3dhf: Difference between revisions

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-[[Image:3dhf.png|left|200px]]
-{{STRUCTURE_3dhf|  PDB=3dhf  |  SCENE=  }}
+==Crystal structure of phosphorylated mimic form of human NAMPT complexed with nicotinamide mononucleotide and pyrophosphate==
+<StructureSection load='3dhf' size='340' side='right'caption='[[3dhf]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3dhf]] 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=3DHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DHF 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=3dhf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dhf OCA], [https://pdbe.org/3dhf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dhf RCSB], [https://www.ebi.ac.uk/pdbsum/3dhf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dhf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NAMPT_HUMAN NAMPT_HUMAN] Catalyzes the condensation of nicotinamide with 5-phosphoribosyl-1-pyrophosphate to yield nicotinamide mononucleotide, an intermediate in the biosynthesis of NAD. It is the rate limiting component in the mammalian NAD biosynthesis pathway (By similarity).
+== 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/dh/3dhf_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=3dhf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nicotinamide phosphoribosyltransferase (NAMPT) is highly evolved to capture nicotinamide (NAM) and replenish the nicotinamide adenine dinucleotide (NAD(+)) pool during ADP-ribosylation and transferase reactions. ATP-phosphorylation of an active-site histidine causes catalytic activation, increasing NAM affinity by 160,000. Crystal structures of NAMPT with catalytic site ligands identify the phosphorylation site, establish its role in catalysis, demonstrate unique overlapping ATP and phosphoribosyltransferase sites, and establish reaction coordinate motion. NAMPT structures with beryllium fluoride indicate a covalent H247-BeF(3)(-) as the phosphohistidine mimic. Activation of NAMPT by H247-phosphorylation causes stabilization of the enzyme-phosphoribosylpyrophosphate complex, permitting efficient capture of NAM. Reactant and product structures establish reaction coordinate motion for NAMPT to be migration of the ribosyl anomeric carbon from the pyrophosphate leaving group to the nicotinamide-N1 while the 5-phosphoryl group, the pyrophosphate moiety, and the nicotinamide ring remain fixed in the catalytic site.
-===Crystal structure of phosphorylated mimic form of human NAMPT complexed with nicotinamide mononucleotide and pyrophosphate===
+A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT.,Burgos ES, Ho MC, Almo SC, Schramm VL Proc Natl Acad Sci U S A. 2009 Aug 4. PMID:19666527<ref>PMID:19666527</ref>
-{{ABSTRACT_PUBMED_19666527}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3dhf" style="background-color:#fffaf0;"></div>
-[[3dhf]] is a 2 chain structure 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=3DHF OCA].
 ==See Also==
-*[[Phosphoribosyltransferase|Phosphoribosyltransferase]]
+*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019666527</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Nicotinamide phosphoribosyltransferase]]
+[[Category: Large Structures]]
-[[Category: Almo, S C.]]
+[[Category: Almo SC]]
-[[Category: Burgos, E S.]]
+[[Category: Burgos ES]]
-[[Category: Ho, M.]]
+[[Category: Ho M]]
-[[Category: Schramm, V L.]]
+[[Category: Schramm VL]]
-[[Category: Beryllium fluoride]]
-[[Category: Glycosyltransferase]]
-[[Category: Namprtase]]
-[[Category: Nicotinamide d-ribonucleotide]]
-[[Category: Nmprtase]]
-[[Category: Phosphoprotein]]
-[[Category: Pyridine nucleotide biosynthesis]]
-[[Category: Pyrophosphate]]
-[[Category: The mimic form of phosporylated histidine]]
-[[Category: Transferase]]
-[[Category: Visfatin]]