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PubMedDate not supplied

Structure and properties of a bacterial polysaccharide from a Klebsiella strain (ATCC 12657).

The chemical structure and the rheological behavior of the Klebsiella polysaccharide ATCC 12657 was studied and compared with data described in the literature and obtained for similar polysaccharides. The acetylated polysaccharide presents in solution a normal viscoelastic behavior with no evidence of an ordered conformation whatever the experimental conditions are. The deacetylated form can induce the formation of physical gels, in the presence of salt excess or ethanol. Microcalorimetry, optical rotation, and rheology experiments demonstrate that a thermally reversible and highly cooperative conformational transition occurs at the same temperature than a sol-gel transition. The melting of the gel and the conformational transition temperatures are dependent on the nature of cations and ionic concentration, whereas the gel strength is only influenced by polymer concentration.

Carbohydrate Conformation↗
PubMed2005

The structural comparison of the bacterial PepX and human DPP-IV reveals sites for the design of inhibitors of PepX activity.

X-prolyl dipeptidyl aminopeptidases (X-PDAP) are enzymes catalysing the release of dipeptides from the amino termini of polypeptides containing a proline or an alanine at the penultimate position. Involved in various mammalian regulation processes, as well as in chronic human diseases, they have been proposed to play a role in pathogenicity for Streptococci. We compared the structure of X-PDAP from Lactococcus lactis (PepX) with its human counterpart DPP-IV. Despite very different overall folds, the residues most implicated for X-PDAP activity are conserved in the same positions and orientations in both enzymes, thus defining a structural signature for the X-PDAP specificity that crosses the species frontiers of evolution. Starting from this observation, we tested some inhibitors of DPP-IV on PepX activity, for which no specific inhibitor is known. We thus found that PepX was highly sensitive to valine-pyrrolidide with a KI of 9.3 microm, close to that reported in DPP-IV inhibition. We finally used the structure of PepX from L. lactis as a template for computer-based homology modeling of PepX from the pathogenic Streptococcus gordonii. Docking simulations of valine-pyrrolidide into the active site of PepX led to the identification of key residues for a rational drug design against PepX from Streptococci. These results could have applications in human health giving new perspectives to the struggle against pathogens.

Adenosine Deaminase↗
PubMed2005

Molecular characterization of fungal community dynamics in the initial stages of composting.

Composting relies on a complex network of bacteria and fungi to process crude organic material. Although it is known that these organisms drive dynamic changes in temperature and pH, little is known about the temporal dynamics of fungal populations during the rise to thermophilic conditions. This study employed F-ARISA (fungal-automated rRNA intergenic spacer analysis) and 18S rRNA gene cloning and sequencing to examine changes in community structure during this period. Sequencing of the 18S rRNA portion of cloned F-ARISA products revealed the presence of four distinct fungal genera including Backusella sp., Mucoraceae, Geotrichum sp. and the yeast Pichia sp. Based on the presence and absence of these ARISA operational taxonomic units (A-OTUs), we observed a shift in fungal community structure between 48 and 60 h. This change in community structure preceded a rise in pH and coincided with an increase in temperature. Clone libraries constructed using fungi-specific 18S rRNA primers contained sequences similar to several other fungal genera including Penicillium sp., Aspergillus sp., Hamigera sp., Neurospora sp. and the yeast Candida sp. While the fungal species richness was relatively low at any time point, the community structure was dynamic and paralleled changes in bacterial community structure.

Fungi↗
PubMed2004

Microbiology, chemistry and biofilm development in a pilot drinking water distribution system with copper and plastic pipes.

