PDBsum entry 3dpp

Chaperone, peptide binding protein

PDB id: 3dpp

Contents

Protein chains

212 a.a. *

13 a.a. *

Ligands

LYS-LEU-TYR-ALC-LEU-PRO-ARG-PRO-THR

SO4

Waters ×309

* Residue conservation analysis

PDB id:

3dpp

Name:

Chaperone, peptide binding protein

Title:

Crystal structure of the substrate binding domain of e. Coli dnak in complex with a long pyrrhocoricin-derived inhibitor peptide (form a)

Structure:

Chaperone protein dnak. Chain: a, b. Fragment: substrate binding domain (unp residues 389 to 607). Synonym: heat shock protein 70, heat shock 70 kda protein, hsp70. Engineered: yes. Inhibitor peptide. Chain: c, d. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Gene: dnak, grop, grpf, seg, b0014, jw0013. Expressed in: escherichia coli. Synthetic: yes. Other_details: the peptide was pyrrhocoricin-derived.

Resolution:

2.50Å R-factor: 0.241 R-free: 0.316

Authors:

A.Roujeinikova

Key ref:

M.Liebscher and A.Roujeinikova (2009). Allosteric coupling between the lid and interdomain linker in DnaK revealed by inhibitor binding studies. J Bacteriol, 191, 1456-1462. PubMed id: 19103929

Date:

09-Jul-08 Release date: 10-Mar-09

Protein chains

P0A6Y8  (DNAK_ECOLI) -  Chaperone protein DnaK from Escherichia coli (strain K12)

Seq: 638 a.a.

Struc: 212 a.a.

Protein chain

P37362  (PYRRH_PYRAP) -  Pyrrhocoricin from Pyrrhocoris apterus

Seq: 20 a.a.

Struc: 13 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

J Bacteriol 191:1456-1462 (2009)

PubMed id: 19103929

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

M.Liebscher, A.Roujeinikova.

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.