6MLB

Crystal structure of the holo retinal-bound domain-swapped dimer Q108K:K40L:T51F mutant of human cellular retinol binding protein II

Summary for 6MLB

• Entry DOI: 10.2210/pdb6mlb/pdb
• Descriptor: Retinol-binding protein 2, GLYCEROL, ACETATE ION, ... (5 entities in total)
• Functional Keywords: ilbp, protein switch, lipid binding protein
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 4
• Total formula weight: 63746.68

Authors

Ghanbarpour, A.,Geiger, J. (deposition date: 2018-09-27, release date: 2019-10-16, Last modification date: 2023-10-11)

Primary citation

Ghanbarpour, A.,Pinger, C.,Esmatpour Salmani, R.,Assar, Z.,Santos, E.M.,Nosrati, M.,Pawlowski, K.,Spence, D.,Vasileiou, C.,Jin, X.,Borhan, B.,Geiger, J.H.
Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches.
J.Am.Chem.Soc., 141:17125-17132, 2019

PubMed Abstract: Protein conformational switches or allosteric proteins play a key role in the regulation of many essential biological pathways. Nonetheless, the implementation of protein conformational switches in protein design applications has proven challenging, with only a few known examples that are not derivatives of naturally occurring allosteric systems. We have discovered that the domain-swapped (DS) dimer of hCRBPII undergoes a large and robust conformational change upon retinal binding, making it a potentially powerful template for the design of protein conformational switches. Atomic resolution structures of the apo- and holo-forms illuminate a simple, mechanical movement involving sterically driven torsion angle flipping of two residues that drive the motion. We further demonstrate that the conformational "readout" can be altered by addition of cross-domain disulfide bonds, also visualized at atomic resolution. Finally, as a proof of principle, we have created an allosteric metal binding site in the DS dimer, where ligand binding results in a reversible 5-fold loss of metal binding affinity. The high resolution structure of the metal-bound variant illustrates a well-formed metal binding site at the interface of the two domains of the DS dimer and confirms the design strategy for allosteric regulation.

PubMed: 31557439
DOI: 10.1021/jacs.9b04664

Experimental method

X-RAY DIFFRACTION (2.15 Å)