3x0s: Difference between revisions

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-'''Unreleased structure'''
-The entry 3x0s is ON HOLD
+==ADP ribose pyrophosphatase from Thermus thermophilus HB8 in E'-state at reaction time of 50 min==
+<StructureSection load='3x0s' size='340' side='right'caption='[[3x0s]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3x0s]] 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=3X0S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X0S FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.1&#8491;</td></tr>
+<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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3x0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x0s OCA], [https://pdbe.org/3x0s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x0s RCSB], [https://www.ebi.ac.uk/pdbsum/3x0s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x0s ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5SKW5_THET8 Q5SKW5_THET8]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-Authors: Furuike Y., Akita Y., Miyahara I., Kamiya N.
+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>
-Description: ADP ribose pyrophosphatase from Thermus thermophilus HB8 in E'-state at reaction time of 50 min
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3x0s" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[ADP-ribose pyrophosphatase 3D structures|ADP-ribose pyrophosphatase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Thermus thermophilus HB8]]
+[[Category: Akita Y]]
+[[Category: Furuike Y]]
+[[Category: Kamiya N]]
+[[Category: Miyahara I]]