5c7t: Difference between revisions

Revision as of 06:23, 7 June 2023

Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase in complex with ADP-ribose

Structural highlights

5c7t is a 2 chain structure with sequence from Bdellovibrio bacteriovorus HD100. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	APR, GOL, PEG, PG0, PGE, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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:https://dx.doi.org/10.1371/journal.pone.0141716

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OCA

[1] 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:https://dx.doi.org/10.1371/journal.pone.0141716

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='5c7t' size='340' side='right'caption='[[5c7t]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5c7t]] 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=5C7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C7T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5c7t]] 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=5C7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C7T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <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>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5c7q|5c7q]]</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=5c7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c7t OCA], [https://pdbe.org/5c7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c7t RCSB], [https://www.ebi.ac.uk/pdbsum/5c7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c7t ProSAT]</span></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='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=5c7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c7t OCA], [http://pdbe.org/5c7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c7t RCSB], [http://www.ebi.ac.uk/pdbsum/5c7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c7t ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q6MIH8_BDEBA Q6MIH8_BDEBA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: ADP-ribose diphosphatase]]
+[[Category: Bdellovibrio bacteriovorus HD100]]
-[[Category: Bdeba]]
 [[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]]

5c7t: Difference between revisions

Revision as of 06:23, 7 June 2023

Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase in complex with ADP-ribose

Structural highlights

Function

Publication Abstract from PubMed

References

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