5c7q

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<StructureSection load='5c7q' size='340' side='right'caption='[[5c7q]], [[Resolution|resolution]] 1.52&Aring;' scene=''>
<StructureSection load='5c7q' size='340' side='right'caption='[[5c7q]], [[Resolution|resolution]] 1.52&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5c7q]] 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=5C7Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C7Q FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5c7q]] 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=5C7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C7Q FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.52&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5c7t|5c7t]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<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>
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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=5c7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c7q OCA], [https://pdbe.org/5c7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c7q RCSB], [https://www.ebi.ac.uk/pdbsum/5c7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c7q ProSAT]</span></td></tr>
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<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>
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<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=5c7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c7q OCA], [http://pdbe.org/5c7q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c7q RCSB], [http://www.ebi.ac.uk/pdbsum/5c7q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c7q ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q6MIH8_BDEBA Q6MIH8_BDEBA]
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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.
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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<ref>PMID:26524597</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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<div class="pdbe-citations 5c7q" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: ADP-ribose diphosphatase]]
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[[Category: Bdellovibrio bacteriovorus HD100]]
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[[Category: Bdeba]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Amzel, L M]]
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[[Category: Amzel LM]]
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[[Category: Gabelli, S B]]
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[[Category: Gabelli SB]]
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[[Category: Pena, A H.de la]]
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[[Category: Suarez A]]
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[[Category: Suarez, A]]
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[[Category: De la Pena AH]]
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[[Category: Hydrolase]]
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[[Category: Nudix]]
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Current revision

Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase

PDB ID 5c7q

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