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4lja

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Revision as of 11:04, 14 December 2022

ClpB NBD2 R621Q from T. thermophilus in complex with AMPPCP and guanidinium chloride

Structural highlights

4lja is a 1 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CLPB_THET8 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]

Publication Abstract from PubMed

ATPases of the AAA+ superfamily are large oligomeric molecular machines that remodel their substrates by converting the energy from ATP hydrolysis into mechanical force. This study focuses on the molecular chaperone ClpB, the bacterial homologue of Hsp104, which reactivates aggregated proteins under cellular stress conditions. Based on high-resolution crystal structures in different nucleotide states, mutational analysis and nucleotide-binding kinetics experiments, the ATPase cycle of the C-terminal nucleotide-binding domain (NBD2), one of the motor subunits of this AAA+ disaggregation machine, is dissected mechanistically. The results provide insights into nucleotide sensing, explaining how the conserved sensor 2 motif contributes to the discrimination between ADP and ATP binding. Furthermore, the role of a conserved active-site arginine (Arg621), which controls binding of the essential Mg2+ ion, is described. Finally, a hypothesis is presented as to how the ATPase activity is regulated by a conformational switch that involves the essential Walker A lysine. In the proposed model, an unusual side-chain conformation of this highly conserved residue stabilizes a catalytically inactive state, thereby avoiding unnecessary ATP hydrolysis.

Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor.,Zeymer C, Barends TR, Werbeck ND, Schlichting I, Reinstein J Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):582-95. doi:, 10.1107/S1399004713030629. Epub 2014 Jan 31. PMID:24531492^[2]

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

References

↑ Motohashi K, Watanabe Y, Yohda M, Yoshida M. Heat-inactivated proteins are rescued by the DnaK.J-GrpE set and ClpB chaperones. Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7184-9. PMID:10377389
↑ Zeymer C, Barends TR, Werbeck ND, Schlichting I, Reinstein J. Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor. Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):582-95. doi:, 10.1107/S1399004713030629. Epub 2014 Jan 31. PMID:24531492 doi:http://dx.doi.org/10.1107/S1399004713030629

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/4lja"

@@ Line 1: / Line 1: @@
 ==ClpB NBD2 R621Q from T. thermophilus in complex with AMPPCP and guanidinium chloride==
-<StructureSection load='4lja' size='340' side='right' caption='[[4lja]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='4lja' size='340' side='right'caption='[[4lja]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4lja]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LJA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4lja]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LJA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lj4|4lj4]], [[4lj5|4lj5]], [[4lj6|4lj6]], [[4lj7|4lj7]], [[4lj8|4lj8]], [[4lj9|4lj9]]</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=4lja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lja OCA], [https://pdbe.org/4lja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lja RCSB], [https://www.ebi.ac.uk/pdbsum/4lja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lja ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">clpB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=4lja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lja OCA], [http://pdbe.org/4lja PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lja RCSB], [http://www.ebi.ac.uk/pdbsum/4lja PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lja ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CLPB_THET8 CLPB_THET8]] 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:10377389</ref>
+[https://www.uniprot.org/uniprot/CLPB_THET8 CLPB_THET8] 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:10377389</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 18: @@
 </div>
 <div class="pdbe-citations 4lja" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Heat Shock Protein structures|Heat Shock Protein structures]]
+*[[3D structures of ClpB|3D structures of ClpB]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Thet8]]
+[[Category: Large Structures]]
-[[Category: Barends, T R.M]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Reinstein, J]]
+[[Category: Barends TRM]]
-[[Category: Schlichting, I]]
+[[Category: Reinstein J]]
-[[Category: Werbeck, N D]]
+[[Category: Schlichting I]]
-[[Category: Zeymer, C]]
+[[Category: Werbeck ND]]
-[[Category: Aaa+ protein]]
+[[Category: Zeymer C]]
-[[Category: Chaperone]]
-[[Category: Disaggregase]]
-[[Category: Molecular chaperone]]
-[[Category: Nucleotide binding domain]]

4lja

From Proteopedia

Revision as of 11:04, 14 December 2022

ClpB NBD2 R621Q from T. thermophilus in complex with AMPPCP and guanidinium chloride

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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