Multidomain organization of eukaryotic guanine nucleotide exchange translation initiation factor eIF‐2B subunits revealed by analysis of conserved sequence motifs

Abstract

Computer‐assisted analysis of amino acid sequences using methods for database screening with individual sequences and with multiple alignment blocks reveals a complex multidomain organization of yeast proteins GCD6 and GCD1, and mammalian homolog of GCD6 — subunits of the eukaryotic translation initiation factor eIF‐2B involved in GDP/GTP exchange on eIF‐2. It is shown that these proteins contain a putative nucleotide‐binding domain related to a variety of nucleotidyltransferases, most of which are involved in nucleoside diphosphate‐sugar formation in bacteria. Three conserved motifs, one of which appears to be a variant of the phosphate‐binding site (P‐loop) and another that may be considered a specific version of the Mg²⁺‐binding site of NTP‐utilizing enzymes, were identified in the nucleotidyltransferase‐related domain. Together with the third unique motif adjacent to the P‐loop, these motifs comprise the signature of a new superfamily of nucleotide‐binding domains. A domain consisting of hexapeptide amino acid repeats with a periodic distribution of bulky hydrophobic residues (isoleucine patch), which previously have been identified in bacterial acetyltransferases, is located toward the C‐terminus from the nucleotidyltransferase‐related domain. Finally, at the very C‐termini of GCD6, eIF‐2Be, and two other eukaryotic translation initiation factors, eIF‐4γ and eIF‐5, there is a previously undetected, conserved domain. It is hypothesized that the nucleotidyltransferase‐related domain is directly involved in the GDP/GTP exchange, whereas the C‐terminal conserved domain may be involved in the interaction of eIF‐2B, eIF‐4γ, and eIF‐5 with eIF‐2.