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New page: left|200px<br /><applet load="1fyd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fyd, resolution 2.25Å" /> '''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"
caption="1fyd, resolution 2.25&Aring;" />
'''CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE AMP, ONE PYROPHOSPHATE ION AND ONE MG2+ ION'''<br />


==Overview==
==CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE AMP, ONE PYROPHOSPHATE ION AND ONE MG2+ ION==
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+).
<StructureSection load='1fyd' size='340' side='right'caption='[[1fyd]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</table>
== Function ==
[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]
== 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/fy/1fyd_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=1fyd ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
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].
*[[NAD synthase|NAD synthase]]
 
__TOC__
==Reference==
</StructureSection>
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]
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: NAD(+) synthase (glutamine-hydrolyzing)]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Brouillette C]]
[[Category: Brouillette, C.]]
[[Category: Brouillette W]]
[[Category: Brouillette, W.]]
[[Category: DeLucas L]]
[[Category: DeLucas, L.]]
[[Category: Devedjiev Y]]
[[Category: Devedjiev, Y.]]
[[Category: Jedrzejas M]]
[[Category: Jedrzejas, M.]]
[[Category: Muccio D]]
[[Category: Muccio, D.]]
[[Category: Singh R]]
[[Category: Singh, R.]]
[[Category: Symersky J]]
[[Category: Symersky, J.]]
[[Category: AMP]]
[[Category: MG]]
[[Category: POP]]
[[Category: amidotransferase]]
[[Category: atp]]
[[Category: lyase]]
[[Category: nh3 dependent]]
[[Category: pyrophosphatase]]
 
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