2d0p: Difference between revisions

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==Strcuture of diol dehydratase-reactivating factor in nucleotide free form==
 
<StructureSection load='2d0p' size='340' side='right' caption='[[2d0p]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
==Structure of diol dehydratase-reactivating factor in nucleotide free form==
<StructureSection load='2d0p' size='340' side='right'caption='[[2d0p]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2d0p]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D0P FirstGlance]. <br>
<table><tr><td colspan='2'>[[2d0p]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D0P FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <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]] 3&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2d0o|2d0o]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d0p RCSB], [http://www.ebi.ac.uk/pdbsum/2d0p PDBsum]</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=2d0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0p OCA], [https://pdbe.org/2d0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d0p RCSB], [https://www.ebi.ac.uk/pdbsum/2d0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0p ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DDRA_KLEOK DDRA_KLEOK] Large subunit of the diol dehydratase-reactivating factor (DDR), which reactivates suicidally inhibited adenosylcobalamin-dependent diol dehydratase (DD, pddA, pddB, pddC). DDR acts as a chaperone, reactivating inactivated DD holoenzyme in the presence of ATP, Mg(2+) and free adenosylcobalamin (AdoCbl), by mediating the exchange of the tightly bound damaged cofactor AdoCbl for a free intact one (PubMed:10529189, PubMed:9405397, PubMed:9920879, PubMed:17916188, PubMed:18586770, PubMed:21040475). Reactivation takes place in two steps: ADP-dependent cobalamin release, then ATP-dependent dissociation of the DD apoenzyme-DDR complex. DDR has weak ATPase activity which is required for DD reactivation (PubMed:10529189, PubMed:17916188, PubMed:21040475). This subunit contains the adenosine nucleotide binding site (PubMed:16338403). Activates glycerol-inactivated, O2-inactivated holoenzyme and inactivated enzyme-cyanocobalamin complex (PubMed:9920879). Also reactivates glycerol-inactivated hologlycerol dehydratase, a DD isozyme (PubMed:17916188).<ref>PMID:10529189</ref> <ref>PMID:16338403</ref> <ref>PMID:17916188</ref> <ref>PMID:18586770</ref> <ref>PMID:21040475</ref> <ref>PMID:9405397</ref> <ref>PMID:9920879</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/2d0p_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/2d0p_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata ConSurf].
</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=2d0p ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structures of ADP bound and nucleotide-free forms of molecular chaperone-like diol dehydratase-reactivating factor (DDR) were determined at 2.0 and 3.0 A, respectively. DDR exists as a dimer of heterodimer (alphabeta)2. The alpha subunit has four domains: ATPase domain, swiveling domain, linker domain, and insert domain. The beta subunit, composed of a single domain, has a similar fold to the beta subunit of diol dehydratase (DD). The binding of an ADP molecule to the nucleotide binding site of DDR causes a marked conformational change of the ATPase domain of the alpha subunit, which would weaken the interactions between the DDR alpha and beta subunits and make the displacement of the DDR beta subunit by DD through the beta subunit possible. The binding of the DD beta subunit to the DDR alpha subunit induces steric repulsion between the DDR alpha and DD alpha subunits that would lead to the release of a damaged cofactor from inactivated holoDD.
Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray structures of diol dehydratase-reactivating factor.,Shibata N, Mori K, Hieda N, Higuchi Y, Yamanishi M, Toraya T Structure. 2005 Dec;13(12):1745-54. PMID:16338403<ref>PMID:16338403</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Klebsiella oxytoca]]
[[Category: Klebsiella oxytoca]]
[[Category: Hieda, N]]
[[Category: Large Structures]]
[[Category: Higuchi, Y]]
[[Category: Hieda N]]
[[Category: Mori, K]]
[[Category: Higuchi Y]]
[[Category: Shibata, N]]
[[Category: Mori K]]
[[Category: Toraya, T]]
[[Category: Shibata N]]
[[Category: Yamanishi, M]]
[[Category: Toraya T]]
[[Category: Chaperone]]
[[Category: Yamanishi M]]
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