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PubMed1993

Recent developments on the regulation and structure of glutamine synthetase enzymes from selected bacterial groups.

The structure of glutamine synthetase (GS) enzymes from diverse bacterial groups fall into three distinct classes. GSI is the typical bacterial GS, GSII is similar to the eukaryotic GS and is found together with GSI in plant symbionts and Streptomyces, while GSIII has been found in two unrelated anaerobic rumen bacteria. In most cases, the structural gene for GS enzyme is regulated in response to nitrogen. However, different regulatory mechanisms, to ensure optimal utilization of nitrogen substrates, control the GS enzyme in each class.

Actinomycetales↗
PubMed2007

Crystal structures of a bacterial 6-phosphogluconate dehydrogenase reveal aspects of specificity, mechanism and mode of inhibition by analogues of high-energy reaction intermediates.

Crystal structures of recombinant Lactococcus lactis 6-phosphogluconate dehydrogenase (LlPDH) in complex with substrate, cofactor, product and inhibitors have been determined. LlPDH shares significant sequence identity with the enzymes from sheep liver and the protozoan parasite Trypanosoma brucei for which structures have been reported. Comparisons indicate that the key residues in the active site are highly conserved, as are the interactions with the cofactor and the product ribulose 5-phosphate. However, there are differences in the conformation of the substrate 6-phosphogluconate which may reflect distinct states relevant to catalysis. Analysis of the complex formed with the potent inhibitor 4-phospho-d-erythronohydroxamic acid, suggests that this molecule does indeed mimic the high-energy intermediate state that it was designed to. The analysis also identified, as a contaminant by-product of the inhibitor synthesis, 4-phospho-d-erythronamide, which binds in similar fashion. LlPDH can now serve as a model system for structure-based inhibitor design targeting the enzyme from Trypanosoma species.

Amino Acid Sequence↗
PubMed1990

Three separate classes of bacterial ice nucleation structures.

Studies of the properties of the ice nucleation structure exposed on the surfaces of various bacteria such as Pseudomonas syringae, Erwinia herbicola, or various strains of Ice+ recombinant Escherichia coli have shown that there are clearly three major related but chemically distinct types of structures on these cells. First, the ability of Ice+ cells to nucleate super-cooled D2O has been examined, and it has been found that this ability (relative to the ability of the same cells to nucleate super-cooled H2O) exhibited three characteristic nucleating patterns. The rarest structure, called class A, is found on only a small fraction of cells in a culture, nucleates H2O at temperatures above -4.4 degrees C, and is an effective nucleator of super-cooled D2O. A second class of structure, called class B, is found on a larger portion of the cells, nucleates H2O between -4.8 and -5.7 degrees C, and is a relatively poor nucleator of super-cooled D2O. The class C structure is found on almost all cells and nucleates at -7.6 degrees C or colder. These three classes of structures were also differentiated by their sensitivities to low concentrations of water-miscible organic solvents such as dioxane or dimethyl sulfoxide. Depending on the specific bacterial strain, the addition of these solvents to bacterial suspensions lowered the nucleation activity of the class A structure by 1,000-fold or more. The nucleation activities of class B structures in the same culture were highly resistant to these compounds and were lowered only by 20 to 40%. The class C structures were more sensitive than Class B structures were, and the nucleation activities decreased 70 to 90%. Finally, the pH sensitivity of these three classes of structures was examined. The class A structure was destroyed in buffers at pH 4.5 lower but was stable in buffers at higher pHs. The class B structure was less sensitive to acidic buffers but was destroyed at pH 5.5 or lower and was stable at higher pHs. However, the class C structure was unaffected by incubation in buffers with pHs of 3.5 to 9.0. Suggestions for the actual nucleation structures of the three classes are proposed.

Deuterium↗
PubMed2001

Crystal structure of a bacterial signal peptidase apoenzyme: implications for signal peptide binding and the Ser-Lys dyad mechanism.

