3x0k

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Current revision (08:48, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3x0k' size='340' side='right'caption='[[3x0k]], [[Resolution|resolution]] 0.97&Aring;' scene=''>
<StructureSection load='3x0k' size='340' side='right'caption='[[3x0k]], [[Resolution|resolution]] 0.97&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3x0k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X0K FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3x0k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X0K FirstGlance]. <br>
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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=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 0.97&#8491;</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;'>[[3x0i|3x0i]], [[3x0j|3x0j]], [[3x0l|3x0l]], [[3x0m|3x0m]], [[3x0n|3x0n]], [[3x0o|3x0o]], [[3x0p|3x0p]], [[3x0q|3x0q]], [[3x0r|3x0r]], [[3x0s|3x0s]]</div></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=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHA0528 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
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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-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x0k OCA], [https://pdbe.org/3x0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x0k RCSB], [https://www.ebi.ac.uk/pdbsum/3x0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x0k ProSAT]</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=3x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x0k OCA], [https://pdbe.org/3x0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x0k RCSB], [https://www.ebi.ac.uk/pdbsum/3x0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x0k ProSAT]</span></td></tr>
</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/Q5SKW5_THET8 Q5SKW5_THET8]
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Adenosine diphosphate ribose pyrophosphatase (ADPRase), a member of the Nudix family proteins, catalyzes the metal-induced and concerted general acid-base hydrolysis of ADP ribose (ADPR) into AMP and ribose-5'-phosphate (R5P). The ADPR-hydrolysis reaction of ADPRase from Thermus thermophilus HB8 (TtADPRase) requires divalent metal cations such as Mn(2+), Zn(2+), or Mg(2+) as cofactors. Here, we report the reaction pathway observed in the catalytic center of TtADPRase, based on cryo-trapping X-ray crystallography at atomic resolutions around 1.0 A using Mn(2+) as the reaction trigger, which was soaked into TtADPRase-ADPR binary complex crystals. Integrating 11 structures along the reaction timeline, five reaction states of TtADPRase were assigned, which were ADPRase alone (E), the ADPRase-ADPR binary complex (ES), two ADPRase-ADPR-Mn(2+) reaction intermediates (ESM, ESMM), and the postreaction state (E'). Two Mn(2+) ions were inserted consecutively into the catalytic center of the ES-state and ligated by Glu86 and Glu82, which are highly conserved among the Nudix family, in the ESM- and ESMM-states. The ADPR-hydrolysis reaction was characterized by electrostatic, proximity, and orientation effects, and by preferential binding for the transition state. A new reaction mechanism is proposed, which differs from previous ones suggested from structure analyses with nonhydrolyzable substrate analogues or point-mutated ADPRases.
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ADP-Ribose Pyrophosphatase Reaction in Crystalline State Conducted by Consecutive Binding of Two Manganese(II) Ions as Cofactors.,Furuike Y, Akita Y, Miyahara I, Kamiya N Biochemistry. 2016 Mar 29;55(12):1801-12. doi: 10.1021/acs.biochem.5b00886. Epub , 2016 Mar 16. PMID:26979298<ref>PMID:26979298</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 3x0k" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[ADP-ribose pyrophosphatase 3D structures|ADP-ribose pyrophosphatase 3D structures]]
*[[ADP-ribose pyrophosphatase 3D structures|ADP-ribose pyrophosphatase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: ADP-ribose diphosphatase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Thet8]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Akita, Y]]
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[[Category: Akita Y]]
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[[Category: Furuike, Y]]
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[[Category: Furuike Y]]
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[[Category: Kamiya, N]]
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[[Category: Kamiya N]]
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[[Category: Miyahara, I]]
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[[Category: Miyahara I]]
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[[Category: Adp ribose]]
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[[Category: Adp ribose hydrolase]]
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[[Category: Cytosol]]
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[[Category: Hydrolase]]
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[[Category: Nudix motif]]
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Current revision

ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ES-state at 0.97 angstrom resolution

PDB ID 3x0k

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