A total of 150 amino acid sequences of vitamin B6-dependent enzymes are known to date, the largest contingent being furnished by the aminotransferases with 51 sequences of 14 different enzymes. All aminotransferase sequences were aligned by using algorithms for sequence comparison, hydropathy patterns and secondary structure predictions. The aminotransferases could be divided into four subgroups on the basis of their mutual structural relatedness. Subgroup I comprises aspartate, alanine, tyrosine, histidinol-phosphate, and phenylalanine aminotransferases; subgroup II acetylornithine, ornithine, omega-amino acid, 4-aminobutyrate and diaminopelargonate aminotransferases; subgroup III D-alanine and branched-chain amino acid aminotransferases, and subgroup IV serine and phosphoserine aminotransferases. (N-1) Profile analysis, a more stringent application of profile analysis [Gribskov, M., McLachlan, A. D. and Eisenberg, D. (1987) Proc. Natl Acad. Sci. USA 84, 4355-4358], established the homology among the enzymes of each subgroup as well as among all subgroups except subgroup III. However, similarity of active-site segments and the hydropathy patterns around invariant residues suggest that subgroup III, though most distantly related, might also be homologous with the other aminotransferases. On the basis of the comprehensive alignment, a new numbering of amino acid residues applicable to aminotransferases (AT) in general is proposed. In the multiply aligned sequences, only four out of a total of about 400 amino acid residues proved invariant in all 51 sequences, i.e. Gly(314AT)197, Asp/Glu(340AT)222, Lys(385AT)258 and Arg(562AT)386, the number not in parentheses corresponding to the structure of porcine cytosolic aspartate aminotransferase. Apparently, the aminotransferases constitute a group of homologous proteins which diverged into subgroups and, with some exceptions, into substrate-specific individual enzymes already in the universal ancestor cell.

Aminotransferases: demonstration of homology and division into evolutionary subgroups

Ethylene is one of the simplest organic molecules with biological activity. At concentrations as low as 0.1 ppm in air, it has been shown to have dramatic effects on plant growth and development [1]. Neljubov [78] was the first to show that ethylene has three major effects in etiolated pea seedlings called the triple response: (1) diageotropic growth, (2) thickening of stem and inhibition of stem elongation, and (3) exaggeration of apical hook curvature. Since then, numerous ethylene effects have been described in light-grown plants such as sex determination in curcurbits, fruit ripening in climacteric fruits, epinastic curvature, flower senescence, and root initiation [1]. Interestingly, ethylene has also been shown to have opposite effects in some plants; for instance, it inhibits stem elongation in most dicots, whereas in some aquatic dicots and rice, it stimulates growth [1, 45, 72].

Ethylene biosynthesis and action: a case of conservation

We identified a set of cytokinin-insensitive mutants by using a screen based on the ethylene-mediated triple response observed after treatment with low levels of cytokinins. One group of these mutants disrupts ACS5, a member of the Arabidopsis gene family that encodes 1-aminocyclopropane-1-carboxylate synthase, the first enzyme in ethylene biosynthesis. The ACS5 isoform is mainly responsible for the sustained rise in ethylene biosynthesis observed in response to low levels of cytokinin and appears to be regulated primarily by a posttranscriptional mechanism. Furthermore, the dominant ethylene-overproducing mutant eto2 was found to be the result of an alteration of the carboxy terminus of ACS5, suggesting that this domain acts as a negative regulator of ACS5 function.

https://www.pnas.org/content/pnas/95/8/4766.full.pdf

Recessive and dominant mutations in the ethylene biosynthetic gene ACS5 of Arabidopsis confer cytokinin insensitivity and ethylene overproduction, respectively

In the framework of the European project aimed at the sequencing of the Bacillus subtilis genome the DNA region located between gerB (314 degrees) and sacXY (333 degrees) was assigned to the Institut Pasteur. In this paper we describe the cloning and sequencing of a segment of 97 kb of contiguous DNA. Ninety-two open reading frames were predicted to encode putative proteins among which only forty-two were found to display significant similarities to known proteins present in databanks, e.g. amino acid permeases, proteins involved in cell wall or antibiotic biosynthesis, various regulatory proteins, proteins of several dehydrogenase families and enzymes II of the phosphotransferase system involved in sugar transport. Additional experiments led to the identification of the products of new B. subtilis genes, e.g. galactokinase and an operon involved in thiamine biosynthesis.

Bacillus subtilis genome project: cloning and sequencing of the 97 kb region from 325° to 333deg;

Cystalysin is a Cβ–Sγ lyase from the oral pathogen Treponema denticola catabolyzing l‐cysteine to produce pyruvate, ammonia and H2S. With its ability to induce cell lysis, cystalysin represents a new class of pyridoxal 5′‐phosphate (PLP)‐dependent virulence factors. The crystal structure of cystalysin was solved at 1.9 A resolution and revealed a folding and quaternary arrangement similar to aminotransferases. Based on the active site architecture, a detailed catalytic mechanism is proposed for the catabolism of S‐containing amino acid substrates yielding H2S and cysteine persulfide. Since no homologies were observed with known haemolysins the cytotoxicity of cystalysin is attributed to this chemical reaction. Analysis of the cystalysin–l‐aminoethoxyvinylglycine (AVG) complex revealed a ‘dead end’ ketimine PLP derivative, resulting in a total loss of enzyme activity. Cystalysin represents an essential factor of adult periodontitis, therefore the structure of the cystalysin–AVG complex may provide the chemical basis for rational drug design.

/pdf/crystal-structure-of-cystalysin-from-treponema-denticola-a-2e2nhj1ky6.pdf

Crystal structure of cystalysin from Treponema denticola: a pyridoxal 5′-phosphate-dependent protein acting as a haemolytic enzyme

Thermostable aspartate aminotransferase from a thermophilic Bacillus species. Gene cloning, sequence determination, and preliminary x-ray characterization.

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Thermostable aspartate aminotransferase from a thermophilic Bacillus species. Gene cloning, sequence determination, and preliminary x-ray characterization.