4UDM

Crystal structure of Im3 in complex with Y52A mutant of E3RNase

Summary for 4UDM

• Entry DOI: 10.2210/pdb4udm/pdb
• Descriptor: COLICIN-E3 IMMUNITY PROTEIN, COLICIN-E3, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: translation, antibiotic, antimicrobial, bacteriocin, bacteriocin immunity, endonuclease, hydrolase, inhibition, nuclease, protein-protein interactions, ribonuclease, ribosome inactivation, toxin
• Biological source: ESCHERICHIA COLI BL21(DE3); More
• Total number of polymer chains: 2
• Total formula weight: 20786.47

Authors

Sharma, A.,Kleanthous, C. (deposition date: 2014-12-10, release date: 2016-01-13, Last modification date: 2023-12-20)

Primary citation

Papadakos, G.,Sharma, A.,Lancaster, L.E.,Bowen, R.,Kaminska, R.,Leech, A.P.,Walker, D.,Redfield, C.,Kleanthous, C.
Consequences of Inducing Intrinsic Disorder in a High-Affinity Protein-Protein Interaction.
J.Am.Chem.Soc., 137:5252-, 2015

PubMed Abstract: The kinetic and thermodynamic consequences of intrinsic disorder in protein-protein recognition are controversial. We address this by inducing one partner of the high-affinity colicin E3 rRNase domain-Im3 complex (K(d) ≈ 10(-12) M) to become an intrinsically disordered protein (IDP). Through a variety of biophysical measurements, we show that a single alanine mutation at Tyr507 within the hydrophobic core of the isolated colicin E3 rRNase domain causes the enzyme to become an IDP (E3 rRNase(IDP)). E3 rRNase(IDP) binds stoichiometrically to Im3 and forms a structure that is essentially identical to the wild-type complex. However, binding of E3 rRNase(IDP) to Im3 is 4 orders of magnitude weaker than that of the folded rRNase, with thermodynamic parameters reflecting the disorder-to-order transition on forming the complex. Critically, pre-steady-state kinetic analysis of the E3 rRNase(IDP)-Im3 complex demonstrates that the decrease in affinity is mostly accounted for by a drop in the electrostatically steered association rate. Our study shows that, notwithstanding the advantages intrinsic disorder brings to biological systems, this can come at severe kinetic and thermodynamic cost.

PubMed: 25856265
DOI: 10.1021/JA512607R

Experimental method

X-RAY DIFFRACTION (2.96 Å)