1r6b: Difference between revisions

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-[[Image:1r6b.jpg|left|200px]]
- {{Structure
+==High resolution crystal structure of ClpA==
-|PDB= 1r6b |SIZE=350|CAPTION= <scene name='initialview01'>1r6b</scene>, resolution 2.25&Aring;
+<StructureSection load='1r6b' size='340' side='right'caption='[[1r6b]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
+<table><tr><td colspan='2'>[[1r6b]] 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=1R6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R6B FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r6b OCA], [https://pdbe.org/1r6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r6b RCSB], [https://www.ebi.ac.uk/pdbsum/1r6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r6b ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1k6k|1K6K]], [[1ksf|1KSF]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r6b OCA], [http://www.ebi.ac.uk/pdbsum/1r6b PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1r6b RCSB]</span>
+== Function ==
-}}
+[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.
+== 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/r6/1r6b_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=1r6b ConSurf].
+<div style="clear:both"></div>
-'''High resolution crystal structure of ClpA'''
+==See Also==
+*[[Heat Shock Protein structures|Heat Shock Protein structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Escherichia coli ClpA, an Hsp100/Clp chaperone and an integral component of the ATP-dependent ClpAP protease, participates in the dissolution and degradation of regulatory proteins and protein aggregates. ClpA consists of three functional domains: an N-terminal domain and two ATPase domains, D1 and D2. The N-domain is attached to D1 by a mobile linker and is made up of two tightly bound, identically folded alpha-helical bundles related by a pseudo 2-fold symmetry. Between the halves of the pseudo-dimer is a large flexible acidic loop that becomes better ordered upon binding of the small adaptor protein, ClpS. We have identified a number of structural features in the N-domain, including a Zn(++) binding motif, several interfaces for binding to ClpS, and a prominent hydrophobic surface area that binds peptides in different configurations. These structural motifs may contribute to binding of protein or peptide substrates with weak affinity and broad specificity. Kinetic studies comparing wild-type ClpA to a mutant ClpA with its N-domain deleted show that the N-domains contribute to the binding of a non-specific protein substrate but not of a folded substrate with the specific SsrA recognition tag. A functional model is proposed in which the N-domains in ClpA function as tentacles to weakly hold on to proteins thereby enhancing local substrate concentration.
-==About this Structure==
-R6B is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R6B OCA].
-==Reference==
-Crystallographic investigation of peptide binding sites in the N-domain of the ClpA chaperone., Xia D, Esser L, Singh SK, Guo F, Maurizi MR, J Struct Biol. 2004 Apr-May;146(1-2):166-79. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15037248 15037248]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Esser, L.]]
+[[Category: Esser L]]
-[[Category: Guo, F.]]
+[[Category: Guo F]]
-[[Category: Maurizi, M R.]]
+[[Category: Maurizi MR]]
-[[Category: Singh, S K.]]
+[[Category: Singh SK]]
-[[Category: Xia, D.]]
+[[Category: Xia D]]
-[[Category: aaa+]]
-[[Category: binding mechanism]]
-[[Category: clpa]]
-[[Category: clp]]
-[[Category: crystal]]
-[[Category: n-terminal domain]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:23:51 2008''