A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase

Protein folds in the all-beta and all-alpha classes

Analysis of the structures in the Protein Databank, released in June 1996, shows that the number of different protein folds, i.e. the number of different arrangements of major secondary structures and/or chain topologies, is 327. Of these folds, approximately 25% belong to the all-alpha class, 20% belong to the all-beta class, 30% belong to the alpha/beta class, and 25% belong to the alpha + beta class. We describe the types of folds now known for the all-beta and all-alpha classes, emphasizing those that have been discovered recently. Detailed theories for the physical determinants of the structures of most of these folds now exist, and these are reviewed.

Association of lipid A disaccharide synthase with aerobic glycerol-3-phosphate dehydrogenase in extracts of Escherichia coli

Variants of the Escherichia coli UDP-GlcNAc O-acyltransferase (LpxA) and of the lipid A disaccharide synthase (LpxB) containing affinity chromatography tags (C-terminal histidine 8 [H8] tails) were constructed in order to investigate whether or not these enzymes interact with other E. coli proteins. These variants (LpxA-H8 and LpxB-H8) had specific activities in vitro that were similar to wild-type enzymes. Crude extracts made from E. coli cells expressing LpxA-H8 or LpxB-H8 were chromatographed over Ni(2+)-NTA-Agarose, and proteins purifying with the tagged proteins were identified by SDS-PAGE, followed by blotting and N-terminal microsequencing. At high levels of LpxB-H8 expression, two heat-shock proteins (DnaK and GroEL) were associated with the disaccharide synthase, but not with the acyltransferase. Another major protein recovered with LpxB-H8 (both at low and high levels of expression) was the aerobic glycerol-3-phosphate dehydrogenase (GlpD). The latter interaction was specific, since GlpD did not bind the affinity resin when the affinity tag was present on the UDP-GlcNAc O-acyltransferase (LpxA-H8). Velocity centrifugation experiments indicated that both wild-type LpxB and GlpD sedimented together under some conditions, but these aggregates were smaller than and distinct from inner membranes. Our findings suggest a possible new mechanism by which the biosynthetic pathways for lipid A and glycerophospholipids may be coordinated.

Differential effect of site-directed mutations in pelC on pectate lyase activity, plant tissue maceration, and elicitor activity

Oligonucleotide site-directed mutations were introduced into the pelC gene of Erwinia chrysanthemi EC16 that directed single or double amino acid changes affecting disulfide linkages, calcium binding, catalysis, and protein folding. Subsequent characterization of the purified PelC mutant proteins demonstrated that pectinolytic function involves amino acids located near the calcium binding site rather than those surrounding an invariant vWiDH sequence. Wild-type PelC and the tested mutant proteins generally macerated plant tissue in proportion to their specific pectinolytic activity in vitro. However, some mutants gave higher maceration activity in plant tissue and elicited greater production of the phytoalexin, glyceollin, in soybean cotyledons than predicted by their in vitro pectinolytic activity. Most notable in this regard were three different mutations at lysine 172 with greatly reduced pectinolytic activity but as much elicitor activity as the wild-type protein. PelE macerated plant tissue 10 times more efficiently than PelC, as observed previously, but surprisingly showed equal activity in the elicitor assay. The results indicate that factors other than pectinolytic activity per se are involved in plant tissue maceration and elicitor activity.

Crystal structure of phage P22 tailspike protein complexed with Salmonella sp. O-antigen receptors

The O-antigenic repeating units of lipopolysaccharides from Salmonella serogroups A, B, and D1 serve as receptors for the phage P22 tailspike protein, which also has receptor destroying endoglycosidase (endorhamnosidase) activity, integrating the functions of both hemagglutinin and neuraminidase in influenza virus. Crystal structures of the tailspike protein in complex with oligosaccharides, comprising two O-antigenic repeating units from Salmonella typhimurium, Salmonella enteritidis, and Salmonella typhi 253Ty were determined at 1.8 A resolution. The active-site topology with Asp-392, Asp-395, and Glu-359 as catalytic residues was identified. Kinetics of binding and cleavage suggest a role of the receptor destroying endorhamnosidase activity primarily for detachment of newly assembled phages.

