7N6K

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Selective promiscuity in the binding of E. coli Hsp70 to an unfolded protein.

Clerico, E.M.Pozhidaeva, A.K.Jansen, R.M.Ozden, C.Tilitsky, J.M.Gierasch, L.M.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2016962118
  • Primary Citation of Related Structures:  
    7JMM, 7JN8, 7JN9, 7JNE, 7N6J, 7N6K, 7N6L, 7N6M

  • 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 Escherichia coli Hsp70 (DnaK) substrate-binding domain (SBD) and peptides encompassing five potential binding sites in the precursor to E. coli 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.


  • Organizational Affiliation

    Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone protein DnaK219Escherichia coli K-12Mutation(s): 0 
Gene Names: dnaKgroPgrpFsegb0014JW0013
UniProt
Find proteins for P0A6Y8 (Escherichia coli (strain K12))
Explore P0A6Y8 
Go to UniProtKB:  P0A6Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6Y8
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Alkaline phosphatase peptide10Escherichia coli K-12Mutation(s): 3 
EC: 3.1.3.1
UniProt
Find proteins for P00634 (Escherichia coli (strain K12))
Explore P00634 
Go to UniProtKB:  P00634
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00634
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.213 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.763α = 90
b = 94.773β = 90
c = 117.109γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5 R35 GM118161

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 2.0: 2021-07-14
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references
  • Version 2.2: 2023-10-18
    Changes: Data collection, Refinement description