3DPP

Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form A)

• PDB DOI: https://doi.org/10.2210/pdb3DPP/pdb

• Classification: Chaperone, Peptide Binding Protein
• Organism(s): Escherichia coli K-12, Pyrrhocoris apterus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-09 Released: 2009-03-10 
• Deposition Author(s): Roujeinikova, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.316 
• R-Value Work: 0.237 
• R-Value Observed: 0.241 

Starting Model: experimental

Literature

Allosteric coupling between the lid and interdomain linker in DnaK revealed by inhibitor binding studies.

Liebscher, M., Roujeinikova, A.

(2009) J Bacteriol 191: 1456-1462

• PubMed: 19103929 
• DOI: https://doi.org/10.1128/JB.01131-08
• Primary Citation of Related Structures:  
  3DPO, 3DPP, 3DPQ


• PubMed Abstract: 
  

  The molecular chaperone DnaK assists protein folding and refolding, translocation across membranes, and regulation of the heat shock response. In Escherichia coli, the protein is a target for insect-derived antimicrobial peptides, pyrrhocoricins. We present here the X-ray crystallographic analysis of the E. coli DnaK substrate-binding domain in complex with pyrrhocoricin-derived peptide inhibitors. The structures show that pyrrhocoricins act as site-specific, dual-mode (competitive and allosteric) inhibitors, occupying the substrate-binding tunnel and disrupting the latch between the lid and the beta-sandwich. Our structural analysis revealed an allosteric coupling between the movements of the lid and the interdomain linker, identifying a previously unknown mechanism of the lid-mediated regulation of the chaperone cycle.

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Organizational Affiliation: 

Martin Luther University Halle-Wittenberg, Saale, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.67 kDa 
• Atom Count: 3,748 
• Modelled Residue Count: 448 
• Deposited Residue Count: 478 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein dnaK	A, B	219	Escherichia coli K-12	Mutation(s): 0  Gene Names: dnaK, groP, grpF, seg, b0014, JW0013
UniProt
Find proteins for P0A6Y8 (Escherichia coli (strain K12)) Explore P0A6Y8  Go to UniProtKB:  P0A6Y8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
inhibitor peptide	C, D	20	N/A	Mutation(s): 0
UniProt
Find proteins for P37362 (Pyrrhocoris apterus) Explore P37362  Go to UniProtKB:  P37362

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALC	C, D	L-PEPTIDE LINKING	C9 H17 N O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.316 
• R-Value Work: 0.237 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.87	α = 90
b = 159.12	β = 90
c = 44.79	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Roujeinikova, A.

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary