6z64
From Proteopedia
(Difference between revisions)
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==Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative== | ==Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative== | ||
| - | <StructureSection load='6z64' size='340' side='right'caption='[[6z64]]' scene=''> | + | <StructureSection load='6z64' size='340' side='right'caption='[[6z64]], [[Resolution|resolution]] 1.89Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z64 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z64 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6z64]] 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=6Z64 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z64 FirstGlance]. <br> |
| - | </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=6z64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z64 OCA], [https://pdbe.org/6z64 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z64 RCSB], [https://www.ebi.ac.uk/pdbsum/6z64 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z64 ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.89Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=Q9K:(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl-(3-azanylpropyl)amino]methyl]oxolane-3,4-diol'>Q9K</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=6z64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z64 OCA], [https://pdbe.org/6z64 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z64 RCSB], [https://www.ebi.ac.uk/pdbsum/6z64 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z64 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == 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> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Nicotinamide adenine dinucleotide (NAD) kinases are essential and ubiquitous enzymes involved in the tight regulation of NAD/nicotinamide adenine dinucleotide phosphate (NADP) levels in many metabolic pathways. Consequently, they represent promising therapeutic targets in cancer and antibacterial treatments. We previously reported diadenosine derivatives as NAD kinase inhibitors with bactericidal activities on Staphylococcus aureus. Among them, one compound (namely NKI1) was found effective in vivo in a mouse infection model. With the aim to gain detailed knowledge about the selectivity and mechanism of action of this lead compound, we planned to develop a chemical probe that could be used in affinity-based chemoproteomic approaches. Here, we describe the first functionalized chemical probe targeting a bacterial NAD kinase. Aminoalkyl functional groups were introduced on NKI1 for further covalent coupling to an activated Sepharose(TM) matrix. Inhibitory properties of functionalized NKI1 derivatives together with X-ray characterization of their complexes with the NAD kinase led to identify candidate compounds that are amenable to covalent coupling to a matrix. | ||
| + | |||
| + | New Chemical Probe Targeting Bacterial NAD Kinase.,Clement DA, Leseigneur C, Gelin M, Coelho D, Huteau V, Lionne C, Labesse G, Dussurget O, Pochet S Molecules. 2020 Oct 22;25(21). pii: molecules25214893. doi:, 10.3390/molecules25214893. PMID:33105870<ref>PMID:33105870</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6z64" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[NAD kinase|NAD kinase]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Listeria monocytogenes EGD-e]] | ||
[[Category: Gelin M]] | [[Category: Gelin M]] | ||
[[Category: Labesse G]] | [[Category: Labesse G]] | ||
Current revision
Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative
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