1v8n: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1v8n.jpg|left|200px]]<br /><applet load="1v8n" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1v8n, resolution 1.74&Aring;" />
-'''Crystal structure analysis of the ADP-ribose pyrophosphatase complexed with Zn'''<br />
-==Overview==
+==Crystal structure analysis of the ADP-ribose pyrophosphatase complexed with Zn==
-ADP-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.
+<StructureSection load='1v8n' size='340' side='right'caption='[[1v8n]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1v8n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V8N 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]] 1.74&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1v8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8n OCA], [https://pdbe.org/1v8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v8n RCSB], [https://www.ebi.ac.uk/pdbsum/1v8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v8n ProSAT], [https://www.topsan.org/Proteins/RSGI/1v8n TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q84CU3_THETH Q84CU3_THETH]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v8/1v8n_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1v8n ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+ADP-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.
-==About this Structure==
+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<ref>PMID:15210687</ref>
-V8N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1V8N OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15210687 15210687]
+</div>
-[[Category: ADP-ribose diphosphatase]]
+<div class="pdbe-citations 1v8n" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+==See Also==
+*[[ADP-ribose pyrophosphatase 3D structures|ADP-ribose pyrophosphatase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermus thermophilus]]
-[[Category: Inoue, Y.]]
+[[Category: Inoue Y]]
-[[Category: Kuramitsu, S.]]
+[[Category: Kuramitsu S]]
-[[Category: Masui, R.]]
+[[Category: Masui R]]
-[[Category: Nakagawa, N.]]
+[[Category: Nakagawa N]]
-[[Category: Ooga, T.]]
+[[Category: Ooga T]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+[[Category: Shibata T]]
-[[Category: Shibata, T.]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S.]]
+[[Category: Yoshiba S]]
-[[Category: Yoshiba, S.]]
-[[Category: ZN]]
-[[Category: mutt family]]
-[[Category: nudix motif]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rsgi]]
-[[Category: structural genomics]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 21:49:07 2007''