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PubMed2006

Structure/function relationships in serotonin transporter: new insights from the structure of a bacterial transporter.

Serotonin transporter (SERT) serves the important function of taking up serotonin (5-HT) released during serotonergic neurotransmission. It is the target for important therapeutic drugs and psychostimulants. SERT catalyzes the influx of 5-HT together with Na+ and Cl- in a 1:1:1 stoichiometry. In the same catalytic cycle, there is coupled efflux of one K+ ion. SERT is one member of a large family of amino acid and amine transporters that is believed to utilize similar mechanisms of transport. A bacterial member of this family was recently crystallized, revealing the structural basis of these transporters. In light of the new structure, previous results with SERT have been re-interpreted, providing new insight into the substrate binding site, the permeation pathway, and the conformational changes that occur during the transport cycle.

Amino Acid Sequence↗
PubMed1996

Crystal structure of a bacterial lipase from Chromobacterium viscosum ATCC 6918 refined at 1.6 angstroms resolution.

The crystal structure of a lipase from the bacterium Chromobacterium viscosum ATCC 6918 (CVL) has been determined by isomorphous replacement and refined at 1.6 angstroms resolution to an R-factor of 17.8%. The lipase has the overall topology of an alpha/beta type protein, which was also found for previously determined lipase structures. The catalytic triad of the active center consists of the residues Ser87, Asp263 and His285. These residues are not exposed to the solvent, but a narrow channel connects them with the molecular surface. This conformation is very similar to the previously reported closed conformation of Pseudomonas glumae lipase (PGL), but superposition of the two lipase structures reveals several conformational differences. r.m.s. deviations greater than 2 angstroms are found for the C alpha-atoms of the polypeptide chains from His15 to Asp28, from Leu49 to Ser54 and from Lys128 to Gln158. Compared to the PGL structure in the CVL structure, three alpha-helical fragments are shorter, one beta-strand is longer and an additional antiparallel beta-sheet is found. In contrast to PGL, CVL displays an oxyanion hole, which is stabilized by the amide nitrogen atoms of Leu17 and Gln88, and a cis-peptide bond between Gln291 and Leu292. CVL contains a Ca2+, like the PGL, which is coordinated by four oxygen atoms from the protein and two water molecules.

Amino Acid Sequence↗
PubMed1980

Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence.

We have derived a secondary structure model for 16S ribosomal RNA on the basis of comparative sequence analysis, chemical modification studies and nuclease susceptibility data. Nucleotide sequences of the E. coli and B. brevis 16S rRNA chains, and of RNAse T1 oligomer catalogs from 16S rRNAs of over 100 species of eubacteria were used for phylogenetic comparison. Chemical modification of G by glyoxal, A by m-chloroperbenzoic acid and C by bisulfite in naked 16S rRNA, and G by kethoxal in active and inactive 30S ribosomal subunits was taken as an indication of single stranded structure. Further support for the structure was obtained from susceptibility to RNases A and T1. These three approaches are in excellent agreement. The structure contains fifty helical elements organized into four major domains, in which 46 percent of the nucleotides of 16S rRNA are involved in base pairing. Phylogenetic comparison shows that highly conserved sequences are found principally in unpaired regions of the molecule. No knots are created by the structure.

Bacillus↗
PubMedDate not supplied

[Possible determination of the structural organization of bacterial and animal rhodopsins by the hydrophobicity of amino acid residues].

From a comparative analysis of the distribution of hydrophobicity in bacterial and animal (bovine) rhodopsins, the following peculiarities in the structure of these proteins have been assumed: 1) each of these proteins has 5 hydrophobic regions of equal length (20-28 residues) able to be arranged across the membrane and one region of doubled length. 2) The alpha-helix of the doubled-length regions (residues N 178-225 for bacterial rhodopsin and N 75-132 for the animal one) is characterized by pronounced amphipaticity and is capable of a retinal dependent movement in the membrane. The model of animal rhodopsin was suggested to have 13 phenylalanine residues forming a chain which "connects" 6 transmembrane segments and runs from one surface of the membrane to the opposite one.

Amino Acid Sequence↗
PubMed2004

Electronic structure of regular bacterial surface layers.

