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Kinetic and ultraviolet-visible spectral techniques were utilized to investigate the interaction of Escherichia coli cystathionine beta lyase (CBL) and aminoethoxyvinylglycine (AVG). The results indicated that AVG can act as a slow-binding inhibitor of CBL. X-ray crystallography revealed the spatial structure of the CBLAVG complex as compatible with a ketimine as the reaction product. The structure suggested a binding mode for rhizobitoxine.

The crystal structures of five complexes of Escherichia coli dihydrodipicolinate synthase (DHDPS) with substrates, substrate analogs and inhibitors are shown. These include the complexes of DHDPS with pyruvate, pyruvate and the L-aspartate beta-semialdehyde analog succinate beta-semialdehyde, the inhibitor alpha-ketopimelic acid, dipicolinic acid and the natural feedback inhibitor L-lysine. The kinetics of inhibition were investigated and the binding site of the L-lysine was determined. (4S)-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid was identified as the only product of the reaction catalyzed by DHDPS.

Escherichia coli threonine synthase (Ts) catalyzes threonine synthesis from HSerP, deamination and half-transamination reactions, depending on the nature of the substrate. The stabilization of kinetically competent quinonoidal intermediate is an outstanding feature of Ts catalysis.

The isolation annd characterization of a carbamate hydrolase gene from Arthrobacter oxydans P52 were reported. A monomeric phenylcarbamate hydrolase (phenmedipham hydrolase) of about 55-kDa molecular weight was purified to homogeneity. It was found that the gene for phenylcarbamate degradation (pcd) is plasmid encoded. The pcd gene encoding the enzyme was then cloned and sequenced. Sequence comparisons revealed homology of the phenmedipham hydrolase with esterases of eukaryotic origin.

Abstract Background Health and disease of organisms are reflected in their phenotypes. Often, a genetic component to a disease is discovered only after clearly defining its phenotype. In the past years, many technologies to systematically generate phenotypes in a high-throughput manner, such as RNA interference or gene knock-out, have been developed and used to decipher functions for genes. However, there have been relatively few efforts to make use of phenotype data beyond the single genotype-phenotype relationships. Results We present results on a study where we use a large set of phenotype data – in textual form – to predict gene annotation. To this end, we use text clustering to group genes based on their phenotype descriptions. We show that these clusters correlate well with several indicators for biological coherence in gene groups, such as functional annotations from the Gene Ontology (GO) and protein-protein interactions. We exploit these clusters for predicting gene function by carrying over annotations from well-annotated genes to other, less-characterized genes in the same cluster. For a subset of groups selected by applying objective criteria, we can predict GO-term annotations from the biological process sub-ontology with up to 72.6% precision and 16.7% recall, as evaluated by cross-validation. We manually verified some of these clusters and found them to exhibit high biological coherence, e.g. a group containing all available antennal Drosophila odorant receptors despite inconsistent GO-annotations. Conclusion The intrinsic nature of phenotypes to visibly reflect genetic activity underlines their usefulness in inferring new gene functions. Thus, systematically analyzing these data on a large scale offers many possibilities for inferring functional annotation of genes. We show that text clustering can play an important role in this process.

THR1, the gene from Saccharomyces cerevisiae, encoding homoserine kinase, one of the threonine biosynthetic enzymes, has been cloned by complementation. The nucleotide sequence of a 3.1-kb region carrying this gene reveals an open reading frame of 356 codons, corresponding to about 40 kDa for the encoded protein. The presence of three canonical GCN4 regulatory sequences in the upstream flanking region suggests that the expression of THR1 is under the general amino acid control. In parallel, the enzyme was purified by four consecutive column chromatographies, monitoring homoserine kinase activity. In SDS gel electrophoresis, homoserine kinase migrates like a 40-kDa protein; the native enzyme appears to be a homodimer. Thc sequence of the first 15 NH2-terminal amino acids, as determined by automated Edman degradation, is in accordance with the amino acid sequence deduced from the nucleotide sequence. Computer-assisted comparison of the yeast enzyme with the corresponding activities from bacterial sources showed that several segments among these proteins are highly conserved. Furthermore, the observed homology patterns suggest that the ancestral sequences might have been composed from separate (functional) domains. A block of very similar amino acids is found in the homoserine kinases towards the carboxy terminus that is also present in many other proteins involved in threonine (or serine) metabolism: this motif, therefore, may represent the binding site for the hydroxyamino acids. Limited similarity was detected between a motif conserved among thc homoserine kinases and consensus sequences found in other mono- or dinucleotide-binding proteins. [ABSTRACT FROM AUTHOR]