group exposed to formaldehyde fumes. The possibility that the hyperemic lung reaction is the consequence of the exposure to formaldehyde fumes should be further explored

Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product

Heparinase II depolymerizes heparin and heparan sulfate glycosaminoglycans, yielding unsaturated oligosaccharide products through an elimination degradation mechanism. This enzyme cleaves the oligosaccharide chain on the nonreducing end of either glucuronic or iduronic acid, sharing this characteristic with a chondroitin ABC lyase. We have determined the first structure of a heparin-degrading lyase, that of heparinase II from Pedobacter heparinus ( formerly Flavobacterium heparinum), in a ligand-free state at 2.15 (A) over circle resolution and in complex with a disaccharide product of heparin degradation at 2.30 (A) over circle resolution. The protein is composed of three domains: an N-terminal alpha-helical domain, a central two-layered beta-sheet domain, and a C-terminal domain forming a two-layered beta-sheet. Heparinase II shows overall structural similarities to the polysaccharide lyase family 8 ( PL8) enzymes chondroitin AC lyase and hyaluronate lyase. In contrast to PL8 enzymes, however, heparinase II forms stable dimers, with the two active sites formed independently within each monomer. The structure of the N- terminal domain of heparinase II is also similar to that of alginate lyases from the PL5 family. A Zn2+ ion is bound within the central domain and plays an essential structural role in the stabilization of a loop forming one wall of the substrate-binding site. The disaccharide binds in a long, deep canyon formed at the top of the N- terminal domain and by loops extending from the central domain. Based on structural comparison with the lyases from the PL5 and PL8 families having bound substrates or products, the disaccharide found in heparinase II occupies the '+1' and '+2' subsites. The structure of the enzyme -product complex, combined with data from previously characterized mutations, allows us to propose a putative chemical mechanism of heparin and heparan -sulfate degradation200626NRC publication: Ye

Crystal structure of ureidoglycolate hydrolase (AllA) from Escherichia coli O157:H7

NRC publication: Ye

Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography

AbstractBackground: Ribosomes are the universal cellular organelles that accomplish the translation of the genetic code into proteins. Electron cryo-microscopy (cryo-EM) has yielded fairly detailed three-dimensional reconstructions of ribosomes. These were used to assist in the determination of higher resolution structures by X-ray crystallography.Results: Molecular replacement studies using cryo-EM reconstructions provided feasible packing schemes for crystals of ribosomes and their two subunits from Thermus thermophilus, and of the large subunits from Haloarcula marismortui. For the large subunits, these studies also confirmed the major heavy-atom sites obtained by single isomorphous replacement combined with anomalous diffraction (SIRAS) and by multiple isomorphous replacement combined with anomalous diffraction (MIRAS) at ∼10 Å. Although adequate starting phases could not be obtained for the small subunits, the crystals of which diffract to 3.0 Å, cryo-EM reconstructions were indispensable for analyzing their 7.2 Å multiple isomorphous replacement (MIR) map. This work indicated that the conformation of the crystallized small subunits resembles that seen within the 70S ribosomes. Subsequently, crystals of particles trapped in their functionally active state were grown.Conclusions: Single-particle cryo-EM can contribute to the progress of crystallography of non-symmetrical, large and flexible macromolecular assemblies. Besides confirming heavy-atom sites, obtained from flat or overcrowded difference Patterson maps, the cryo-EM reconstructions assisted in elucidating packing arrangements. They also provided tools for the identification of the conformation within the crystals and for the estimation of the level of inherent non-isomorphism

Sequence-structure relationships in polysaccharide co-polymerase (PCP) proteins

Polysaccharides are ubiquitously distributed on the cell surface of bacteria. These polymers are involved in many processes, including immune avoidance and bacteria–host interactions, which are especially important for pathogenic organisms. In many instances, the lengths of these polysaccharides are not random, but rather distribute around some mean value, termed the modal length. A large family of proteins, called polysaccharide co-polymerases (PCPs), found in both Gram-negative and Gram-positive species regulate polysaccharide modal length. Recent crystal structures of Wzz proteins from Escherichia coli and Salmonella typhimurium provide the first atomic-resolution information for one family of PCPs, the PCP1 group. These crystal structures have important implications for the structures of other PCP families.Renato Morona, Leanne Purins, Ante Tocilj, Allan Matte and Miroslaw Cygle