Sequence comparisons betweenAgrobacterium tumefaciens T-DNA-encoded octopine and nopaline dehydrogenases and other nucleotide-requiring enzymes: Structural and evolutionary implications

Abstract

The nucleotide sequences of the two T-DNA-encoded crown gall imino acid dehydrogenases octopine dehydrogenase and nopaline dehydrogenase were compared with each other and with the sequences of other dehydrogenases. A multistep strategy comprising computer sequence analysis and secondary- and antigenic-structure predictions was used. An alignment of octopine and nopaline dehydrogenase was obtained in which a 20-amino-acid N-terminal arm and six fairly long gaps in the C-terminal moiety were introduced. The aligned sequences have identities of 26% at the amino acid level and 38% at the nucleotide level. They appear to contain two domains. The N-terminal coenzyme-binding domains are similar to those of the well-characterized NAD(P) dehydrogenases. Conserved fragments were found in the C-terminal catalytic domains that likely contain essential residues for catalysis. Comparison of the sequences with those of two other 2-keto acid dehydrogenases, lactate and malate dehydrogenase, suggests that as in those enzymes, histidine, aspartic acid, and arginine residues are located at the octopine and nopaline dehydrogenase active sites. The crown gall enzymes could not be classified with any known family of dehydrogenases. Their evolutionary origin remains unknown. However, predictions concerning their internal organization may provide new insight into protein evolution.