7N6L

Crystal structure of the substrate-binding domain of E. coli DnaK in complex with the peptide EANQQKPLLGLFADG

Replaces:  7JMZ

Summary for 7N6L

• Entry DOI: 10.2210/pdb7n6l/pdb
• Descriptor: Chaperone protein DnaK, Alkaline phosphatase peptide, GLYCEROL, ... (5 entities in total)
• Functional Keywords: complex, molecular chaperone, protein/peptide, chaperone, chaperone-hydrolase complex, chaperone/hydrolase
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 2
• Total formula weight: 25798.87

Authors

Jansen, R.M.,Ozden, C.,Gierasch, L.M.,Garman, S.C. (deposition date: 2021-06-08, release date: 2021-06-23, Last modification date: 2023-10-18)

Primary citation

Clerico, E.M.,Pozhidaeva, A.K.,Jansen, R.M.,Ozden, C.,Tilitsky, J.M.,Gierasch, L.M.
Selective promiscuity in the binding of E. coli Hsp70 to an unfolded protein.
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: Heat shock protein 70 (Hsp70) chaperones bind many different sequences and discriminate between incompletely folded and folded clients. Most research into the origins of this "selective promiscuity" has relied on short peptides as substrates to dissect the binding, but much less is known about how Hsp70s bind full-length client proteins. Here, we connect detailed structural analyses of complexes between the Hsp70 (DnaK) substrate-binding domain (SBD) and peptides encompassing five potential binding sites in the precursor to alkaline phosphatase (proPhoA) with SBD binding to full-length unfolded proPhoA. Analysis of SBD complexes with proPhoA peptides by a combination of X-ray crystallography, methyl-transverse relaxation optimized spectroscopy (methyl-TROSY), and paramagnetic relaxation enhancement (PRE) NMR and chemical cross-linking experiments provided detailed descriptions of their binding modes. Importantly, many sequences populate multiple SBD binding modes, including both the canonical N to C orientation and a C to N orientation. The favored peptide binding mode optimizes substrate residue side-chain compatibility with the SBD binding pockets independent of backbone orientation. Relating these results to the binding of the SBD to full-length proPhoA, we observe that multiple chaperones may bind to the protein substrate, and the binding sites, well separated in the proPhoA sequence, behave independently. The hierarchy of chaperone binding to sites on the protein was generally consistent with the apparent binding affinities observed for the peptides corresponding to these sites. Functionally, these results reveal that Hsp70s "read" sequences without regard to the backbone direction and that both binding orientations must be considered in current predictive algorithms.

PubMed: 34625496
DOI: 10.1073/pnas.2016962118

Experimental method

X-RAY DIFFRACTION (2.4 Å)