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2wod

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[[Image:2wod.png|left|200px]]
 
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==Crystal Structure of the dinitrogenase reductase-activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP- ribsoyllysine==
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The line below this paragraph, containing "STRUCTURE_2wod", creates the "Structure Box" on the page.
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<StructureSection load='2wod' size='340' side='right'caption='[[2wod]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2wod]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"dicrospirillum_rubrum"_enderlein_1925 "dicrospirillum rubrum" enderlein 1925]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WOD FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZZC:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[[(2R,3R)-2,3-DIHYDROXY-4-OXO-PENTOXY]-OXIDO-PHOSPHORYL]+PHOSPHATE'>ZZC</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2woe|2woe]], [[2woc|2woc]]</div></td></tr>
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{{STRUCTURE_2wod| PDB=2wod | SCENE= }}
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2wod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wod OCA], [https://pdbe.org/2wod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wod RCSB], [https://www.ebi.ac.uk/pdbsum/2wod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wod ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wo/2wod_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2wod ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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ADP-ribosylation is a ubiquitous regulatory posttranslational modification involved in numerous key processes such as DNA repair, transcription, cell differentiation, apoptosis, and the pathogenic mechanism of certain bacterial toxins. Despite the importance of this reversible process, very little is known about the structure and mechanism of the hydrolases that catalyze removal of the ADP-ribose moiety. In the phototrophic bacterium Rhodospirillum rubrum, dinitrogenase reductase-activating glycohydrolase (DraG), a dimanganese enzyme that reversibly associates with the cell membrane, is a key player in the regulation of nitrogenase activity. DraG has long served as a model protein for ADP-ribosylhydrolases. Here, we present the crystal structure of DraG in the holo and ADP-ribose bound forms. We also present the structure of a reaction intermediate analogue and propose a detailed catalytic mechanism for protein de-ADP-ribosylation involving ring opening of the substrate ribose. In addition, the particular manganese coordination in DraG suggests a rationale for the enzyme's preference for manganese over magnesium, although not requiring a redox active metal for the reaction.
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===CRYSTAL STRUCTURE OF THE DINITROGENASE REDUCTASE-ACTIVATING GLYCOHYDROLASE (DRAG) FROM RHODOSPIRILLUM RUBRUM IN COMPLEX WITH ADP-RIBSOYLLYSINE===
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Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG.,Berthold CL, Wang H, Nordlund S, Hogbom M Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14247-52. Epub 2009 Aug 12. PMID:19706507<ref>PMID:19706507</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19706507}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2wod" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19706507 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19706507}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Dicrospirillum rubrum enderlein 1925]]
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[[2wod]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOD OCA].
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[[Category: Large Structures]]
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[[Category: Berthold, C L]]
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==Reference==
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[[Category: Hogbom, M]]
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<ref group="xtra">PMID:019706507</ref><references group="xtra"/>
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[[Category: Nordlund, S]]
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[[Category: Rhodospirillum rubrum]]
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[[Category: Wang, H]]
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[[Category: Berthold, C L.]]
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[[Category: Hogbom, M.]]
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[[Category: Nordlund, S.]]
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[[Category: Wang, H.]]
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[[Category: Adp-ribosylglycohydrolase]]
[[Category: Adp-ribosylglycohydrolase]]
[[Category: Dimanganese-dependent]]
[[Category: Dimanganese-dependent]]

Current revision

Crystal Structure of the dinitrogenase reductase-activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP- ribsoyllysine

PDB ID 2wod

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