We studied the changes in water quality and formation of biofilms occurring in a pilot-scale water distribution system with two generally used pipe materials: copper and plastic (polyethylene, PE). The formation of biofilms with time was analysed as the number of total bacteria, heterotrophic plate counts and the concentration of ATP in biofilms. At the end of the experiment (after 308 days), microbial community structure, viable biomass and gram-negative bacterial biomass were analysed via lipid biomarkers (phospholipid fatty acids and lipopolysaccharide 3-hydroxy fatty acids), and the numbers of virus-like particles and total bacteria were enumerated by SYBR Green I staining. The formation of biofilm was slower in copper pipes than in the PE pipes, but after 200 days there was no difference in microbial numbers between the pipe materials. Copper ion led to lower microbial numbers in water during the first 200 days, but thereafter there were no differences between the two pipe materials. The number of virus-like particles was lower in biofilms and in outlet water from the copper pipes than PE pipes. Pipe material influenced also the microbial and gram-negative bacterial community structure in biofilms and water.

Biofilms↗
PubMed1982

Sugar transport by the bacterial phosphotransferase system. Primary structure and active site of a general phosphocarrier protein (HPr) from Salmonella typhimurium.

The general histidine-containing phosphocarrier protein (HPr) of the Salmonella phosphotransferase system is required for the phosphorylation of all sugar substrates by this system. The complete amino acid sequence of HPr, consisting of 84 amino acid residues, has been established. The sequence was determined by cleaving the protein with cyanogen bromide, trypsin, and with a protease from Staphylococcus aureus, followed by isolation and amino acid sequence determination of the resulting peptides. The Salmonella typhimurium protein contains two histidine residues, at positions 15 and 75, respectively. The phosphoryl group in phospho-HPr was linked to the His-15 residue. Based on several lines of evidence, the HPr protein from Escherichia coli appears to be identical with the protein from S. typhimurium. The HPr protein from S. aureus has also been isolated in this laboratory and was shown to differ from the HPr proteins described above both with respect to amino acid composition and the inability of the S. aureus and E. coli HPR proteins to substitute for each other in the in vitro sugar phosphorylation assays. The complete amino acid sequence of S. aureus HPr has been reported (Beyreuther, K., Raufuss, H., Schrecker, O., and Hengstenberg, W. (1977) Eur. J. Biochem. 75, 275-286), and its secondary structure has been predicted; this protein contains 70 amino acid residues and only one histidine. In the present studies, three methods were used to predict the secondary structure of S. typhimurium HPr, the results were combined, and a secondary structure for the protein is proposed. Although the amino acid compositions and sequences of the S. typhimurium and S. aureus HPr proteins are quite different, 13 residues are identical in the sequence of the two proteins, and most of these are located near the active site histidine residue. In addition, the predicted secondary structures of the two proteins are quite similar; the additional 14 residues in S. typhimurium, located at the carboxyl terminal end, are predicted to form an alpha-helix.

Amino Acid Sequence↗
PubMed2001

Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment.

Soil structure depends on the association between mineral soil particles (sand, silt, and clay) and organic matter, in which aggregates of different size and stability are formed. Although the chemistry of organic materials, total microbial biomass, and different enzyme activities in different soil particle size fractions have been well studied, little information is available on the structure of microbial populations in microhabitats. In this study, topsoil samples of different fertilizer treatments of a long-term field experiment were analyzed. Size fractions of 200 to 63 microm (fine sand fraction), 63 to 2 microm (silt fraction), and 2 to 0.1 microm (clay fraction) were obtained by a combination of low-energy sonication, wet sieving, and repeated centrifugation. Terminal restriction fragment length polymorphism analysis and cloning and sequencing of 16S rRNA genes were used to compare bacterial community structures in different particle size fractions. The microbial community structure was significantly affected by particle size, yielding higher diversity of microbes in small size fractions than in coarse size fractions. The higher biomass previously found in silt and clay fractions could be attributed to higher diversity rather than to better colonization of particular species. Low nutrient availability, protozoan grazing, and competition with fungal organisms may have been responsible for reduced diversities in larger size fractions. Furthermore, larger particle sizes were dominated by alpha-Proteobacteria, whereas high abundance and diversity of bacteria belonging to the Holophaga/Acidobacterium division were found in smaller size fractions. Although very contrasting organic amendments (green manure, animal manure, sewage sludge, and peat) were examined, our results demonstrated that the bacterial community structure was affected to a greater extent by the particle size fraction than by the kind of fertilizer applied. Therefore, our results demonstrate specific microbe-particle associations that are affected to only a small extent by external factors.

