3x0s: Difference between revisions
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==ADP ribose pyrophosphatase from Thermus thermophilus HB8 in E'-state at reaction time of 50 min== | ==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]] 1.10Å' scene=''> | <StructureSection load='3x0s' size='340' side='right'caption='[[3x0s]], [[Resolution|resolution]] 1.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3x0s]] is a 1 chain structure with sequence from [ | <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=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.1Å</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=' | <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> | ||
< | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q5SKW5_THET8 Q5SKW5_THET8] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[ADP-ribose pyrophosphatase|ADP-ribose pyrophosphatase]] | *[[ADP-ribose pyrophosphatase 3D structures|ADP-ribose pyrophosphatase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Thermus thermophilus HB8]] | ||
[[Category: Akita | [[Category: Akita Y]] | ||
[[Category: Furuike | [[Category: Furuike Y]] | ||
[[Category: Kamiya | [[Category: Kamiya N]] | ||
[[Category: Miyahara | [[Category: Miyahara I]] | ||
Latest revision as of 16:38, 8 November 2023
ADP ribose pyrophosphatase from Thermus thermophilus HB8 in E'-state at reaction time of 50 minADP ribose pyrophosphatase from Thermus thermophilus HB8 in E'-state at reaction time of 50 min
Structural highlights
FunctionPublication Abstract from PubMedAdenosine 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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