3QML

The structural analysis of Sil1-Bip complex reveals the mechanism for Sil1 to function as a novel nucleotide exchange factor

Summary for 3QML

• Entry DOI: 10.2210/pdb3qml/pdb
• Related: 3QFP 3QFU
• Descriptor: 78 kDa glucose-regulated protein homolog, Nucleotide exchange factor SIL1, PHOSPHATE ION, ... (5 entities in total)
• Functional Keywords: armadillo like repeats, chaperone-protein transport complex, chaperone/protein transport
• Biological source: Saccharomyces cerevisiae (brewer's yeast,lager beer yeast,yeast); More
• Cellular location: Endoplasmic reticulum lumen: P16474 Q08199
• Total number of polymer chains: 4
• Total formula weight: 159139.45

Authors

Yan, M.,Li, J.Z.,Sha, B.D. (deposition date: 2011-02-04, release date: 2011-06-29, Last modification date: 2024-02-21)

Primary citation

Yan, M.,Li, J.,Sha, B.
Structural analysis of the Sil1-Bip complex reveals the mechanism for Sil1 to function as a nucleotide-exchange factor.
Biochem.J., 438:447-455, 2011

PubMed Abstract: 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.

PubMed: 21675960
DOI: 10.1042/BJ20110500

Experimental method

X-RAY DIFFRACTION (2.31 Å)