2d0o

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:45, 13 March 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2d0o.gif|left|200px]]
 
-
<!--
+
==Structure of diol dehydratase-reactivating factor complexed with ADP and Mg2+==
-
The line below this paragraph, containing "STRUCTURE_2d0o", creates the "Structure Box" on the page.
+
<StructureSection load='2d0o' size='340' side='right'caption='[[2d0o]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2d0o]] 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=2D0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D0O FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</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&#8491;</td></tr>
-
-->
+
<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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_2d0o| PDB=2d0o | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0o OCA], [https://pdbe.org/2d0o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d0o RCSB], [https://www.ebi.ac.uk/pdbsum/2d0o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0o ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Strcuture of diol dehydratase-reactivating factor complexed with ADP and Mg2+'''
+
== 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 ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
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.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/2d0o_consurf.spt"</scriptWhenChecked>
-
2D0O is a [[Protein complex]] structure of sequences 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=2D0O OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
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://www.ncbi.nlm.nih.gov/pubmed/16338403 16338403]
+
</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=2d0o 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: Chaperone]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 23:28:47 2008''
+

Current revision

Structure of diol dehydratase-reactivating factor complexed with ADP and Mg2+

PDB ID 2d0o

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2d0o"
Personal tools