Back in time to the Gly-rich prototype of the phosphate binding elementary function

• Published in: Current research in structural biology 2024-01, Vol.7, p.100142-100142, Article 100142
• Main Authors: Zheng, Zejun, Goncearenco, Alexander, Berezovsky, Igor N.
• Format: Article
• Language: English
• Subjects: Amino acid chronology; Closed loops; Elementary function; Gly-rich prototype; P-loop NTPases; Prebiotic evolution; Protein evolution; Protein function; Review; Rossmann and Rossmann-like
• ISSN: 2665-928X; 2665-928X
• DOI: 10.1016/j.crstbi.2024.100142

Binding of nucleotides and their derivatives is one of the most ancient elementary functions dating back to the Origin of Life. We review here the works considering one of the key elements in binding of (di)nucleotide-containing ligands – phosphate binding. We start from a brief discussion of major participants, conditions, and events in prebiotic evolution that resulted in the Origin of Life. Tracing back to the basic functions, including metal and phosphate binding, and, potentially, formation of primitive protein-protein interactions, we focus here on the phosphate binding. Critically assessing works on the structural, functional, and evolutionary aspects of phosphate binding, we perform a simple computational experiment reconstructing its most ancient and generic sequence prototype. The profiles of the phosphate binding signatures have been derived in form of position-specific scoring matrices (PSSMs), their peculiarities depending on the type of the ligands have been analyzed, and evolutionary connections between them have been delineated. Then, the apparent prototype that gave rise to all relevant phosphate-binding signatures had also been reconstructed. We show that two major signatures of the phosphate binding that discriminate between the binding of dinucleotide- and nucleotide-containing ligands are GxGxxG and GxxGxG, respectively. It appears that the signature archetypal for dinucleotide-containing ligands is more generic, and it can frequently bind phosphate groups in nucleotide-containing ligands as well. The reconstructed prototype's key signature GxGGxG underlies the role of glycine residues in providing flexibility and interactions necessary for binding the phosphate groups. The prototype also contains other ancient amino acids, valine, and alanine, showing versatility towards evolutionary design and functional diversification. [Display omitted] •Back in time to the Prototype of the phosphate binding.•The Gly-rich Prototype became a cornerstone of many functions.•Design versatility of the phosphate binding prototype.