Homology of pyridoxal‐5′‐phosphate‐dependent aminotransferases with the cobC (cobalamin synthesis), nifS (nitrogen fixation), pabC (p‐aminobenzoate synthesis) and malY (abolishing endogenous induction of the maltose system) gene products

Abstract

Bacterial deletion mutants have indicated that the gene products of cobC, nifS, pabC and malY participate in important metabolic pathways, i.e. cobalamin synthesis, nitrogen fixation, synthesis of p‐aminobenzoate and the regulation of the maltose system, respectively. However, the proteins themselves and their specific functions have not yet been identified. In the course of our studies on the evolutionary relationships among aminotransferases, we have found that the above gene products are homologous to aminotransferases. Profile analysis [Gribskov, M., Lüthy, R. & Eisenberg, D. (1990) Methods Enzymol. 183, 146–159] based on the amino acid sequences of certain subgroups of aminotransferases as probes attributed significant Z scores in the range 5–20 SD to the deduced amino acid sequences of the above gene products as included in the protein data base. Reciprocal profile analyses confirmed the homologies. All known aminotransferases are pyridoxal‐5′‐phosphate‐dependent enzymes and catalyze the reversible transfer of amino groups from amino acids to oxo acids. The sequence homologies suggest that the above gene products are aminotransferases or other closely related pyridoxal‐5′‐phosphate‐dependent enzymes probably catalyzing transformations of amino acids involving cleavage of a bond at Cα.

The biosynthetic gene cluster for coronamic acid, an ethylcyclopropyl amino acid, contains genes homologous to amino acid-activating enzymes and thioesterases

“…Two possible reactions would be characterized either by (i) an intermediacy of PLP bound to L-isoleucine followed by nonenzymatic tautomerization and release of L-alloisoleucine or by (ii) deamination of L-isoleucine to form 2-keto-(3S)-methylvaleric acid followed by keto-enol tautomerization, subsequent amination, and release of L-alloisoleucine (31). The cofactor PLP is known to play an important role in a variety of amino acid-modifying enzymes and is bound to them via a conserved lysine residue (2,34 (43,55). However, we did not find a conserved -24(GG)/-12(GC) motif upstream of the transcriptional start site as would be presumed for a oa54-dependent promoter (35,55).…”

lcd from Streptococcus anginosus encodes a C-S lyase with α,β-elimination activity that degrades l-cysteine The DDBJ accession number for the Streptococcus anginosus lcd gene sequence reported in this paper is AB084812.

“…2), and is located between residues 209 and 256 in various members of the α family (Alexander et al, 1994). In addition, six of the eight residues that are found in most aminotransferases in the α family are conserved (Mehta et al, 1989 ;Mehta & Christen, 1993 ;Alexander et al, 1994) (Fig. 2).…”

“…Pyridoxal-5h-phosphate-dependent enzymes have been classified into the α, β and γ families based on sequence alignments and the construction of protein profiles (Alexander et al, 1994). All four amino acid residues that are invariant in the comprehensive alignment of aminotransferases belonging to the α family (Mehta & Christen, 1993) are conserved in Lcd (Fig. 2).…”

“…Four amino acid residues that are invariant in the comprehensive alignment of aminotransferases belonging to the α family (Mehta & Christen, 1993) are highlighted. The eight residues conserved in most aminotransferases in the α family are boxed.…”

Evolutionary recruitment of biochemically specialized subdivisions of Family I within the protein superfamily of aminotransferases

“…Subfamily I is presumably dedicated to an unknown aminotransferase reaction required for cobalamin biosynthesis (37). Subfamily I␦ is specialized for mediating the interconversion of L-alanine and pyruvate.…”