3dzf: Difference between revisions

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-[[Image:3dzf.png|left|200px]]
-<!--
+==Crystal structure of human CD38 extracellular domain complexed with a covalent intermediate, ara-F-ribose-5'-phosphate==
-The line below this paragraph, containing "STRUCTURE_3dzf", creates the "Structure Box" on the page.
+<StructureSection load='3dzf' size='340' side='right'caption='[[3dzf]], [[Resolution|resolution]] 2.01&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'>[[3dzf]] is a 6 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=3DZF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DZF 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]] 2.01&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RF5:2-DEOXY-2-FLUORO-5-O-PHOSPHONO-ALPHA-D-ARABINOFURANOSE'>RF5</scene></td></tr>
-{{STRUCTURE_3dzf|  PDB=3dzf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dzf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dzf OCA], [https://pdbe.org/3dzf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dzf RCSB], [https://www.ebi.ac.uk/pdbsum/3dzf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dzf 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/dz/3dzf_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=3dzf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Enzymatic utilization of nicotinamide adenine dinucleotide (NAD) has increasingly been shown to have fundamental roles in gene regulation, signal transduction, and protein modification. Many of the processes require the cleavage of the nicotinamide moiety from the substrate and the formation of a reactive intermediate. Using X-ray crystallography, we show that human CD38, an NAD-utilizing enzyme, is capable of catalyzing the cleavage reactions through both covalent and noncovalent intermediates, depending on the substrate used. The covalent intermediate is resistant to further attack by nucleophiles, resulting in mechanism-based enzyme inactivation. The noncovalent intermediate is stabilized mainly through H-bond interactions, but appears to remain reactive. Our structural results favor the proposal of a noncovalent intermediate during normal enzymatic utilization of NAD by human CD38 and provide structural insights into the design of covalent and noncovalent inhibitors targeting NAD-utilization pathways.
-===Crystal structure of human CD38 extracellular domain complexed with a covalent intermediate, ara-F-ribose-5'-phosphate===
+Covalent and noncovalent intermediates of an NAD utilizing enzyme, human CD38.,Liu Q, Kriksunov IA, Jiang H, Graeff R, Lin H, Lee HC, Hao Q Chem Biol. 2008 Oct 20;15(10):1068-78. PMID:18940667<ref>PMID:18940667</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18940667}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3dzf" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18940667 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_18940667}}
-==About this Structure==
-[[3dzf]] is a 6 chain structure of [[Cluster of Differentiation 38]] with 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=3DZF OCA].
 ==See Also==
-*[[Cluster of Differentiation 38|Cluster of Differentiation 38]]
+*[[Cluster of Differentiation CD38|Cluster of Differentiation CD38]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018940667</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Graeff, R.]]
+[[Category: Large Structures]]
-[[Category: Hao, Q.]]
+[[Category: Graeff R]]
-[[Category: Jiang, H.]]
+[[Category: Hao Q]]
-[[Category: Kriksunov, I A.]]
+[[Category: Jiang H]]
-[[Category: Lee, H C.]]
+[[Category: Kriksunov IA]]
-[[Category: Lin, H.]]
+[[Category: Lee HC]]
-[[Category: Liu, Q.]]
+[[Category: Lin H]]
-[[Category: Alpha bundle]]
+[[Category: Liu Q]]
-[[Category: Beta sheet]]
-[[Category: Covalent intermediate]]
-[[Category: Diabetes mellitus]]
-[[Category: Glycoprotein]]
-[[Category: Hydrolase]]
-[[Category: Membrane]]
-[[Category: Nad]]
-[[Category: Receptor]]
-[[Category: Signal-anchor]]
-[[Category: Transmembrane]]