We report here the x-ray crystal structure of a soluble catalytically active fragment of the Escherichia coli type I signal peptidase (SPase-(Delta2-75)) in the absence of inhibitor or substrate (apoenzyme). The structure was solved by molecular replacement and refined to 2.4 A resolution in a different space group (P4(1)2(1)2) from that of the previously published acyl-enzyme inhibitor-bound structure (P2(1)2(1)2) (Paetzel, M., Dalbey, R.E., and Strynadka, N.C.J. (1998) Nature 396, 186-190). A comparison with the acyl-enzyme structure shows significant side-chain and main-chain differences in the binding site and active site regions, which result in a smaller S1 binding pocket in the apoenzyme. The apoenzyme structure is consistent with SPase utilizing an unusual oxyanion hole containing one side-chain hydroxyl hydrogen (Ser-88 OgammaH) and one main-chain amide hydrogen (Ser-90 NH). Analysis of the apoenzyme active site reveals a potential deacylating water that was displaced by the inhibitor. It has been proposed that SPase utilizes a Ser-Lys dyad mechanism in the cleavage reaction. A similar mechanism has been proposed for the LexA family of proteases. A structural comparison of SPase and members of the LexA family of proteases reveals a difference in the side-chain orientation for the general base lysine, both of which are stabilized by an adjacent hydroxyl group. To gain insight into how signal peptidase recognizes its substrates, we have modeled a signal peptide into the binding site of SPase. The model is built based on the recently solved crystal structure of the analogous enzyme LexA (Luo, Y., Pfuetzner, R. A., Mosimann, S., Paetzel, M., Frey, E. A., Cherney, M., Kim, B., Little, J. W., and Strynadka, N. C. J. (2001) Cell 106, 1-10) with its bound cleavage site region.

Apoenzymes↗
PubMed2003

Three-dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homodimer.

The small multidrug resistance family of transporters is widespread in bacteria and is responsible for bacterial resistance to toxic aromatic cations by proton-linked efflux. We have determined the three-dimensional (3D) structure of the Escherichia coli multidrug transporter EmrE by electron cryomicroscopy of 2D crystals, including data to 7.0 A resolution. The structure of EmrE consists of a bundle of eight transmembrane alpha-helices with one substrate molecule bound near the centre. The substrate binding chamber is formed from six helices and is accessible both from the aqueous phase and laterally from the lipid bilayer. The most remarkable feature of the structure of EmrE is that it is an asymmetric homodimer. The possible arrangement of the two polypeptides in the EmrE dimer is discussed based on the 3D density map.

Antiporters↗
PubMed2000

Crystal structure of the bacterial protein export chaperone secB.

SecB is a bacterial molecular chaperone involved in mediating translocation of newly synthesized polypeptides across the cytoplasmic membrane of bacteria. The crystal structure of SecB from Haemophilus influenzae shows that the molecule is a tetramer organized as a dimer of dimers. Two long channels run along the side of the molecule. These are bounded by flexible loops and lined with conserved hydrophobic amino acids, which define a suitable environment for binding non-native polypeptides. The structure also reveals an acidic region on the top surface of the molecule, several residues of which have been implicated in binding to SecA, its downstream target.

Adenosine Triphosphatases↗
PubMed2005

Effects of long-term benzene pollution on bacterial diversity and community structure in groundwater.

In this study we analysed the relationship between bacterial community structures and geochemistry of groundwater in a sandstone aquifer (SIReN site) impacted mainly by BTEX hydrocarbons (benzene, toluene, ethylbenzene and xylenes), of which benzene is most abundant. The long-term presence of benzene reduced bacterial diversity: in groundwaters contaminated with more than 1.8 x 10(4) microg l(-1) of benzene, bacterial diversity was half of that in clean groundwaters. Terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rDNA revealed that the community structures were very similar in uncontaminated groundwaters, whereas communities subjected to long-term benzene contamination were different, not only from uncontaminated groundwater communities, but also from each other. Canonical correspondence analysis of the community profiles and the geochemical data showed that this divergence in community structure was not primarily caused by the direct toxic or stressful effects of benzene, but by the environmental changes brought about by benzene metabolism, in particular a decrease in redox potential.