Bacteria↗
PubMed1975

Relation of structure to function in bacterial endotoxins. VIII. Biological activities in a polysaccharide-rich fraction.

This is the first report describing in vivo biologic activities elicited by a non-toxic, polysaccharide-rich, water soluble fraction obtained by partial acidic hydrolysis from endotoxic lipopolysaccharide. The two activities present in this preparation were a) mouse bone marrow cell colony formation stimulation (CSF) and b) protection of mice against lethal irradiation. With polysaccharide-deficient rough mutants of salmonella minnesota, the CSF-inducing activity could be restricted to the "core" region of the LPS structure. Sixty-minute hydrolysis with 1 N HCl at 100 degrees C or 0.1 M sodium metaperiodate oxidation at cold room temperature completely abolished CSF-inducing activity of the preparation, whereas it showed considerable resistance to mild alkaline hydrolysis. These findings indicate that the active component in this preparation is carbohydrate in nature. Lipid preparations from smooth LPS or from Re rough mutants are either much less active or completely inactive in the above two assays. The fully active polysaccharide rich preparation was found to be inert in seven other characteristic endotoxicity parameters.

Adjuvants, Immunologic↗
PubMed2006

Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices.

Changes in the diversity and structure of soil microbial communities may offer a key to understanding the impact of environmental factors on soil quality in agriculturally managed systems. Twenty-five years of biodynamic, bio-organic, or conventional management in the DOK long-term experiment in Switzerland significantly altered soil bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, the relation between bacterial diversity and bacterial community structures and their discrimination potential were investigated by sequence and T-RFLP analyses of 1,904 bacterial 16S rRNA gene clones derived from the DOK soils. Standard anonymous diversity indices such as Shannon, Chao1, and ACE or rarefaction analysis did not allow detection of management-dependent influences on the soil bacterial community. Bacterial community structures determined by sequence and T-RFLP analyses of the three gene libraries substantiated changes previously observed by soil bacterial community level T-RFLP profiling. This supported the value of high-throughput monitoring tools such as T-RFLP analysis for assessment of differences in soil microbial communities. The gene library approach also allowed identification of potential management-specific indicator taxa, which were derived from nine different bacterial phyla. These results clearly demonstrate the advantages of community structure analyses over those based on anonymous diversity indices when analyzing complex soil microbial communities.

Agriculture↗
PubMed2002

Short-term changes in bacterial community fingerprints and potential activities in an alfisol supplemented with solid waste leachates.

We investigated the effect on soil functioning of adding leachates from municipal solid waste incinerator (MSWI) ashes to laboratory columns (bare soil) and to field experimental plots (bare soil or grass cover). Leachate of MSWI-solidified air pollution control residues (SAPCr) contained more salts but less heavy metals than did MSWI-bottom ash (BA) leachate. Leachate-supplemented soils (BA soil, SAPCr soil) and control (water added) soil (W) were analyzed after 30 days. Potential denitrifying activity (PDA) and potential N2 fixation (acetylene reduction assay, ARA) were measured in controlled conditions. PDA was significantly lower in SAPCr soil than in W soil, both in the laboratory (-45%) and in bare soil in the field (-31%). ARA values were lower in bare SAPCr soil (-54%) and in bare BA (-25%) soil. Both activities remained unaffected by leachate supplementation in soil under permanent grass cover. Automated ribosomal intergenic spacer analysis (A-RISA) fingerprints and RFLP of nifH gene pools were used to assess changes in the structure of bacterial community. Multivariate analysis of these fingerprints revealed that SAPCr leachate had a stronger effect than BA leachate on the total and N2-fixing bacterial communities. Similar results were obtained for laboratory and bare soil field plots, but leachates did not affect nifH gene pools from soil under permanent grass cover. The stronger impact of SAPCr leachate on both structure of bacterial communities and activities supports the conclusion that observed effects would result from the abundance of salts rather than from heavy metal toxicity.

