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1fyd

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(New page: 200px<br /><applet load="1fyd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fyd, resolution 2.25&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:1fyd.jpg|left|200px]]<br /><applet load="1fyd" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1fyd, resolution 2.25&Aring;" />
 
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'''CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE AMP, ONE PYROPHOSPHATE ION AND ONE MG2+ ION'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE AMP, ONE PYROPHOSPHATE ION AND ONE MG2+ ION==
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The NH(3)-dependent NAD(+) synthetase (NADS) participates in the, biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) by transforming, nicotinic acid adenine dinucleotide (NaAD) to NAD(+). The structural, behavior of the active site, including stabilization of flexible loops, 82-87 and 204-225, has been studied by determination of the crystal, structures of complexes of NADS with natural substrates and a substrate, analog. Both loops are stabilized independently of NaAD and solely from, the ATP-binding site. Analysis of the binding contacts suggests that the, minor loop 82-87 is stabilized primarily by a hydrogen bond with the, adenine base of ATP. Formation of a coordination complex with Mg(2+) in, the ATP-binding site may contribute to the stabilization of the major loop, 204-225. The major loop has a role in substrate recognition and, stabilization, in addition to the protection of the reaction intermediate, described previously. A second and novel Mg(2+) position has been observed, closer to the NaAD-binding site in the structure crystallized at pH 7.5, where the enzyme is active. This could therefore be the catalytically, active Mg(2+).
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<StructureSection load='1fyd' size='340' side='right'caption='[[1fyd]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1fyd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FYD FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fyd OCA], [https://pdbe.org/1fyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fyd RCSB], [https://www.ebi.ac.uk/pdbsum/1fyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fyd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NADE_BACSU NADE_BACSU] Catalyzes a key step in NAD biosynthesis, transforming deamido-NAD into NAD by a two-step reaction.[HAMAP-Rule:MF_00193]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fy/1fyd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1fyd ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1FYD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with MG, AMP and POP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/NAD(+)_synthase_(glutamine-hydrolyzing) NAD(+) synthase (glutamine-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.1 6.3.5.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1FYD OCA].
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*[[NAD synthase|NAD synthase]]
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__TOC__
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==Reference==
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</StructureSection>
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Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis., Devedjiev Y, Symersky J, Singh R, Jedrzejas M, Brouillette C, Brouillette W, Muccio D, Chattopadhyay D, DeLucas L, Acta Crystallogr D Biol Crystallogr. 2001 Jun;57(Pt 6):806-12. Epub 2001, May 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11375500 11375500]
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[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: NAD(+) synthase (glutamine-hydrolyzing)]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Brouillette C]]
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[[Category: Brouillette, C.]]
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[[Category: Brouillette W]]
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[[Category: Brouillette, W.]]
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[[Category: DeLucas L]]
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[[Category: DeLucas, L.]]
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[[Category: Devedjiev Y]]
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[[Category: Devedjiev, Y.]]
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[[Category: Jedrzejas M]]
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[[Category: Jedrzejas, M.]]
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[[Category: Muccio D]]
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[[Category: Muccio, D.]]
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[[Category: Singh R]]
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[[Category: Singh, R.]]
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[[Category: Symersky J]]
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[[Category: Symersky, J.]]
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[[Category: AMP]]
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[[Category: MG]]
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[[Category: POP]]
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[[Category: amidotransferase]]
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[[Category: atp]]
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[[Category: lyase]]
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[[Category: nh3 dependent]]
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[[Category: pyrophosphatase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:27:59 2007''
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Current revision

CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE AMP, ONE PYROPHOSPHATE ION AND ONE MG2+ ION

PDB ID 1fyd

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