2o3u: Difference between revisions

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-[[Image:2o3u.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2o3u", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2o3u|  PDB=2o3u  |  SCENE=  }}
-'''Structural Basis for Formation and Hydrolysis of Calcium Messenger Cyclic ADP-ribose by Human CD38'''
+==Structural Basis for Formation and Hydrolysis of Calcium Messenger Cyclic ADP-ribose by Human CD38==
+<StructureSection load='2o3u' size='340' side='right'caption='[[2o3u]], [[Resolution|resolution]] 2.11&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2o3u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O3U 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]] 2.11&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NGD:[[(2R,3S,4R,5R)-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]+[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl+hydrogen+phosphate'>NGD</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=2o3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o3u OCA], [https://pdbe.org/2o3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o3u RCSB], [https://www.ebi.ac.uk/pdbsum/2o3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o3u ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CD38_HUMAN CD38_HUMAN] Synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.
+== 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/o3/2o3u_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2o3u ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human CD38 is a multifunctional ectoenzyme responsible for catalyzing the conversions from nicotinamide adenine dinucleotide (NAD) to cyclic ADP-ribose (cADPR) and from cADPR to ADP-ribose (ADPR). Both cADPR and ADPR are calcium messengers that can mobilize intracellular stores and activate influx as well. In this study, we determined three crystal structures of the human CD38 enzymatic domain complexed with cADPR at 1.5-A resolution, with its analog, cyclic GDP-ribose (cGDPR) (1.68 A) and with NGD (2.1 A) a substrate analog of NAD. The results indicate that the binding of cADPR or cGDPR to the active site induces structural rearrangements in the dipeptide Glu(146)-Asp(147) by as much as 2.7 A) providing the first direct evidence of a conformational change at the active site during catalysis. In addition, Glu(226) is shown to be critical not only in catalysis but also in positioning of cADPR at the catalytic site through strong hydrogen bonding interactions. Structural details obtained from these complexes provide a step-by-step description of the catalytic processes in the synthesis and hydrolysis of cADPR.
-==Overview==
+Structural basis for formation and hydrolysis of the calcium messenger cyclic ADP-ribose by human CD38.,Liu Q, Kriksunov IA, Graeff R, Lee HC, Hao Q J Biol Chem. 2007 Feb 23;282(8):5853-61. Epub 2006 Dec 20. PMID:17182614<ref>PMID:17182614</ref>
-Human CD38 is a multifunctional ectoenzyme responsible for catalyzing the conversions from nicotinamide adenine dinucleotide (NAD) to cyclic ADP-ribose (cADPR) and from cADPR to ADP-ribose (ADPR). Both cADPR and ADPR are calcium messengers that can mobilize intracellular stores and activate influx as well. In this study, we determined three crystal structures of the human CD38 enzymatic domain complexed with cADPR at 1.5-A resolution, with its analog, cyclic GDP-ribose (cGDPR) (1.68 A) and with NGD (2.1 A) a substrate analog of NAD. The results indicate that the binding of cADPR or cGDPR to the active site induces structural rearrangements in the dipeptide Glu(146)-Asp(147) by as much as 2.7 A) providing the first direct evidence of a conformational change at the active site during catalysis. In addition, Glu(226) is shown to be critical not only in catalysis but also in positioning of cADPR at the catalytic site through strong hydrogen bonding interactions. Structural details obtained from these complexes provide a step-by-step description of the catalytic processes in the synthesis and hydrolysis of cADPR.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-O3U is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O3U OCA].
+</div>
+<div class="pdbe-citations 2o3u" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural basis for formation and hydrolysis of the calcium messenger cyclic ADP-ribose by human CD38., Liu Q, Kriksunov IA, Graeff R, Lee HC, Hao Q, J Biol Chem. 2007 Feb 23;282(8):5853-61. Epub 2006 Dec 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17182614 17182614]
+*[[Cluster of Differentiation CD38|Cluster of Differentiation CD38]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Graeff, R.]]
+[[Category: Graeff R]]
-[[Category: Hao, Q.]]
+[[Category: Hao Q]]
-[[Category: Kriksunov, I A.]]
+[[Category: Kriksunov IA]]
-[[Category: Lee, H C.]]
+[[Category: Lee HC]]
-[[Category: Liu, Q.]]
+[[Category: Liu Q]]
-[[Category: Human cd38 e226q mutant]]
-[[Category: Ngd binding and hydrolysis]]
-[[Category: The catalytic pocket]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 10:17:47 2008''