Bacteria↗
PubMed1998

NADP-dependent bacterial alcohol dehydrogenases: crystal structure, cofactor-binding and cofactor specificity of the ADHs of Clostridium beijerinckii and Thermoanaerobacter brockii.

We have determined the X-ray structures of the NADP(H)-dependent alcohol dehydrogenase of Clostridiim beijerinckii (CBADH) in the apo and holo-enzyme forms at 2.15 A and 2.05 A resolution, respectively, and of the holo-alcohol dehydrogenase of Thermoanaerobacter brockii (TBADH) at 2.5 A. These are the first structures of prokaryotic alcohol dehydrogenase to be determined as well as that of the first NADP(H)-dependent alcohol dehydrogenase. CBADH and TBADH 75% have sequence identity and very similar three-dimensional structures. Both are tetramers of 222 symmetry. The monomers are composed of two domains: a cofactor-binding domain and a catalytic domain. These are separated by a deep cleft at the bottom of which a single zinc atom is bound in the catalytic site. The tetramers are composed of two dimers, each structurally homologous to the dimer of alcohol dehydrogenases of vertebrates. The dimers form tetramers by means of contacts between surfaces opposite the interdomain cleft thus leaving it accessible from the surface of the tetramer. The tetramer encloses a large internal cavity with a positive surface potential. A molecule of NADP(H) binds in the interdomain cleft to the cofactor-binding domain of each monomer. The specificity of the two bacterial alcohol dehydrogenases toward NADP(H) is determined by residues Gly198, Ser199, Arg200 and Tyr218, with the latter three making hydrogen bonds with the 2'-phosphate oxygen atoms of the cofactor. Upon NADP(H) binding to CBADH, Tyr218 undergoes a rotation of approximately 120 degrees about chi1 which facilitates stacking interactions with the adenine moiety and hydrogen bonding with one of the phosphate oxygen atoms. In apo-CBADH the catalytic zinc is tetracoordinated by side-chains of residues Cys37, His59, Asp150 and Glu60; in holo-CBADH, Glu60 is retracted from zinc in three of the four monomers whereas in holo-TBADH, Glu60 does not participate in Zn coordination. In both holo-enzymes, but not in the apo-enzyme, residues Ser39 and Ser113 are in the second coordination sphere of the catalytic zinc. The carboxyl group of Asp150 is oriented with respect to the active carbon of NADP(H) so as to form hydrogen bonds with both pro-S and pro-R hydrogen atoms.

Alcohol Oxidoreductases↗
PubMed2006

Correlating structure with function in bacterial multicomponent monooxygenases and related diiron proteins.

Bacterial multicomponent monooxygenases (BMMs) catalyze the O2-dependent hydroxylation of hydrocarbons at a carboxylate-bridged diiron center similar to those that occur in a variety of dimetallic oxygen-utilizing enzymes. BMMs have found numerous biodegradation and biocatalytic applications. Recent investigations have begun to reveal how BMMs perform their C-H bond activation chemistry and why these enzymes may be mechanistically different from other related diiron proteins. The structures of the BMM component proteins and of complexes between them provide insights into the tuning of the dinuclear iron center and the enzyme mechanism. Selected findings are compared and contrasted with the properties of other carboxylate-bridged diiron proteins, revealing common structural and functional themes.

Bacteria↗
PubMed1996

Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization.

