1v8i: Difference between revisions

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-{{Seed}}
-[[Image:1v8i.png|left|200px]]
-<!--
+==Crystal Structure Analysis of the ADP-ribose pyrophosphatase==
-The line below this paragraph, containing "STRUCTURE_1v8i", creates the "Structure Box" on the page.
+<StructureSection load='1v8i' size='340' side='right'caption='[[1v8i]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1v8i]] 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=1V8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V8I FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.76&#8491;</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=1v8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8i OCA], [https://pdbe.org/1v8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v8i RCSB], [https://www.ebi.ac.uk/pdbsum/1v8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v8i ProSAT], [https://www.topsan.org/Proteins/RSGI/1v8i TOPSAN]</span></td></tr>
-{{STRUCTURE_1v8i|  PDB=1v8i  |  SCENE=  }}
+</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/v8/1v8i_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=1v8i 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.
-===Crystal Structure Analysis of the ADP-ribose pyrophosphatase===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1v8i" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15210687}}, adds the Publication Abstract to the page
+*[[ADP-ribose pyrophosphatase 3D structures|ADP-ribose pyrophosphatase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15210687 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15210687}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-V8I is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8I OCA].
-==Reference==
-<ref group="xtra">PMID:15210687</ref><references group="xtra"/>
-[[Category: ADP-ribose diphosphatase]]
 [[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: Bacteria]]
-[[Category: Nudix motif]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 07:09:43 2009''