Crystallization and preliminary crystallographic analysis of tetrahydrodipicolinate-N-succinyltransferase

Crystals of tetrahydrodipicolinate-N-succinyltransferase have been obtained from solutions containing 2-propanol and polyethylene glycol 4,000. These crystals belong to the monoclinic space group P2(1), diffract X-rays to a resolution of 2.2 A, and contain one trimer per asymmetric unit.

Progress towards understanding beta-sheet structure

This review is focused on recent advances in our understanding of beta-sheet structure. It is intended to supplement previous surveys describing the early characterization and study of beta-sheet structure. The first two sections of this review provide a brief introduction to beta-sheet structure referencing the prior comprehensive reviews in this area as well as integrating new concepts. The next part outlines the typical problems encountered in solution studies on beta-sheet structures. The most useful spectroscopic and biophysical techniques used to characterize beta-sheet structures are described in the fourth section. Current hypotheses regarding the folding of predominantly beta-sheet proteins are discussed in some detail in the fifth segment. The efforts of a number of laboratories to utilize peptides or peptidomimetics to serve as small beta-sheet model systems are reviewed in the penultimate section. Finally, the efforts of a number of research groups focusing on the de novo design of beta-sheet-based proteins are outlined.

Function of the htrB high temperature requirement gene of Escherichia coli in the acylation of lipid A: HtrB catalyzed incorporation of laurate

By assaying lysates of Escherichia coli generated with the hybrid lambda bacteriophages of an ordered library (Kohara, Y., Akiyama, K., and Isono, K. (1987) Cell 50, 495-508), we identified two clones (lambda232 and lambda233) capable of overexpressing the lauroyl transferase that functions after 3-deoxy-D-manno-octulosonic acid (Kdo) addition in lipid A biosynthesis (Brozek, K. A., and Raetz, C. R. H. (1990) J. Biol. Chem. 265, 15410-15417). The E. coli DNA inserts in lambda232 and lambda233 suggested that a known gene (htrB) required for rapid growth above 33 degrees C might encode the lauroyl transferase. Using the intermediate (Kdo)2-lipid IVA as the laurate acceptor, extracts of strains with transposon insertions in htrB were found to contain no lauroyl transferase activity. Cells harboring hybrid htrB+ plasmids overproduced transferase activity 100-200-fold. The overproduced transferase was solubilized with a non-ionic detergent and purified further by DEAE-Sepharose chromatography. With lauroyl acyl carrier protein as the donor, the purified enzyme rapidly incorporated one laurate residue into (Kdo)2-lipid IVA. The rate of laurate incorporation was reduced by several orders of magnitude when either one or both Kdos were absent in the acceptor. With a matched set of acyl-acyl carrier proteins, the enzyme incorporated laurate 3-8 times faster than decanoate or myristate, respectively. Transfer of palmitate, palmitoleate, or R-3-hydroxymyristate was very slow. Taken together with previous studies, our findings indicate that htrB encodes a key, late functioning acyltransferase of lipid A biosynthesis.

Crystallization and preliminary diffraction studies of NodL, a rhizobial O-acetyl-transferase involved in the host-specific nodulation of legume roots

The NodL specified O-acetyltransferase from the microbial symbiont Rhizobium leguminosarum has been over-expressed in Escherichia coli and purified using affinity-elution dye chromatography as the key step. The protein has been crystallized at 20 degrees C in 18% PEG 600, 0.1 M Tris/HCl buffer, pH 8.5, containing 1% dioxane, 0.25% octyl-beta-glucoside, and 5 mM coenzyme A using the hanging drop vapor diffusion method. Ambient temperature X-ray diffraction studies reveal the space group to be hexagonal (P6(3)22) with lattice constants a = b = 77.08 A, c = 160.6 A, and alpha = beta = 90 degrees, gamma = 120 degrees. Crystals that are flash-frozen to 120 K diffract beyond 2.7 A.