The bacterial community structure in the winter cover and pelagic zone of a high mountain lake was analyzed by in situ hybridization with fluorescently labeled rRNA-targeted oligonucleotide probes. Cells fixed on membrane filters were hybridized with a probe specific for the domain Bacteria as well as with probes for the alpha, beta, and gamma subclasses of the class Proteobacteria and the Cytophaga-Flavobacterium group. The fraction of bacteria detectable after hybridization with the bacterial probe EUB ranged from 40 to 81% of 4(prm1),6-diamidino-2-phenylindole (DAPI) counts. The bacterial assemblage varied considerably between and within different habitats (snow, slush, and lake water) but was in most cases dominated by members of the beta subclass (6.5 to 116% of bacteria detectable with probe EUB). The sum of bacteria hybridizing with group-specific probes was usually lower than the fraction detectable with probe EUB. Image analysis was used to characterize morphology and the size-specific biomass distribution of bacterial assemblages, which clearly separated the three habitats. Although the measured secondary production parameters and the fraction of 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyltetrazolium chloride-reducing bacteria varied by more than an order of magnitude in the different slush and pelagic layers, detectability with the fluorescent probe EUB was constantly high. Physiological strategies of bacteria under nutrient limitation and at low temperatures are discussed in the context of the ribosome content of single cells. This study confirms the suitability of fluorescently labeled rRNA-targeted probes for the characterization of bacterial population structures even in oligotrophic habitats.

Journal Article↗
PubMed1984

Structural studies on the bacterial cell wall peptidoglycan pseudomurein. I. Conformational energy calculations on the glycan strands in C1 conformation and comparison with murein.

Conformational energy calculations have been used to explore the conformations which may be realized for the sugar moiety of murein and pseudomurein. For the building blocks of the pseudomurein sugar strands, i.e. for the monosaccharides beta-D-N-acetylglucosamine (NAG) and alpha-L-N-acetyltalosaminuronic acid (NAT), both in C1 ring conformation, as well as for their 1,3 and 1,4 linked disaccharides, the favoured conformations were obtained. The helical parameters of sugar strands of both linkage types, which describe the regular structure of the corresponding polysaccharides, poly-(1,3-NAT-NAG) and poly-(1,4-NAT-NAG), were calculated. Both types of polysaccharides poly-(NAG-NAT) considered in this study favoured extended conformations, which in the case of 1,3 linked polymers showed less gain of length per saccharide unit compared to 1,4 linked poly-(NAG-NAT) residues. For a 1,3 linked sugar moiety of pseudomurein every pair of neighbouring peptides attached to glycan chain pointed in favoured conformations approximately to opposite sides of the strands, whereas in a 1,4 linked poly-(NAG-NAT) the peptides protruded approximately to the same side of the glycan moiety. A comparison between pseudomurein and murein revealed that the sugar moieties of both peptidoglycans have similar features in respect to their overall structure, i.e. both favoured more or less extended structures. In contrast to these data the shapes of the resulting polysaccharide moieties were remarkably different. In poly-(1,3-NAG-NAT) the glycan chains possessed a zig-zag-like arrangement, whereas for glycan chains of the murein type relatively flat structures were preferred. These remaining differences in the conformational arrangement between both peptidoglycans depend strongly on the C1 chair conformation of NAT. It is, therefore, attractive to speculate about an hypothetical pseudomurein sugar chain configuration comprising beta-L-N-acetyltalosaminuronic acid in its 1C conformation.

Acetylglucosamine↗
PubMed1999

Phylogenetic Composition, Spatial Structure, and Dynamics of Lotic Bacterial Biofilms Investigated by Fluorescent in Situ Hybridization and Confocal Laser Scanning Microscopy.

