1wxh: Difference between revisions

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 ==E.coli NAD Synthetase, NAD==
-<StructureSection load='1wxh' size='340' side='right' caption='[[1wxh]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1wxh' size='340' side='right'caption='[[1wxh]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1wxh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WXH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WXH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1wxh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WXH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WXH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wxe|1wxe]], [[1wxf|1wxf]], [[1wxg|1wxg]], [[1wxi|1wxi]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_synthase NAD(+) synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.1.5 6.3.1.5] </span></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=1wxh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wxh OCA], [https://pdbe.org/1wxh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wxh RCSB], [https://www.ebi.ac.uk/pdbsum/1wxh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wxh ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wxh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wxh OCA], [http://pdbe.org/1wxh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wxh RCSB], [http://www.ebi.ac.uk/pdbsum/1wxh PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NADE_ECOLI NADE_ECOLI]] Catalyzes a key step in NAD biosynthesis, transforming deamido-NAD into NAD by a two-step reaction.
+[https://www.uniprot.org/uniprot/NADE_ECOLI NADE_ECOLI] Catalyzes a key step in NAD biosynthesis, transforming deamido-NAD into NAD by a two-step reaction.
 == 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/wx/1wxh_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wx/1wxh_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1wxh ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Nicotinamide adenine dinucleotide synthetases (NADS) catalyze the amidation of nicotinic acid adenine dinucleotide (NAAD) to yield the enzyme cofactor nicotinamide adenine dinucleotide (NAD). Here we describe the crystal structures of the ammonia-dependent homodimeric NADS from Escherichia coli alone and in complex with natural substrates and with the reaction product NAD. The structures disclosed two NAAD/NAD binding sites at the dimer interface and an adenosine triphosphate (ATP) binding site within each subunit. Comparison with the Bacillus subtilis NADS showed pronounced chemical differences in the NAAD/NAD binding sites and less prominent differences in the ATP binding pockets. In addition, the E. coli NADS structures revealed unexpected dynamical rearrangements in the NAAD/NAD binding pocket upon NAAD-to-NAD conversion, which define a catalysis state and a substrate/product exchange state. The two states are adopted by concerted movement of the nicotinysyl moieties of NAAD and NAD, Phe-170, and residues 224-228, which may be triggered by differential coordination of a magnesium ion to NAAD and NAD. Phylogenetic structure comparisons suggest that the present results are relevant for designing species-specific antibiotics.
-Structures of Escherichia coli NAD synthetase with substrates and products reveal mechanistic rearrangements.,Jauch R, Humm A, Huber R, Wahl MC J Biol Chem. 2005 Apr 15;280(15):15131-40. Epub 2005 Feb 7. PMID:15699042<ref>PMID:15699042</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1wxh" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[NAD synthase|NAD synthase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Huber, R]]
+[[Category: Large Structures]]
-[[Category: Humm, A]]
+[[Category: Huber R]]
-[[Category: Jauch, R]]
+[[Category: Humm A]]
-[[Category: Wahl, M C]]
+[[Category: Jauch R]]
-[[Category: E coli]]
+[[Category: Wahl MC]]
-[[Category: Ligase]]
-[[Category: Nad]]
-[[Category: Nade]]