We report photoemission and near-edge x-ray absorption fine structure measurements of the occupied and unoccupied valence electronic states of the regular surface layer of Bacillus sphaericus, which is widely used as the protein template for the fabrication of metallic nanostructures. The two-dimensional protein crystal shows a semiconductorlike behavior with a gap value of approximately 3.0 eV and the Fermi energy close to the bottom of the lowest unoccupied molecular orbital. We anticipate that these results will open up new possibilities for the electric addressability of biotemplated low-dimensional hybrid structures.

Bacillus↗
PubMed2026

Species-specific structuring of gut bacterial and fungal communities in honey bees Apis cerana and Apis mellifera.

Honey bee gut microbiome studies have primarily emphasized bacteria, leaving fungal communities comparatively overlooked despite their ecological and functional importance. Whole-genome shotgun metagenomics of Apis cerana and Apis mellifera revealed fungal assemblages dominated by Ascomycota, with Basidiomycota and Microsporidia in minor proportions, alongside gut bacterial communities composed mainly of Pseudomonadota, Bacillota, and Actinomycetota. The bacterial diversity was markedly higher in A. mellifera (Shannon = 5.90; Simpson = 0.98) than in A. cerana (Shannon = 4.01; Simpson = 0.94; p > 0.05), while fungal diversity remained comparable between species (p > 0.05). Beta-diversity analyses revealed strong host-specific clustering for both bacterial (PERMANOVA R2 = 0.7989, p > 0.05) and fungal communities (R2 = 0.7218, p > 0.05), indicating distinct microbial organization driven by host species. Bacterial-fungal co-occurrence patterns exhibited host-specific structuring, suggesting differential inter-kingdom community organization between A. cerana and A. mellifera. Linear Discriminant Analysis Effect Size (LEfSe) identified 93 discriminatory fungal taxa (45 enriched in A. cerana, 48 in A. mellifera), highlighting yeast-dominated signatures in A. mellifera and Basidiomycota-affiliated enrichments in A. cerana. KEGG and CAZy profiling revealed host- and kingdom-specific functional differences, with bacterial communities of A. mellifera showing distinct representation of carbohydrate metabolism and nutrient-cycling functions, while fungal communities exhibited a comparatively narrower functional repertoire. Together, these findings provide a high-resolution view of honey bee bacterial and fungal microbiomes, highlighting strong host-driven divergence in taxonomy, function, and cross-kingdom interactions.

Animals↗
PubMed1999

The bacterial K+ channel structure and its implications for neuronal channels.

Voltage-gated K+ (Kv) channels play a central role in generating action potentials and rhythmic patterns, as well as in dendritic signal processing in neurons. Recently, the first structure of a member of the K+ channel family was solved. Although this channel is from bacteria and has a streamlined body plan with no voltage gating, it establishes the architecture of the functional core of the voltage-gated (K+) channels and their relatives. This architecture explains the crucial features of ion permeation and blockade, and gives some strong hints about gating. The bacterial K+ channel structure is the central piece in a puzzle; it remains to be seen how it will fit together with other domains of the Kv channels, with auxiliary subunits, and with other signal transduction molecules.

Bacterial Proteins↗
PubMed1994

Bacterial lipopolysaccharide has structural similarity to ceramide and stimulates ceramide-activated protein kinase in myeloid cells.

Bacterial lipopolysaccharide (LPS), tumor necrosis factor (TNF)-alpha and interleukin-1 beta (IL-1 beta) stimulate similar cellular responses. TNF-alpha and IL-1 beta are known to initiate signaling through a pathway involving hydrolysis of sphingomyelin to ceramide (Kolesnick, R. N., and Golde, D. W. (1994) Cell 77, 325-328). In this system, ceramide acts as a second messenger stimulating a ceramide-activated serine/threonine protein kinase. The present studies demonstrate that LPS, like TNF and IL-1, stimulates ceramide-activated protein kinase activity in human leukemia (HL-60) cells and in freshly isolated human neutrophils. Lipid A, the biologically active core of LPS, enhanced kinase activity in a time- and concentration-dependent manner. As little as 10 nM lipid A was effective, and a maximal effect occurred with 500 nM lipid A, increasing kinase activity 5-fold. Native LPS similarly induced kinase activation. This effect of LPS was markedly enhanced by LPS binding protein and required the LPS receptor CD14. In contrast to TNF and IL-1, LPS did not cause sphingomyelin hydrolysis and thus stimulates ceramide-activated protein kinase without generating ceramide. Molecular modeling showed strong structural similarity between ceramide and a region of lipid A. Based on these observations, we propose that LPS stimulates cells by mimicking the second messenger function of ceramide.