> Abstract The phylogenetic composition, three-dimensional structure and dynamics of bacterial communities in river biofilms generated in a rotating annular reactor system were studied by fluorescent in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM). Biofilms grew on independently removable polycarbonate slides exposed in the reactor system with natural river water as inoculum and sole nutrient and carbon source. The microbial biofilm community developed from attached single cells and distinct microcolonies via a more confluent structure characterized by various filamentous bacteria to a mature biofilm rich in polymeric material with fewer cells on a per-area basis after 56 days. During the different stages of biofilm development, characteristic microcolonies and cell morphotypes could be identified as typical features of the investigated lotic biofilms. In situ analysis using a comprehensive suite of rRNA-targeted probes visualized individual cells within the alpha-, beta-, and gamma-Proteobacteria as well as the Cytophaga-Flavobacterium group as major parts of the attached community. The relative abundance of these major groups was determined by using digital image analysis to measure specific cell numbers as well as specific cell area after in situ probing. Within the lotic biofilm community, 87% of the whole bacterial cell area and 79% of the total cell counts hybridized with a Bacteria specific probe. During initial biofilm development, beta-Proteobacteria dominated the bacterial population. This was followed by a rapid increase of alpha-Proteobacteria and bacteria affiliated to the Cytophaga-Flavobacterium group. In mature biofilms, alpha-Proteobacteria and Cytophaga-Flavobacteria continued to be the prevalent bacterial groups. Beta-Proteobacteria constituted the morphologically most diverse group within the biofilm communities, and more narrow phylogenetic staining revealed the importance of distinct phylotypes within the beta1-Proteobacteria for the composition of the microbial community. The presence of sulfate-reducing bacteria affiliated to the Desulfovibrionaceae and Desulfobacteriaceae confirmed the range of metabolic potential within the lotic biofilms.http://link.springer-ny.com/link/service/journals/00248/bibs/37n4p225.html

Journal Article↗
PubMed2006

Rhizosphere microbial activity during phytoremediation of diesel-contaminated soil.

To know microbial activity and diesel-removal efficiency influencing through plant roots, we examined the effect of the rhizosphere on phytoremediation of diesel-contaminated soils by alfalfa (Medicago sativa L.). Pots were treated with and without diesel and allowed to stabilize for 7 weeks, at which time four experimental/control groups were prepared: (1) planted diesel-contaminated soil, (2) unplanted diesel-contaminated soil, (3) planted uncontaminated soil, and (4) unplanted uncontaminated soil. Samples of rhizosphere and bulk soils were separately taken from all planted pots. After 7 weeks of alfalfa growth from seeds, the removal efficiencies in rhizosphere and bulk soil samples were 82.5% and 36.5 approximately 59.4%, respectively. The total microbial activity was highest in diesel-contaminated rhizosphere soils. Significantly more culturable soil bacteria and hydrocarbon-degraders were found in diesel-contaminated rhizosphere soil versus unplanted and uncontaminated bulk soil, with a greater increase seen in hydrocarbon-degraders (172-fold) versus general soil bacteria (14-fold). DGGE (Denaturing Gel Gradient Electrophoresis) analysis revealed that the bacterial community structure was most highly influenced by the combined presence of diesel contamination and plant roots (39.13% similarity compared to the control), but that diesel contamination alone had a higher influence (42.31% similarity compared to the control) than the rhizosphere (50.00% similarity compared to the control). Sequence analysis and BLAST searches revealed that all samples were dominated by members of alpha -, gamma -, delta - and epsilon -proteobacteria, and Chloroflexi. The rhizosphere samples additionally contained novel dominant members of alpha -proteobacteria and Cytophaga-Flexibacter-Bacteroides, while the diesel samples contained additional dominant alpha -proteobacteria and the rhizosphere plus diesel samples contained other epsilon -proteobacteria. Collectively, these findings indicate that the presence of plant roots (i.e., a rhizosphere) had a greater effect on bacterial activity in diesel contamination than did the absence of diesel contamination, whereas diesel contamination had a greater effect on bacterial community structure. These novel findings provide new insight into the mechanisms of phytoremediation.

Biodegradation, Environmental↗
PubMed1983

[Cellular structure of propionibacteria during their multiplication].

