Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family

5 years ago

Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family

Barber-Zucker, B., R., Shaanan, Zarivach, S.

Divalent transition metal cations (DTMCs), such as Fe, Zn and Mn, participate in many biological processes, like DNA synthesis, enzymatic activities and the synthesis of different biological minerals. Understanding how specific DTMCs are transported to and within the cell and what controls their binding selectivity to different proteins is crucial for defining the mechanisms of metalloproteins and designing new proteins with novel function. To better understand such processes, we scanned the RCSB Protein Data Bank, performed a structural-based comprehensive analysis of seven DTMCs and found their amino acid binding and coordination geometry propensities. We then used the results of this analysis to characterize the correlation between metal selectivity, specific binding site composition and phylogenetic classification of the cation diffusion facilitator (CDF) protein family, a family of DTMC transporters found throughout evolution and sharing a conserved structure, yet with different members displaying distinct metal selectivity. Our analysis shows that DTMCs differ, at times significantly, in terms of their binding propensities, and that in each CDF clade, the metal selectivity-related binding site has a unique and conserved sequence signature. Here we show that only limited correlation exists between the composition of the DMTC binding site in each clade and the metal selectivity shown by its proteins. Considering this binding site composition and previous results, we suggest that CDF phylogenetic classification cannot determine metal selectivity.

Publisher URL: http://biorxiv.org/cgi/content/short/164509v1

DOI: 10.1101/164509