|
|
| (One intermediate revision not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='2woc' size='340' side='right'caption='[[2woc]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='2woc' size='340' side='right'caption='[[2woc]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2woc]] is a 3 chain structure with sequence from [http://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=2WOC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2WOC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2woc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WOC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WOC FirstGlance]. <br> |
| - | </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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2wod|2wod]], [[2woe|2woe]]</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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribosyl-[dinitrogen_reductase]_hydrolase ADP-ribosyl-[dinitrogen reductase] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.24 3.2.2.24] </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=2woc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woc OCA], [https://pdbe.org/2woc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2woc RCSB], [https://www.ebi.ac.uk/pdbsum/2woc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2woc ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2woc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2woc OCA], [http://pdbe.org/2woc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2woc RCSB], [http://www.ebi.ac.uk/pdbsum/2woc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2woc ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DRAG_RHORU DRAG_RHORU] Involved in the regulation of nitrogen fixation activity by the reversible ADP-ribosylation of one subunit of the homodimeric dinitrogenase reductase component of the nitrogenase enzyme complex. The ADP-ribosyltransferase (DraT) transfers the ADP-ribose group from NAD to dinitrogenase reductase. The ADP-ribose group is removed through the action of the ADP-ribosylglycohydrolase (DraG, this entry). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 32: |
Line 33: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Dicrospirillum rubrum enderlein 1925]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Berthold, C L]] | + | [[Category: Rhodospirillum rubrum]] |
| - | [[Category: Hogbom, M]] | + | [[Category: Berthold CL]] |
| - | [[Category: Nordlund, S]] | + | [[Category: Hogbom M]] |
| - | [[Category: Wang, H]] | + | [[Category: Nordlund S]] |
| - | [[Category: Adp-ribosylglycohydrolase]]
| + | [[Category: Wang H]] |
| - | [[Category: Dimanganese]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Mono-adp-ribosylhydrolase]]
| + | |
| - | [[Category: Nitrogen fixation]]
| + | |
| Structural highlights
Function
DRAG_RHORU Involved in the regulation of nitrogen fixation activity by the reversible ADP-ribosylation of one subunit of the homodimeric dinitrogenase reductase component of the nitrogenase enzyme complex. The ADP-ribosyltransferase (DraT) transfers the ADP-ribose group from NAD to dinitrogenase reductase. The ADP-ribose group is removed through the action of the ADP-ribosylglycohydrolase (DraG, this entry).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Berthold CL, Wang H, Nordlund S, Hogbom M. Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG. Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14247-52. Epub 2009 Aug 12. PMID:19706507
|