Bacteria↗
PubMed2005

Bacterial chromosome segregation: structure and DNA binding of the Soj dimer--a conserved biological switch.

Soj and Spo0J of the Gram-negative hyperthermophile Thermus thermophilus belong to the conserved ParAB family of bacterial proteins implicated in plasmid and chromosome partitioning. Spo0J binds to DNA near the replication origin and localises at the poles following initiation of replication. Soj oscillates in the nucleoid region in an ATP- and Spo0J-dependent fashion. Here, we show that Soj undergoes ATP-dependent dimerisation in solution and forms nucleoprotein filaments with DNA. Crystal structures of Soj in three nucleotide states demonstrate that the empty and ADP-bound states are monomeric, while a hydrolysis-deficient mutant, D44A, is capable of forming a nucleotide 'sandwich' dimer. Soj ATPase activity is stimulated by Spo0J or the N-terminal 20 amino-acid peptide of Spo0J. Our analysis shows that dimerisation and activation involving a peptide containing a Lys/Arg is conserved for Soj, ParA and MinD and their modulators Spo0J, ParB and MinE, respectively. By homology to the nitrogenase iron protein and the GTPases Ffh/FtsY, we suggest that Soj dimerisation and regulation represent a conserved biological switch.

Adenosine Triphosphate↗
PubMed2000

Structural differences of bacterial and mammalian K+ channels.

Using a peptide toxin, kaliotoxin (KTX), we gained new insight into the topology of the pore region of a voltage-gated potassium channel, mKv1.1. In order to find new interactions between mKv1.1 and KTX, we investigated the pH dependence of KTX block which was stronger at pH(o) 6.2 compared with pH(o) 7.4. Using site-directed mutagenesis on the channel and the toxin, we found that protonation of His(34) in KTX caused the pH(o) dependence of KTX block. Glu(350) and Glu(353) in mKv1.1, which interact with His(34) in KTX, were calculated to be 4 and 7 A away from His(34)/KTX, respectively. Docking of KTX into a homology model of mKv1.1 based on the KcsA crystal structure using this and other known interactions as constraints showed structural differences between mKv1.1 and KcsA within the turret (amino acids 348-357). To satisfy our data, we would have to modify the KcsA crystal structure for the mKv1.1 channel orienting Glu(350) 7 A and Glu(353) 4 A more toward the center of the pore compared with KcsA. This would place Glu(350) 15 A and Glu(353) 11 A away from the center of the pore instead of the distances for the equivalent KcsA residues with 22 A for Gly(53) and 15 A for Gly(56), respectively. Bacterial and mammalian potassium channels may have structural differences regarding the turret of the outer pore vestibule. This topological difference between both channel types may have substantial influence on structure-guided development of new drugs for mammalian potassium channels by rational drug design.

Amino Acid Sequence↗
PubMed1999

Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution.

The 30S ribosomal subunit binds messenger RNA and the anticodon stem-loop of transfer RNA during protein synthesis. A crystallographic analysis of the structure of the subunit from the bacterium Thermus thermophilus is presented. At a resolution of 5.5 A, the phosphate backbone of the ribosomal RNA is visible, as are the alpha-helices of the ribosomal proteins, enabling double-helical regions of RNA to be identified throughout the subunit, all seven of the small-subunit proteins of known crystal structure to be positioned in the electron density map, and the fold of the entire central domain of the small-subunit ribosomal RNA to be determined.

Bacterial Proteins↗
PubMed1998

Crystal structure of a bacterial signal peptidase in complex with a beta-lactam inhibitor.

