3GJN

Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins

Summary for 3GJN

• Entry DOI: 10.2210/pdb3gjn/pdb
• Descriptor: Colicin-E9 immunity protein, Colicin-E7, ZINC ION, ... (4 entities in total)
• Functional Keywords: protein-protein complex, bacteriocin immunity, antibiotic, antimicrobial, bacteriocin, endonuclease, hydrolase, metal-binding, nuclease
• Biological source: Escherichia coli; More
• Total number of polymer chains: 4
• Total formula weight: 51880.75

Authors

Dym, O.,Tawfik, D.S. (deposition date: 2009-03-09, release date: 2009-09-15, Last modification date: 2023-11-01)

Primary citation

Levin, K.B.,Dym, O.,Albeck, S.,Magdassi, S.,Keeble, A.H.,Kleanthous, C.,Tawfik, D.S.
Following evolutionary paths to protein-protein interactions with high affinity and selectivity
Nat.Struct.Mol.Biol., 16:1049-1055, 2009

PubMed Abstract: How do intricate multi-residue features such as protein-protein interfaces evolve? To address this question, we evolved a new colicin-immunity binding interaction. We started with Im9, which inhibits its cognate DNase ColE9 at 10(-14) M affinity, and evolved it toward ColE7, which it inhibits promiscuously (Kd > 10(-8) M). Iterative rounds of random mutagenesis and selection toward higher affinity for ColE7, and selectivity (against ColE9 inhibition), led to an approximately 10(5)-fold increase in affinity and a 10(8)-fold increase in selectivity. Analysis of intermediates along the evolved variants revealed that changes in the binding configuration of the Im protein uncovered a latent set of interactions, thus providing the key to the rapid divergence of new Im7 variants. Overall, protein-protein interfaces seem to share the evolvability features of enzymes, that is, the exploitation of promiscuous interactions and alternative binding configurations via 'generalist' intermediates, and the key role of compensatory stabilizing mutations in facilitating the divergence of new functions.

PubMed: 19749752
DOI: 10.1038/nsmb.1670

Experimental method

X-RAY DIFFRACTION (2.48 Å)