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5ofo

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Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state, bound to the model substrate casein

5ofo, resolution 4.60Å

Structural highlights

5ofo is a 6 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:	Electron Microscopy, Resolution 4.6Å
Ligands:
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CLPB_ECOLI Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.^[1] ^[2] ^[3] CLPA_ECOLI ATP-dependent specificity component of the ClpAP protease. It directs the protease to specific substrates. It has unfoldase activity. The primary function of the ClpA-ClpP complex appears to be the degradation of unfolded or abnormal proteins.

Publication Abstract from PubMed

Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including Escherichia coli ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through the central pore of tandem adenosine triphosphatase (ATPase) rings. To visualize protein disaggregation, we determined cryo-electron microscopy structures of inactive and substrate-bound ClpB in the presence of adenosine 5'-O-(3-thiotriphosphate), revealing closed AAA+ rings with a pronounced seam. In the substrate-free state, a marked gradient of resolution, likely corresponding to mobility, spans across the AAA+ rings with a dynamic hotspot at the seam. On the seam side, the coiled-coil regulatory domains are locked in a horizontal, inactive orientation. On the opposite side, the regulatory domains are accessible for Hsp70 binding, substrate targeting, and activation. In the presence of the model substrate casein, the polypeptide threads through the entire pore channel and increased nucleotide occupancy correlates with higher ATPase activity. Substrate-induced domain displacements indicate a pathway of regulated substrate transfer from Hsp70 to the ClpB pore, inside which a spiral of loops contacts the substrate. The seam pore loops undergo marked displacements, along with ordering of the regulatory domains. These asymmetric movements suggest a mechanism for ATPase activation and substrate threading during disaggregation.

Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase.,Deville C, Carroni M, Franke KB, Topf M, Bukau B, Mogk A, Saibil HR Sci Adv. 2017 Aug 4;3(8):e1701726. doi: 10.1126/sciadv.1701726. eCollection 2017 , Aug. PMID:28798962^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Barnett ME, Zolkiewska A, Zolkiewski M. Structure and activity of ClpB from Escherichia coli. Role of the amino-and -carboxyl-terminal domains. J Biol Chem. 2000 Dec 1;275(48):37565-71. PMID:10982797 doi:http://dx.doi.org/10.1074/jbc.M005211200
↑ Mogk A, Schlieker C, Strub C, Rist W, Weibezahn J, Bukau B. Roles of individual domains and conserved motifs of the AAA+ chaperone ClpB in oligomerization, ATP hydrolysis, and chaperone activity. J Biol Chem. 2003 May 16;278(20):17615-24. Epub 2003 Mar 6. PMID:12624113 doi:http://dx.doi.org/10.1074/jbc.M209686200
↑ Kedzierska S, Akoev V, Barnett ME, Zolkiewski M. Structure and function of the middle domain of ClpB from Escherichia coli. Biochemistry. 2003 Dec 9;42(48):14242-8. PMID:14640692 doi:http://dx.doi.org/10.1021/bi035573d
↑ Deville C, Carroni M, Franke KB, Topf M, Bukau B, Mogk A, Saibil HR. Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase. Sci Adv. 2017 Aug 4;3(8):e1701726. doi: 10.1126/sciadv.1701726. eCollection 2017 , Aug. PMID:28798962 doi:http://dx.doi.org/10.1126/sciadv.1701726

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ofo"

@@ Line 1: / Line 1: @@
 ==Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state, bound to the model substrate casein==
-<StructureSection load='5ofo' size='340' side='right' caption='[[5ofo]], [[Resolution|resolution]] 4.60&Aring;' scene=''>
+<SX load='5ofo' size='340' side='right' viewer='molstar' caption='[[5ofo]], [[Resolution|resolution]] 4.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ofo]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OFO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ofo]] is a 6 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=5OFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OFO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5og1|5og1]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></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=5ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofo OCA], [http://pdbe.org/5ofo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ofo RCSB], [http://www.ebi.ac.uk/pdbsum/5ofo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofo ProSAT]</span></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=5ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofo OCA], [https://pdbe.org/5ofo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ofo RCSB], [https://www.ebi.ac.uk/pdbsum/5ofo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CLPB_ECOLI CLPB_ECOLI]] Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.<ref>PMID:10982797</ref> <ref>PMID:12624113</ref> <ref>PMID:14640692</ref>
+[https://www.uniprot.org/uniprot/CLPB_ECOLI CLPB_ECOLI] Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.<ref>PMID:10982797</ref> <ref>PMID:12624113</ref> <ref>PMID:14640692</ref> [https://www.uniprot.org/uniprot/CLPA_ECOLI CLPA_ECOLI] ATP-dependent specificity component of the ClpAP protease. It directs the protease to specific substrates. It has unfoldase activity. The primary function of the ClpA-ClpP complex appears to be the degradation of unfolded or abnormal proteins.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5ofo" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Heat Shock Protein structures|Heat Shock Protein structures]]
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Bukau, B]]
+[[Category: Escherichia coli K-12]]
-[[Category: Carroni, M]]
+[[Category: Large Structures]]
-[[Category: Deville, C]]
+[[Category: Bukau B]]
-[[Category: Franke, K B]]
+[[Category: Carroni M]]
-[[Category: Mogk, A]]
+[[Category: Deville C]]
-[[Category: Saibil, H R]]
+[[Category: Franke KB]]
-[[Category: Topf, M]]
+[[Category: Mogk A]]
-[[Category: Aaa]]
+[[Category: Saibil HR]]
-[[Category: Chaperone]]
+[[Category: Topf M]]
-[[Category: Clpb]]
-[[Category: Disaggregase]]

5ofo

From Proteopedia

Current revision

Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state, bound to the model substrate casein

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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