Sil1 functions as a NEF (nucleotide-exchange factor) for the ER (endoplasmic
reticulum) Hsp70 (heat-shock protein of 70 kDa) Bip in eukaryotic cells. Sil1
may catalyse the ADP release from Bip by interacting directly with the ATPase
domain of Bip. In the present study we show the complex crystal structure of the
yeast Bip and the NEF Sil1 at the resolution of 2.3 Å (1 Å=0.1 nm). In the
Sil1-Bip complex structure, the Sil1 molecule acts as a 'clamp' which binds lobe
IIb of the Bip ATPase domain. The binding of Sil1 causes the rotation of lobe
IIb ~ 13.5° away from the ADP-binding pocket. The complex formation also
induces lobe Ib to swing in the opposite direction by ~ 3.7°. These
conformational changes open up the nucleotide-binding pocket in the Bip ATPase
domain and disrupt the hydrogen bonds between Bip and bound ADP, which may
catalyse ADP release. Mutation of the Sil1 residues involved in binding the Bip
ATPase domain compromise the binding affinity of Sil1 to Bip, and these Sil1
mutants also abolish the ability to stimulate the ATPase activity of Bip.
