Conserved Structural Motifs across Diverse Vitamin B12 Binding Proteins

Author(s): Pushya Pradeep, Deepesh Nagarajan.

Vitamin B12, a significant organometallic porphyrin derivative, is an essential growth factor in most organisms. Its primary function is as a cofactor in a diverse range of enzymes, belonging to diverse protein families. Understanding the conserved binding-site characteristics that enable different proteins to recognise the same ligand is therefore of significant importance. In-depth binding-site comparisons, ligand-based site alignments, clustering, and tree computing were performed employing a non-redundant dataset of known vitaminB12 binding proteins to derive the principles for vitamin B12 recognition. The 53 protein structures that bind to vitamin B12 can be clustered into 14 categories, and contain 8 unique binding motifs. Knowledge of these binding-site determinants could be used to detect the function of unknown proteins. An example analysis on the Swiss-Prot database revealed 15 proteins from pathogenic species with identified sequence motifs, indicating that they may have potential vitamin B12 binding activity and have potential as therapeutic targets.