6F7T

Crystal Structure of an Fab fragment in complex with a peptide from Bacillus subtilis RNase Y

Summary for 6F7T

• Entry DOI: 10.2210/pdb6f7t/pdb
• Descriptor: FAB RY79-90, LIGHT CHAIN, FAB RY79-90, HEAVY CHAIN, Ribonuclease Y, ... (5 entities in total)
• Functional Keywords: fab-peptide complex, lambda x light chain, rnase y, immune system
• Biological source: Mus musculus; More
• Total number of polymer chains: 6
• Total formula weight: 96097.43

Authors

Golinelli-Pimpaneau, B.,Hardouin, P. (deposition date: 2017-12-11, release date: 2018-10-31, Last modification date: 2024-01-17)

Primary citation

Hardouin, P.,Velours, C.,Bou-Nader, C.,Assrir, N.,Laalami, S.,Putzer, H.,Durand, D.,Golinelli-Pimpaneau, B.
Dissociation of the Dimer of the Intrinsically Disordered Domain of RNase Y upon Antibody Binding.
Biophys. J., 115:2102-2113, 2018

PubMed Abstract: Although RNase Y acts as the key enzyme initiating messenger RNA decay in Bacillus subtilis and likely in many other Gram-positive bacteria, its three-dimensional structure remains unknown. An antibody belonging to the rare immunoglobulin G (IgG) 2b λx isotype was raised against a 12-residue conserved peptide from the N-terminal noncatalytic domain of B. subtilis RNase Y (BsRNaseY) that is predicted to be intrinsically disordered. Here, we show that this domain can be produced as a stand-alone protein called Nter-BsRNaseY that undergoes conformational changes between monomeric and dimeric forms. Circular dichroism and size exclusion chromatography coupled with multiangle light scattering or with small angle x-ray scattering indicate that the Nter-BsRNaseY dimer displays an elongated form and a high content of α-helices, in agreement with the existence of a central coiled-coil structure appended with flexible ends, and that the monomeric state of Nter-BsRNaseY is favored upon binding the fragment antigen binding (Fab) of the antibody. The dissociation constants of the IgG/BsRNaseY, IgG/Nter-BsRNaseY, and IgG/peptide complexes indicate that the affinity of the IgG for Nter-BsRNaseY is in the nM range and suggest that the peptide is less accessible in BsRNaseY than in Nter-BsRNaseY. The crystal structure of the Fab in complex with the peptide antigen shows that the peptide adopts an elongated U-shaped conformation in which the unique hydrophobic residue of the peptide, Leu6, is completely buried. The peptide/Fab complex may mimic the interaction of a microdomain of the N-terminal domain of BsRNaseY with one of its cellular partners within the degradosome complex. Altogether, our results suggest that BsRNaseY may become accessible for protein interaction upon dissociation of its N-terminal domain into the monomeric form.

PubMed: 30447990
DOI: 10.1016/j.bpj.2018.10.016

Experimental method

X-RAY DIFFRACTION (2.6 Å)