2i2c: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
<StructureSection load='2i2c' size='340' side='right'caption='[[2i2c]], [[Resolution|resolution]] 1.85Å' scene=''> | <StructureSection load='2i2c' size='340' side='right'caption='[[2i2c]], [[Resolution|resolution]] 1.85Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2i2c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[2i2c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_monocytogenes_EGD-e Listeria monocytogenes EGD-e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I2C FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTA:(2S,3S,4R,5R,2S,3S,4R,5R)-2,2-[DITHIOBIS(METHYLENE)]BIS[5-(6-AMINO-9H-PURIN-9-YL)TETRAHYDROFURAN-3,4-DIOL]'>DTA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTA:(2S,3S,4R,5R,2S,3S,4R,5R)-2,2-[DITHIOBIS(METHYLENE)]BIS[5-(6-AMINO-9H-PURIN-9-YL)TETRAHYDROFURAN-3,4-DIOL]'>DTA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=2i2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2c OCA], [https://pdbe.org/2i2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i2c RCSB], [https://www.ebi.ac.uk/pdbsum/2i2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i2c ProSAT]</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=2i2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i2c OCA], [https://pdbe.org/2i2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i2c RCSB], [https://www.ebi.ac.uk/pdbsum/2i2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i2c ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/NADK1_LISMO NADK1_LISMO] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]<ref>PMID:17686780</ref> <ref>PMID:22608967</ref> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 39: | Line 37: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Listeria monocytogenes EGD-e]] | ||
[[Category: Labesse | [[Category: Labesse G]] | ||
[[Category: Poncet-Montange | [[Category: Poncet-Montange G]] | ||
Latest revision as of 13:05, 30 August 2023
Crystal structure of LmNADK1Crystal structure of LmNADK1
Structural highlights
FunctionNADK1_LISMO Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361][1] [2] 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 PubMedHere we describe the crystal structures of the NAD kinase (LmNADK1) from Listeria monocytogenes in complex with its substrate NAD, its product NADP, or two synthesized NAD mimics. We identified one of the NAD mimics, di-adenosine diphosphate, as a new substrate for LmNADK1, whereas we showed that the closely related compound di-5'-thioadenosine is a novel non-natural inhibitor for this enzyme. These structures suggest a mechanism involving substrate-assisted catalysis. Indeed, sequence/structure comparison and directed mutagenesis have previously shown that NAD kinases (NADKs) and the distantly related 6-phosphofructokinases share the same catalytically important GGDGT motif. However, in this study we have shown that these enzymes use the central aspartate of this motif differently. Although this acidic residue chelates the catalytic Mg(2+) ion in 6-phosphofructokinases, it activates the phospho-acceptor (NAD) in NADKs. Sequence/structure comparisons suggest that the role of this aspartate would be conserved in NADKs and the related sphingosine and diacylglycerol kinases. NAD kinases use substrate-assisted catalysis for specific recognition of NAD.,Poncet-Montange G, Assairi L, Arold S, Pochet S, Labesse G J Biol Chem. 2007 Nov 23;282(47):33925-34. Epub 2007 Aug 8. PMID:17686780[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||