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==Crystallographic Capture of Quinolinate Synthase (NadA) from Pyrococcus horikoshii in its Substrates and Product-Bound States== | |||
<StructureSection load='4zk6' size='340' side='right'caption='[[4zk6]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4zk6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZK6 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]] 1.895Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NTM:QUINOLINIC+ACID'>NTM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=4zk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zk6 OCA], [https://pdbe.org/4zk6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zk6 RCSB], [https://www.ebi.ac.uk/pdbsum/4zk6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zk6 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/NADA_PYRHO NADA_PYRHO] Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate (By similarity). | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Quinolinic acid (QA) is a common intermediate in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) and its derivatives in all organisms that synthesize the molecule de novo. In most prokaryotes, it is formed from the condensation of dihydroxyacetone phosphate (DHAP) and aspartate-enamine by the action of quinolinate synthase (NadA). NadA contains a [4Fe-4S] cluster cofactor with a unique, non-cysteinyl-ligated, iron ion (Fea), which is proposed to bind the hydroxyl group of a postulated intermediate in the last step of the reaction to facilitate a dehydration. However, direct evidence for this role in catalysis has yet to be provided. Herein, we present the structure of NadA in the presence of the product of its reaction, QA. We find that N1 and the C7 carboxylate group of QA ligate to Fea in a bidentate fashion, which is confirmed by Hyperfine Sublevel Correlation (HYSCORE) spectroscopy. This binding mode would place the C5 hydroxyl group of the postulated final intermediate distal to Fea and virtually incapable of coordinating to it. The structure shows that three strictly conserved amino acids, Glu198, Tyr109, and Tyr23, are in close proximity to the bound product. Substitution of these amino acids with Gln, Phe, and Phe, respectively, leads to complete loss of activity. | |||
Structure of Quinolinate Synthase from Pyrococcus horikoshii in the Presence of Its Product, Quinolinic Acid.,Esakova OA, Silakov A, Grove TL, Saunders AH, McLaughlin MI, Yennawar NH, Booker SJ J Am Chem Soc. 2016 Jun 15;138(23):7224-7. doi: 10.1021/jacs.6b02708. Epub 2016, Jun 2. PMID:27224840<ref>PMID:27224840</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Booker | <div class="pdbe-citations 4zk6" style="background-color:#fffaf0;"></div> | ||
[[Category: Esakova | == References == | ||
[[Category: Grove | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Pyrococcus horikoshii OT3]] | |||
[[Category: Booker SJ]] | |||
[[Category: Esakova OA]] | |||
[[Category: Grove TL]] | |||
[[Category: Saunders AH]] | |||
[[Category: Yennawar NH]] | |||
Latest revision as of 11:19, 27 September 2023
Crystallographic Capture of Quinolinate Synthase (NadA) from Pyrococcus horikoshii in its Substrates and Product-Bound StatesCrystallographic Capture of Quinolinate Synthase (NadA) from Pyrococcus horikoshii in its Substrates and Product-Bound States
Structural highlights
FunctionNADA_PYRHO Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate (By similarity). Publication Abstract from PubMedQuinolinic acid (QA) is a common intermediate in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) and its derivatives in all organisms that synthesize the molecule de novo. In most prokaryotes, it is formed from the condensation of dihydroxyacetone phosphate (DHAP) and aspartate-enamine by the action of quinolinate synthase (NadA). NadA contains a [4Fe-4S] cluster cofactor with a unique, non-cysteinyl-ligated, iron ion (Fea), which is proposed to bind the hydroxyl group of a postulated intermediate in the last step of the reaction to facilitate a dehydration. However, direct evidence for this role in catalysis has yet to be provided. Herein, we present the structure of NadA in the presence of the product of its reaction, QA. We find that N1 and the C7 carboxylate group of QA ligate to Fea in a bidentate fashion, which is confirmed by Hyperfine Sublevel Correlation (HYSCORE) spectroscopy. This binding mode would place the C5 hydroxyl group of the postulated final intermediate distal to Fea and virtually incapable of coordinating to it. The structure shows that three strictly conserved amino acids, Glu198, Tyr109, and Tyr23, are in close proximity to the bound product. Substitution of these amino acids with Gln, Phe, and Phe, respectively, leads to complete loss of activity. Structure of Quinolinate Synthase from Pyrococcus horikoshii in the Presence of Its Product, Quinolinic Acid.,Esakova OA, Silakov A, Grove TL, Saunders AH, McLaughlin MI, Yennawar NH, Booker SJ J Am Chem Soc. 2016 Jun 15;138(23):7224-7. doi: 10.1021/jacs.6b02708. Epub 2016, Jun 2. PMID:27224840[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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