The aim of the present study was to determine the structure of bacterial cells from Propionibacterium genus as well as their structure during the cellular division. On the basis of the observations made in the electron transmission microscope, in uranyl-acetates-tained preparations of ultra-thin specimens of bacteria, it was stated that propionic bacteria appeared in a shape of short rods, possessing regular profiles of cell walls as opposed to Gram-negative bacteria with a very creased edge line. Besides, it was observed that division of cells had place by formation of septum, most probably preceded by the division of mezosome, which is a signal for creating the divisional wall. In the conducted studies, the following phenomena were started: presence of membraneous structure of mezosomes, which is linked with the chain of circular DNA in bacterial cell, appearance of numerous ribosomes in the regions of tangled threads of nucleic acids, and existence of other undefinite elements. Mezosome present in the cell of propionic bacteria is probably linked with the cell wall at least in two places and on the surface of external cell wall at the site of its linking; it causes the change in electronic density, demonstrated by the undefined holes or scars in cell wall. This finding gives the possibility of distinguishing this genus of Propionibacterium, in the respect of morphology, from other bacteria what, in the opinion of the authors, is a new achievement in the studies on the structure of propionic bacteria.

Cell Division↗
PubMed2000

The atomic-resolution structure of a novel bacterial esterase.

BACKGROUND: A novel bacterial esterase that cleaves esters on halogenated cyclic compounds has been isolated from an Alcaligenes species. This esterase 713 is encoded by a 1062 base pair gene. The presence of a leader sequence of 27 amino acids suggests that this enzyme is exported from the cytosol. Esterase 713 has been over-expressed in Agrobacterium without this leader sequence. Its amino acid sequence shows no significant homology to any known protein sequence. RESULTS: The crystal structure of esterase 713 has been determined by multiple isomorphous replacement and refined to 1. 1 A resolution. The subunits of this dimeric enzyme comprise a single domain with an alpha/beta hydrolase fold. The catalytic triad has been identified as Ser206-His298-Glu230. The acidic residue of the catalytic triad (Glu230) is located on the beta6 strand of the alpha/beta hydrolase fold, whereas most other alpha/beta hydrolase enzymes have the acidic residue located on the beta7 strand. The oxyanion hole is formed by the mainchain nitrogens of Cys71 and Gln207 as identified by the binding of a substrate analogue, (S)-7-iodo-2,3,4,5-tetrahydro-4-methyl-3-oxo-1H-1, 4-benzodiazepine-2-acetic acid. Cys71 forms a disulphide bond with the neighbouring Cys72. CONCLUSIONS: Despite negligible sequence homology, esterase 713 has structural similarities to a number of other esterases and lipases. Residues of the oxyanion hole were confirmed by structural comparison with Rhizomucor miehei lipase. It is proposed that completion of a functional active site requires the formation of the disulphide bond between adjacent residues Cys71 and Cys72 on export of the esterase into the oxidising environment of the periplasmic space.

Alcaligenes↗
PubMed2006

Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota.

The publicly available annotated archaeal genome sequences (23 complete and three partial annotations, October 2005) were searched for the presence of potential two-component open reading frames (ORFs) using gene category lists and BLASTP. A total of 489 potential two-component genes were identified from the gene category lists and BLASTP. Two-component genes were found in 14 of the 21 Euryarchaeal sequences (October 2005) and in neither the Crenarchaeota nor the Nanoarchaeota. A total of 20 predicted protein domains were identified in the putative two-component ORFs that, in addition to the histidine kinase and receiver domains, also includes sensor and signalling domains. The detailed structure of these putative proteins is shown, as is the distribution of each class of two-component genes in each species. Potential members of orthologous groups have been identified, as have any potential operons containing two or more two-component genes. The number of two-component genes in those Euryarchaeal species which have them seems to be linked more to lifestyle and habitat than to genome complexity, with most examples being found in Methanospirillum hungatei, Haloarcula marismortui, Methanococcoides burtonii and the mesophilic Methanosarcinales group. The large numbers of two-component genes in these species may reflect a greater requirement for internal regulation. Phylogenetic analysis of orthologous groups of five different protein classes, three probably involved in regulating taxis, suggests that most of these ORFs have been inherited vertically from an ancestral Euryarchaeal species and point to a limited number of key horizontal gene transfer events.

Bacterial Proteins↗