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| | <StructureSection load='5c8l' size='340' side='right'caption='[[5c8l]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='5c8l' size='340' side='right'caption='[[5c8l]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5c8l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bdeba Bdeba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C8L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C8L FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5c8l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bdellovibrio_bacteriovorus_HD100 Bdellovibrio bacteriovorus HD100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C8L FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5c7q|5c7q]], [[5c7t|5c7t]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nudF, Bd3179 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264462 BDEBA])</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=5c8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c8l OCA], [https://pdbe.org/5c8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c8l RCSB], [https://www.ebi.ac.uk/pdbsum/5c8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c8l ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] </span></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=5c8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c8l OCA], [http://pdbe.org/5c8l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c8l RCSB], [http://www.ebi.ac.uk/pdbsum/5c8l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c8l ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q6MIH8_BDEBA Q6MIH8_BDEBA] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: ADP-ribose diphosphatase]] | + | [[Category: Bdellovibrio bacteriovorus HD100]] |
| - | [[Category: Bdeba]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Amzel, L M]] | + | [[Category: Amzel LM]] |
| - | [[Category: Gabelli, S B]] | + | [[Category: Gabelli SB]] |
| - | [[Category: Pena, A H.de la]]
| + | [[Category: Suarez A]] |
| - | [[Category: Suarez, A]] | + | [[Category: De la Pena AH]] |
| - | [[Category: Hydrolase]] | + | |
| - | [[Category: Nudix]]
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| Structural highlights
Function
Q6MIH8_BDEBA
Publication Abstract from PubMed
Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 -- a Nudix hydrolase from Bdellovibrio bacteriovorus-that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 A Calpha RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the alpha-beta-alpha NDPSase fold differentiates NDPSases from ADPRases.
Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.,de la Pena AH, Suarez A, Duong-Ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB PLoS One. 2015 Nov 2;10(11):e0141716. doi: 10.1371/journal.pone.0141716., eCollection 2015. PMID:26524597[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ de la Pena AH, Suarez A, Duong-Ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB. Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus. PLoS One. 2015 Nov 2;10(11):e0141716. doi: 10.1371/journal.pone.0141716., eCollection 2015. PMID:26524597 doi:http://dx.doi.org/10.1371/journal.pone.0141716
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