The signal peptidase (SPase) from Escherichia coli is a membrane-bound endopeptidase with two amino-terminal transmembrane segments and a carboxy-terminal catalytic region which resides in the periplasmic space. SPase functions to release proteins that have been translocated into the inner membrane from the cell interior, by cleaving off their signal peptides. We report here the X-ray crystal structure of a catalytically active soluble fragment of E. coli SPase (SPase delta2-75). We have determined this structure at 1.9 A resolution in a complex with an inhibitor, a beta-lactam (5S,6S penem), which is covalently bound as an acyl-enzyme intermediate to the gamma-oxygen of a serine residue at position 90, demonstrating that this residue acts as the nucleophile in the hydrolytic mechanism of signal-peptide cleavage. The structure is consistent with the use by SPase of Lys 145 as a general base in the activation of the nucleophilic Ser90, explains the specificity requirement at the signal-peptide cleavage site, and reveals a large exposed hydrophobic surface which could be a site for an intimate association with the membrane. As enzymes that are essential for cell viability, bacterial SPases present a feasible antibacterial target: our determination of the SPase structure therefore provides a template for the rational design of antibiotic compounds.

Bacterial Proteins↗
PubMed1999

Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases.

Bacteria produce and secrete lipases, which can catalyze both the hydrolysis and the synthesis of long-chain acylglycerols. These reactions usually proceed with high regioselectivity and enantioselectivity, and, therefore, lipases have become very important stereoselective biocatalysts used in organic chemistry. High-level production of these biocatalysts requires the understanding of the mechanisms underlying gene expression, folding, and secretion. Transcription of lipase genes may be regulated by quorum sensing and two-component systems; secretion can proceed either via the Sec-dependent general secretory pathway or via ABC transporters. In addition, some lipases need folding catalysts such as the lipase-specific foldases and disulfide-bond-forming proteins to achieve a secretion-competent conformation. Three-dimensional structures of bacterial lipases were solved to understand the catalytic mechanism of lipase reactions. Structural characteristics include an alpha/beta hydrolase fold, a catalytic triad consisting of a nucleophilic serine located in a highly conserved Gly-X-Ser-X-Gly pentapeptide, and an aspartate or glutamate residue that is hydrogen bonded to a histidine. Four substrate binding pockets were identified for triglycerides: an oxyanion hole and three pockets accommodating the fatty acids bound at position sn-1, sn-2, and sn-3. The differences in size and the hydrophilicity/hydrophobicity of these pockets determine the enantiopreference of a lipase. The understanding of structure-function relationships will enable researchers to tailor new lipases for biotechnological applications. At the same time, directed evolution in combination with appropriate screening systems will be used extensively as a novel approach to develop lipases with high stability and enantioselectivity.

Bacteria↗
PubMedDate not supplied

Ampicillin/sulbactam versus cefazolin or cefoxitin in the treatment of skin and skin-structure infections of bacterial etiology.

This randomized, double-blind study compared 1 g of ampicillin plus 0.5 g of sulbactam with 0.5 g of cefazolin in the treatment of cellulitis and with 1 g of cefoxitin in other skin and skin-structure infections. Study drugs were administered intravenously every 6 hours to 58 hospitalized patients. Each indication was evaluated separately. In cellulitis, ampicillin/sulbactam and cefazolin produced clinical cure or improvement in 100% and 91.7% of patients, respectively; duration of hospitalization was 7.7 and 7.2 days. In other skin and skin-structure infections, results for ampicillin/sulbactam and cefoxitin, respectively, were clinical cure or improvement, 80% and 64.7%; treatment failures, 0% and 11.8%; bacterial eradication, 40% and 53%; and duration of hospitalization, 7.7 and 9.4 days. No unusual or unexpected adverse experiences related to any study drug occurred. One patient treated with ampicillin/sulbactam died of a pulmonary embolism, and 1 patient treated with cefoxitin was discontinued from the study following amputation of an infected foot. These events were not considered drug-related. The treatment groups showed no statistically significant differences in efficacy or safety.

Adolescent↗