Amino Acid Sequence↗
PubMed2006

Structural polymorphism in bacterial EspA filaments revealed by cryo-EM and an improved approach to helical reconstruction.

The traditional Fourier-Bessel approach to three-dimensional reconstruction from electron microscopic (EM) images of helical polymers involves averaging over filaments, assuming a homogeneous structure and symmetry. We have used a real-space reconstruction approach to study the EspA filaments formed by enteropathogenic E. coli. In negative stain, the symmetry of these filaments is ambiguous, and we suggest that such ambiguities may be more prevalent than realized. Using cryo-EM of frozen-hydrated filaments, we find that these filaments have a fixed twist with 5.6 subunits per turn but an axial rise per subunit that varies from about 3.6 A to 5.6 A. Reconstructions at approximately 15 A resolution show a switching between the more compressed and extended filaments in the packing of putative alpha helices around the hollow lumen. Outside of a crystal, where there is nothing to maintain long-range order, the structural polymorphism in helical polymers may be much greater than has been assumed.

Cryoelectron Microscopy↗
PubMedDate not supplied

[The role of the structural components of bacterial lipopolysaccharide in its inductive immunosuppressive activity].

The inductive immunosuppressive activity of lipopolysaccharides (LPS) and structural parts (O-chains,cor,lipid A) obtained from bacteria of the genus Shigella and Escherichia coli was studied. LPS preparations were extracted by phenol-water method. Its structural components were obtained by the acetic acid hydrolysis and gel filtration. It has been shown that all these preparations did not change the level of delayed type hypersensitivity (DTH) to test-antigen in mice in the case of intraperitoneal injection. They did not also induce immunosuppressive activity in avirulent bacterial strains. After the redox treatment all LPS preparations acquired the ability to induce immunosuppressive property in avirulent bacteria. As a result of redox treatment the immunosuppressive activity appeared in lipid A preparations. O-chains and cor preparations were not active. Immunosuppressive activity was lost after treatment with phenol. It is supposed that active chemical groups are located in lipid A.

Animals↗
PubMed1995

Observation of the helical structure of the bacterial polysaccharide acetan by atomic force microscopy.

A method has been developed that has been found to give reproducible images of uncoated polysaccharides by Atomic Force Microscopy (AFM). Aqueous solutions of the polysaccharide are deposited as drops onto freshly cleaved mica surfaces, air dried, and then imaged under butanol. The method has been used to obtain images of the bacterial polysaccharide acetan. In regions within the deposited sample, where the molecules are aligned side-by-side, it has been possible to observe a periodic structure along the polysaccharide chain, attributable to the helical structure of acetan.

Acetobacter↗
PubMed2001

Analysis of the role of bacterial endospore cortex structure in resistance properties and demonstration of its conservation amongst species.

AIMS: The aim of this work was to compare the chemical structure of the spore cortex of a range of species, and to determine any correlation between cortex structure and spore resistance properties. METHODS AND RESULTS: The fine chemical structure of the cortex of Bacillus subtilis, Bacillus megaterium, Bacillus cereus and Clostridium botulinum was examined by muropeptide analysis using reverse phase HPLC. There is a conserved basic structure between peptidoglycan of these species, with the only difference being the level of de-N-acetylation of an amino sugar. In order to determine if an alteration in cortex structure correlates with heat resistance properties, the peptidoglycan structure and properties of B. subtilis spores prepared under different conditions were compared. Peptidoglycan from spores prepared in Nutrient Broth (NB) showed reduction in single L-alanine substituted muramic acid to only 13.9% compared with 20.6% in CCY-grown spores. NB-prepared spores are also unstable, with 161-fold less heat resistance (60 min, 85 degrees C) and 43 times less Mn(2+) content than CCY-grown spores. Addition of MnCl(2) to NB led to a peptidoglycan profile similar to CCY-grown spores, sevenfold more heat resistance (60 min, 85 degrees C) and an 86-fold increase in Mn(2+) content. Addition of CCY salts to NB led all parameters to be comparable with CCY-grown spore levels. CONCLUSION: It has been shown that peptidoglycan structure is conserved in four spore-forming bacteria. Also, spore heat resistance is multifactorial and cannot be accounted for by any single parameter. SIGNIFICANCE AND IMPACT OF THE STUDY: Endospores made by diverse species most likely have common mechanisms of heat resistance. However, the molecular basis for their resistance remains elusive.

