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==Crystal structure of the substrate binding domain of E.coli DnaK in complex with the designer peptide NRLILTG==
==Crystal structure of the substrate binding domain of E.coli DnaK in complex with the designer peptide NRLILTG==
<StructureSection load='4ezy' size='340' side='right' caption='[[4ezy]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
<StructureSection load='4ezy' size='340' side='right'caption='[[4ezy]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4ezy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EZY FirstGlance]. <br>
<table><tr><td colspan='2'>[[4ezy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EZY FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dkx|1dkx]], [[1dky|1dky]], [[1dkz|1dkz]], [[3dpo|3dpo]], [[3dpp|3dpp]], [[3dpq|3dpq]], [[3qnj|3qnj]], [[4e81|4e81]], [[4ezn|4ezn]], [[4ezo|4ezo]], [[4ezp|4ezp]], [[4ezq|4ezq]], [[4ezr|4ezr]], [[4ezs|4ezs]], [[4ezt|4ezt]], [[4ezu|4ezu]], [[4ezv|4ezv]], [[4ezw|4ezw]], [[4ezx|4ezx]], [[4ezz|4ezz]], [[4f00|4f00]], [[4f01|4f01]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0014, dnaK, groP, grpF, JW0013, seg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ezy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ezy OCA], [https://pdbe.org/4ezy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ezy RCSB], [https://www.ebi.ac.uk/pdbsum/4ezy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ezy ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ezy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ezy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ezy RCSB], [http://www.ebi.ac.uk/pdbsum/4ezy PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/DNAK_ECOLI DNAK_ECOLI]] Plays an essential role in the initiation of phage lambda DNA replication, where it acts in an ATP-dependent fashion with the DnaJ protein to release lambda O and P proteins from the preprimosomal complex. DnaK is also involved in chromosomal DNA replication, possibly through an analogous interaction with the DnaA protein. Also participates actively in the response to hyperosmotic shock.[HAMAP-Rule:MF_00332]  
[https://www.uniprot.org/uniprot/DNAK_ECOLI DNAK_ECOLI] Plays an essential role in the initiation of phage lambda DNA replication, where it acts in an ATP-dependent fashion with the DnaJ protein to release lambda O and P proteins from the preprimosomal complex. DnaK is also involved in chromosomal DNA replication, possibly through an analogous interaction with the DnaA protein. Also participates actively in the response to hyperosmotic shock.[HAMAP-Rule:MF_00332]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Hsp70 chaperones have been implicated in assisting protein folding of newly synthesized polypeptide chains, refolding of misfolded proteins, and protein trafficking. For these functions, the chaperones need to exhibit a significant promiscuity in binding to different sequences of hydrophobic peptide stretches. To characterize the structural basis of sequence specificity and flexibility of the Escherichia coli Hsp70 chaperone DnaK, we have analyzed crystal structures of the substrate binding domain of the protein in complex with artificially designed peptides as well as small proline-rich antimicrobial peptides. Proline-rich antimicrobial peptides from mammals and insects were identified to target DnaK after cell penetration. Interestingly, the complex crystal structures reveal two different peptide binding modes. The peptides can bind either in a forward or in a reverse direction to the conventional substrate binding cleft of DnaK in an extended conformation. Superposition of the two binding modes shows a remarkable similarity in the side-chain orientations and hydrogen-bonding pattern despite the reversed peptide orientation. The DnaK chaperone has evolved to bind peptides in both orientations in the substrate binding cleft with comparable energy without rearrangements of the protein. Optimal hydrophobic interactions with binding pockets -2 to 0 appear to be the main determinant for the orientation and sequence position of peptide binding.
 
Structural Studies on the Forward and Reverse Binding Modes of Peptides to the Chaperone DnaK.,Zahn M, Berthold N, Kieslich B, Knappe D, Hoffmann R, Strater N J Mol Biol. 2013 Apr 2. pii: S0022-2836(13)00208-8. doi:, 10.1016/j.jmb.2013.03.041. PMID:23562829<ref>PMID:23562829</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==See Also==
</div>
*[[Heat Shock Protein structures|Heat Shock Protein structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Escherichia coli k-12]]
[[Category: Escherichia coli K-12]]
[[Category: Straeter, N]]
[[Category: Large Structures]]
[[Category: Zahn, M]]
[[Category: Straeter N]]
[[Category: Chaperone]]
[[Category: Zahn M]]
[[Category: Peptide binding mode]]

Latest revision as of 14:07, 1 March 2024

Crystal structure of the substrate binding domain of E.coli DnaK in complex with the designer peptide NRLILTGCrystal structure of the substrate binding domain of E.coli DnaK in complex with the designer peptide NRLILTG

Structural highlights

4ezy is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.85Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DNAK_ECOLI Plays an essential role in the initiation of phage lambda DNA replication, where it acts in an ATP-dependent fashion with the DnaJ protein to release lambda O and P proteins from the preprimosomal complex. DnaK is also involved in chromosomal DNA replication, possibly through an analogous interaction with the DnaA protein. Also participates actively in the response to hyperosmotic shock.[HAMAP-Rule:MF_00332]

See Also

4ezy, resolution 1.85Å

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