Aminotransferases: demonstration of homology and division into evolutionary subgroups

Abstract

A total of 150 amino acid sequences of vitamin €3,-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 I1 acetylornithine, ornithine, o-amino acid, 4-aminobutyrate and diaminopelargonate aminotransferases ; subgroup 111 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. Nut1 Acud. Sci. USA 84, 4355-43581, established the homology among the enzymes of each subgroup as well as among all subgroups except subgroup 111. However, similarity of active-site segments and the hydropathy patterns around invariant residues suggest that subgroup 111, 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.The aminotransferases catalyze the reversible transfer of amino groups from amino acids to 0x0 acids, one of the numerous transformations of amino acids that are performed by vitamin-B,-dependent enzymes. Among the various groups of pyridoxal-5'-phosphate-dependent enzymes, the aminotransferases excel by the highest number of reported amino acid sequences, i.e. one third of the total of about 150 sequences of pyridoxal-5'-phosphate-dependent enzymes known to date. The homology of aspartate, tyrosine and histidinol-phosphate aminotransferases has already been reported. On alignment of 16 amino acid sequences of these enzymes, 12 amino acid residues, mainly ligands of the coenzyme or the substrate, proved invariant out of a total of about 400 residues (Mehta et al., 1989). Since the publication of that report, the number of known aminotransferase sequences has doubled.In a continuation of our studies on the evolutionary relationships among vitamin B,-dependent enzymes, all known sequences of aminotransferases were aligned on the basis of sequence similarity, hydropathy pa...

Active site model for γ‐aminobutyrate aminotransferase explains substrate specificity and inhibitor reactivities

“…These include: Gly 11 1, His 139, Gly 140, Glu 210, Pro 21 1, Asp 243, Glu 244, Gln 246, Lys 272, Thr 303*, and Arg 406. Three of these (Asp 243, Lys 272, and Arg 406) are invariant among all aminotransferases capable of acting on a-amino acids (Mehta et al, 1993). In the GABA-AT model, these residues are located in positions spatially identical to those in the DGD structure (Fig.…”

“…GABA-AT belongs to aminotransferase subgroup 11, one of four currently recognized subgroups of aminotransferases (Mehta et al, 1993). At least IO enzymes with approximately 30 known sequences belong to this subgroup.…”

“…The coordinates for the structure of one of these enzymes, dialkylglycine decarboxylase, are available (Toney et al, , 1995. This abundance of sequence information and the conservation throughout these sequences (Mehta et al, 1993) of several residues found to be in the active site of DGD suggest that homology modeling of the GABA-AT structure could lead to a realistic model for its active site structure. The homology modeling-deduced active site structure is presented and analyzed in this report.…”

Similarity between pyridoxal/pyridoxamine phosphate‐dependent enzymes involved in dideoxy and deoxyaminosugar biosynthesis and other pyridoxal phosphate enzymes

“…This is confirmed by profile analysis with the probe P9 (ERBS-SACER plus homologues). In fact, it assigns to 1 PLP-dependent enzyme a 2-score >5.0, considered a threshold for definitive structural relationship, and to several others a score >3.0, con- sidered meaningful (Mehta et al, 1993). The alignment among DAS and ERBS-SACER with its homologues indicates the presence of a lysine/histidine and an aspartate residue at positions equivalent to AAT K258 and D222, respectively (Fig.…”

“…Although sequence similarity is weak (pairwise identity percentage to AAT, DGD, and SHMT is 13, 14, and 12%, respectively), the lysine in position 258 (K258) of AAT, which forms a Schiff base with the PLP cofactor, and the aspartate in position 222 (D222 in AAT), which H bonds to the pyridine ring N1, are both conserved in the ERBS-SACER sequence (these residues will be referred to with their AAT numbering). These 2 residues are among those conserved in all aminotransferases (Mehta et al, 1993). The eryCl gene product is involved in the biosynthesis of erythromycin, very likely at the step of desosamine synthesis or its attachment to the macrolide ring (Dhillon et al, 1989).…”