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New page: left|200px<br /><applet load="1kqp" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kqp, resolution 1.03Å" /> '''NH3-DEPENDENT NAD+ S... |
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== | ==NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION== | ||
The final step of NAD+ biosynthesis includes an amide transfer to | <StructureSection load='1kqp' size='340' side='right'caption='[[1kqp]], [[Resolution|resolution]] 1.03Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1kqp]] 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=1KQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KQP 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]] 1.03Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADJ:NICOTINAMIDE-ADENINE-DINUCLEOTIDE-ADENYLATE+INTERMEDIATE'>ADJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=1kqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqp OCA], [https://pdbe.org/1kqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kqp RCSB], [https://www.ebi.ac.uk/pdbsum/1kqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqp 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/kq/1kqp_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=1kqp ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The final step of NAD+ biosynthesis includes an amide transfer to nicotinic acid adenine dinucleotide (NaAD) catalyzed by NAD+ synthetase. This enzyme was co-crystallized in microgravity with natural substrates NaAD and ATP at pH 8.5. The crystal was exposed to ammonium ions, synchrotron diffraction data were collected and the atomic model was refined anisotropically at 1 A resolution to R = 11.63%. Both binding sites are occupied by the NAD-adenylate intermediate, pyrophosphate and two magnesium ions. The atomic resolution of the structure allows better definition of non-planar peptide groups, reveals a low mean anisotropy of protein and substrate atoms and indicates the H-atom positions of the phosphoester group of the reaction intermediate. The phosphoester group is protonated at the carbonyl O atom O7N, suggesting a carbenium-ion structure stabilized by interactions with two solvent sites presumably occupied by ammonia and a water molecule. A mechanism is proposed for the second catalytic step, which includes a nucleophilic attack by the ammonia molecule on the intermediate. | |||
NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution.,Symersky J, Devedjiev Y, Moore K, Brouillette C, DeLucas L Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1138-46. Epub 2002, Jun 20. PMID:12077433<ref>PMID:12077433</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1kqp" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[NAD synthase|NAD synthase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus subtilis]] | [[Category: Bacillus subtilis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Brouillette C]] | |||
[[Category: Brouillette | [[Category: DeLucas L]] | ||
[[Category: DeLucas | [[Category: Devedjiev Y]] | ||
[[Category: Devedjiev | [[Category: Moore K]] | ||
[[Category: Moore | [[Category: Symersky J]] | ||
[[Category: Symersky | |||
Latest revision as of 12:02, 16 August 2023
NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTIONNH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION
Structural highlights
FunctionNADE_BACSU Catalyzes a key step in NAD biosynthesis, transforming deamido-NAD into NAD by a two-step reaction.[HAMAP-Rule:MF_00193] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe final step of NAD+ biosynthesis includes an amide transfer to nicotinic acid adenine dinucleotide (NaAD) catalyzed by NAD+ synthetase. This enzyme was co-crystallized in microgravity with natural substrates NaAD and ATP at pH 8.5. The crystal was exposed to ammonium ions, synchrotron diffraction data were collected and the atomic model was refined anisotropically at 1 A resolution to R = 11.63%. Both binding sites are occupied by the NAD-adenylate intermediate, pyrophosphate and two magnesium ions. The atomic resolution of the structure allows better definition of non-planar peptide groups, reveals a low mean anisotropy of protein and substrate atoms and indicates the H-atom positions of the phosphoester group of the reaction intermediate. The phosphoester group is protonated at the carbonyl O atom O7N, suggesting a carbenium-ion structure stabilized by interactions with two solvent sites presumably occupied by ammonia and a water molecule. A mechanism is proposed for the second catalytic step, which includes a nucleophilic attack by the ammonia molecule on the intermediate. NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution.,Symersky J, Devedjiev Y, Moore K, Brouillette C, DeLucas L Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1138-46. Epub 2002, Jun 20. PMID:12077433[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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