Amino Acids↗
PubMed2006

Structural classification of bacterial response regulators: diversity of output domains and domain combinations.

CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. In this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. Previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. Transcriptional regulators of the OmpR, NarL, and NtrC families were found to comprise almost 60% of all response regulators; transcriptional regulators with other DNA-binding domains (LytTR, AraC, Spo0A, Fis, YcbB, RpoE, and MerR) account for an additional 6%. The remaining one-third is represented by the stand-alone REC domain (approximately 14%) and its combinations with a variety of enzymatic (GGDEF, EAL, HD-GYP, CheB, CheC, PP2C, and HisK), RNA-binding (ANTAR and CsrA), protein- or ligand-binding (PAS, GAF, TPR, CAP_ED, and HPt) domains, or newly described domains of unknown function. The diversity of domain architectures and the abundance of alternative domain combinations suggest that fusions between the REC domain and various output domains is a widespread evolutionary mechanism that allows bacterial cells to regulate transcription, enzyme activity, and/or protein-protein interactions in response to environmental challenges. The complete list of response regulators encoded in each of the 200 analyzed genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html.

Amino Acid Sequence↗
PubMed2004

Crystal structure of the bacterial nucleoside transporter Tsx.

Tsx is a nucleoside-specific outer membrane (OM) transporter of Gram-negative bacteria. We present crystal structures of Escherichia coli Tsx in the absence and presence of nucleosides. These structures provide a mechanism for nucleoside transport across the bacterial OM. Tsx forms a monomeric, 12-stranded beta-barrel with a long and narrow channel spanning the outer membrane. The channel, which is shaped like a keyhole, contains several distinct nucleoside-binding sites, two of which are well defined. The base moiety of the nucleoside is located in the narrow part of the keyhole, while the sugar occupies the wider opening. Pairs of aromatic residues and flanking ionizable residues are involved in nucleoside binding. Nucleoside transport presumably occurs by diffusion from one binding site to the next.

Amino Acid Sequence↗
PubMed2005

Crystal structure of a bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA.

Type IB DNA topoisomerases are found in all eukarya, two families of eukaryotic viruses (poxviruses and mimivirus), and many genera of bacteria. They alter DNA topology by cleaving and resealing one strand of duplex DNA via a covalent DNA-(3-phosphotyrosyl)-enzyme intermediate. Bacterial type IB enzymes were discovered recently and are described as poxvirus-like with respect to their small size, primary structures, and bipartite domain organization. Here we report the 1.75-A crystal structure of Deinococcus radiodurans topoisomerase IB (DraTopIB), a prototype of the bacterial clade. DraTopIB consists of an amino-terminal (N) beta-sheet domain (amino acids 1-90) and a predominantly alpha-helical carboxyl-terminal (C) domain (amino acids 91-346) that closely resemble the corresponding domains of vaccinia virus topoisomerase IB. The five amino acids of DraTopIB that comprise the catalytic pentad (Arg-137, Lys-174, Arg-239, Asn-280, and Tyr-289) are preassembled into the active site in the absence of DNA in a manner nearly identical to the pentad configuration in human topoisomerase I bound to DNA. This contrasts with the apoenzyme of vaccinia topoisomerase, in which three of the active site constituents are either displaced or disordered. The N and C domains of DraTopIB are splayed apart in an "open" conformation, in which the surface of the catalytic domain containing the active site is exposed for DNA binding. A comparison with the human topoisomerase I-DNA cocrystal structure suggests how viral and bacterial topoisomerase IB enzymes might bind DNA circumferentially via movement of the N domain into the major groove and clamping of a disordered loop of the C domain around the helix.

Amino Acid Sequence↗
PubMedDate not supplied

Regulation of translation termination: conserved structural motifs in bacterial and eukaryotic polypeptide release factors.

Translation termination requires codon-dependent polypeptide release factors. The mechanism of stop codon recognition by release factors is unknown and holds considerable interest since it entails protein-RNA recognition rather than the well-understood mRNA-tRNA interaction in codon-anticodon pairing. Bacteria have two codon-specific release factors and our picture of prokaryotic translation is changing because a third factor, which stimulates the other two, has now been found. Moreover, a highly conserved eukaryotic protein family possessing properties of polypeptide release factor has now been sought. This review summarizes our current understanding of the structural and functional organization of release factors as well as our recent findings of highly conserved structural motifs in bacterial and eukaryotic polypeptide release factors.

Amino Acid Sequence↗