1jbk: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="1jbk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jbk, resolution 1.8Å" /> '''Crystal Structure of ...
 
No edit summary
 
(17 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1jbk.jpg|left|200px]]<br /><applet load="1jbk" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1jbk, resolution 1.8&Aring;" />
'''Crystal Structure of the First Nucelotide Binding Domain of ClpB'''<br />


==Overview==
==Crystal Structure of the First Nucelotide Binding Domain of ClpB==
E. coli Hsp100 ClpB was recently identified as a critical part in a, multi-chaperone system to play important roles in protein folding, protein, transport and degradation in cell physiology. ClpB contains two, nucleotide-binding domains (NBD1 and NBD2) within their primary sequences., NBD1 and NBD2 of ClpB can be classified as members of the large ATPase, family known as ATPases associated with various cellular activities (AAA)., To investigate how ClpB performs its ATPase activities for its chaperone, activity, we have determined the crystal structure of ClpB, nucleotide-binding domain 1 (NBD1) by MAD method to 1.80 A resolution. The, NBD1 monomer structure contains one domain that comprises 11 alpha-helices, and six beta-strands. When compared with the typical AAA structures, the, crystal structure of ClpB NBD1 reveals a novel AAA topology with, six-stranded beta-sheet as its core. The N-terminal portion of NBD1, structure has an extra beta-strand flanked by two extra alpha-helices that, are not present in other AAA structures. Moreover, the NBD1 structure does, not have a C-terminal helical domain as other AAA proteins do. No, nucleotide molecule is bound with ClpB NBD1 in the crystal structure, probably due to lack of the C-terminal helix domain in the structure., Isothermal titration calorimetry (ITC) studies of ClpB NBD1 and other ClpB, deletion mutations showed that either ClpB NBD1 or NBD2 alone does not, bind to nucleotides. However, ClpB NBD2 combined with ClpB C-terminal, fragment can interact with one ADP or ATP molecule. ITC data also, indicated that full-length ClpB could bind two ADP molecules or one ATP, analogue ATPgammaS molecule. Further ATPase activity studies of ClpB and, ClpB deletion mutants showed that only wild-type ClpB have ATPase, activity. None of ClpB NBD1 domain, NBD2 domain and NBD2 with C-terminal, fragment has detectable ATPase activities. On the basis of our structural, and mutagenesis data, we proposed a "see-saw" model to illustrate the, mechanisms by which ClpB performs its ATPase activities for chaperone, functions.
<StructureSection load='1jbk' size='340' side='right'caption='[[1jbk]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1jbk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JBK FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1jbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jbk OCA], [https://pdbe.org/1jbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jbk RCSB], [https://www.ebi.ac.uk/pdbsum/1jbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jbk ProSAT]</span></td></tr>
</table>
== Function ==
[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>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jb/1jbk_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jbk ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1JBK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JBK OCA].
*[[Heat Shock Protein structures|Heat Shock Protein structures]]
 
*[[3D structures of ClpB|3D structures of ClpB]]
==Reference==
== References ==
Crystal structure of E. coli Hsp100 ClpB nucleotide-binding domain 1 (NBD1) and mechanistic studies on ClpB ATPase activity., Li J, Sha B, J Mol Biol. 2002 May 10;318(4):1127-37. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12054807 12054807]
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Bingdong, S.]]
[[Category: Bingdong S]]
[[Category: Jingzhi, L.]]
[[Category: Jingzhi L]]
[[Category: MG]]
[[Category: beta barrel]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:04:55 2007''

Latest revision as of 10:38, 7 February 2024

Crystal Structure of the First Nucelotide Binding Domain of ClpBCrystal Structure of the First Nucelotide Binding Domain of ClpB

Structural highlights

1jbk is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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

1jbk, resolution 1.80Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1jbk&oldid=4045216"