1v8i: Difference between revisions
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==Crystal Structure Analysis of the ADP-ribose pyrophosphatase== | ==Crystal Structure Analysis of the ADP-ribose pyrophosphatase== | ||
<StructureSection load='1v8i' size='340' side='right' caption='[[1v8i]], [[Resolution|resolution]] 1.76Å' scene=''> | <StructureSection load='1v8i' size='340' side='right' caption='[[1v8i]], [[Resolution|resolution]] 1.76Å' scene=''> | ||
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1v8l|1v8l]], [[1v8m|1v8m]], [[1v8n|1v8n]], [[1v8r|1v8r]], [[1v8s|1v8s]], [[1v8t|1v8t]], [[1v8u|1v8u]], [[1v8v|1v8v]], [[1v8w|1v8w]], [[1v8y|1v8y]]</td></tr> | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1v8l|1v8l]], [[1v8m|1v8m]], [[1v8n|1v8n]], [[1v8r|1v8r]], [[1v8s|1v8s]], [[1v8t|1v8t]], [[1v8u|1v8u]], [[1v8v|1v8v]], [[1v8w|1v8w]], [[1v8y|1v8y]]</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='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=1v8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8i OCA], [http://pdbe.org/1v8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v8i RCSB], [http://www.ebi.ac.uk/pdbsum/1v8i PDBsum], [http://www.topsan.org/Proteins/RSGI/1v8i TOPSAN]</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=1v8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8i OCA], [http://pdbe.org/1v8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v8i RCSB], [http://www.ebi.ac.uk/pdbsum/1v8i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v8i ProSAT], [http://www.topsan.org/Proteins/RSGI/1v8i TOPSAN]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v8/1v8i_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v8/1v8i_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
Revision as of 10:55, 28 March 2018
Crystal Structure Analysis of the ADP-ribose pyrophosphataseCrystal Structure Analysis of the ADP-ribose pyrophosphatase
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedADP-ribose pyrophosphatase (ADPRase) catalyzes the divalent metal ion-dependent hydrolysis of ADP-ribose to ribose 5'-phosphate and AMP. This enzyme plays a key role in regulating the intracellular ADP-ribose levels, and prevents nonenzymatic ADP-ribosylation. To elucidate the pyrophosphatase hydrolysis mechanism employed by this enzyme, structural changes occurring on binding of substrate, metal and product were investigated using crystal structures of ADPRase from an extreme thermophile, Thermus thermophilus HB8. Seven structures were determined, including that of the free enzyme, the Zn(2+)-bound enzyme, the binary complex with ADP-ribose, the ternary complexes with ADP-ribose and Zn(2+) or Gd(3+), and the product complexes with AMP and Mg(2+) or with ribose 5'-phosphate and Zn(2+). The structural and functional studies suggested that the ADP-ribose hydrolysis pathway consists of four reaction states: bound with metal (I), metal and substrate (II), metal and substrate in the transition state (III), and products (IV). In reaction state II, Glu-82 and Glu-70 abstract a proton from a water molecule. This water molecule is situated at an ideal position to carry out nucleophilic attack on the adenosyl phosphate, as it is 3.6 A away from the target phosphorus and almost in line with the scissile bond. Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal.,Yoshiba S, Ooga T, Nakagawa N, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S, Masui R J Biol Chem. 2004 Aug 27;279(35):37163-74. Epub 2004 Jun 21. PMID:15210687[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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