2d0p: Difference between revisions

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New page: left|200px<br /><applet load="2d0p" size="350" color="white" frame="true" align="right" spinBox="true" caption="2d0p, resolution 3.00Å" /> '''Strcuture of diol de...
 
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[[Image:2d0p.gif|left|200px]]<br /><applet load="2d0p" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2d0p, resolution 3.00&Aring;" />
'''Strcuture of diol dehydratase-reactivating factor in nucleotide free form'''<br />


==Overview==
==Structure of diol dehydratase-reactivating factor in nucleotide free form==
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.
<StructureSection load='2d0p' size='340' side='right'caption='[[2d0p]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<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>
2D0P is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0P OCA].  
</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='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>
==Reference==
<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>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16338403 16338403]
</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 ==
[[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/d0/2d0p_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=2d0p ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Klebsiella oxytoca]]
[[Category: Klebsiella oxytoca]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Hieda, N.]]
[[Category: Hieda N]]
[[Category: Higuchi, Y.]]
[[Category: Higuchi Y]]
[[Category: Mori, K.]]
[[Category: Mori K]]
[[Category: Shibata, N.]]
[[Category: Shibata N]]
[[Category: Toraya, T.]]
[[Category: Toraya T]]
[[Category: Yamanishi, M.]]
[[Category: Yamanishi M]]
[[Category: CA]]
[[Category: SO4]]
[[Category: chaperone]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 18:52:27 2008''

Latest revision as of 13:45, 13 March 2024

Structure of diol dehydratase-reactivating factor in nucleotide free form

2d0p, resolution 3.00Å

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