3pn1

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<StructureSection load='3pn1' size='340' side='right'caption='[[3pn1]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3pn1' size='340' side='right'caption='[[3pn1]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3pn1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PN1 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3pn1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PN1 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IVH:2-(BUTYLSULFANYL)ADENOSINE'>IVH</scene>, <scene name='pdbligand=IWH:1-(2,4-DIMETHYLBENZYL)-6-OXO-1,6-DIHYDROPYRIDINE-3-CARBOXAMIDE'>IWH</scene></td></tr>
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</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&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ligA, lig, ligN, HI_1100 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IVH:2-(BUTYLSULFANYL)ADENOSINE'>IVH</scene>, <scene name='pdbligand=IWH:1-(2,4-DIMETHYLBENZYL)-6-OXO-1,6-DIHYDROPYRIDINE-3-CARBOXAMIDE'>IWH</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pn1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn1 OCA], [https://pdbe.org/3pn1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pn1 RCSB], [https://www.ebi.ac.uk/pdbsum/3pn1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pn1 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=3pn1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn1 OCA], [https://pdbe.org/3pn1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pn1 RCSB], [https://www.ebi.ac.uk/pdbsum/3pn1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pn1 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/DNLJ_HAEIN DNLJ_HAEIN]] DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA (By similarity).
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[https://www.uniprot.org/uniprot/DNLJ_HAEIN DNLJ_HAEIN] DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA (By similarity).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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DNA ligases are indispensable enzymes playing a critical role in DNA replication, recombination, and repair in all living organisms. Bacterial NAD(+)-dependent DNA ligase (LigA) was evaluated for its potential as a broad-spectrum antibacterial target. A novel class of substituted adenosine analogs was discovered by target-based high throughput screening (HTS), and optimized to become more effective and selective inhibitors of LigA. The adenosine analogs inhibited LigA activity from Escherichia coli, Haemophilus influenzae, Mycoplasma pneumoniae, Streptococcus pneumoniae, and Staphylococcus aureus, with inhibitory activities in the nanomolar range. They were selective for bacterial NAD(+)-dependent DNA ligases, not showing inhibitory activity toward the ATP-dependent human DNA ligase 1 or bacteriophage T4 ligase. Enzyme kinetic measurements demonstrated that the compounds bind competitively with NAD(+). X-ray crystallography demonstrated that the adenosine analogs bind in the AMP-binding pocket of the LigA adenylation domain. Antibacterial activity was observed for pathogenic Gram-positive and atypical bacteria such as S. aureus, S. pneumoniae, Streptococcus pyogenes, and M. pneumoniae, as well as Gram-negative pathogens such as H. influenzae and Moraxella catarrhalis. The mode-of-action was verified using recombinant strains with altered LigA expression, an Okazaki fragment accumulation assay, and isolation of resistant strains with ligA mutations. In vivo efficacy was demonstrated in a murine S. aureus thigh-infection model and a murine S. pneumoniae lung-infection model. Treatment with the adenosine analogs reduced the bacterial burden (CFUs) in the corresponding infected organ tissue by up to 1,000-fold, thus validating LigA as a target for antibacterial therapy.
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Novel Bacterial NAD+-dependent DNA Ligase Inhibitors with Broad Spectrum Activity and Antibacterial Efficacy In Vivo.,Mills SD, Eakin AE, Buurman ET, Newman JV, Gao N, Huynh H, Johnson KD, Lahiri S, Shapiro AB, Walkup GK, Yang W, Stokes SS Antimicrob Agents Chemother. 2010 Dec 28. PMID:21189350<ref>PMID:21189350</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3pn1" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacterium influenzae lehmann and neumann 1896]]
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[[Category: Haemophilus influenzae]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Buurman, E]]
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[[Category: Buurman E]]
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[[Category: Eakin, A]]
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[[Category: Eakin A]]
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[[Category: Gao, N]]
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[[Category: Gao N]]
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[[Category: Huynh, H]]
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[[Category: Huynh H]]
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[[Category: Johnson, K]]
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[[Category: Johnson K]]
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[[Category: Lahiri, S]]
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[[Category: Lahiri S]]
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[[Category: Mills, S]]
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[[Category: Mills S]]
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[[Category: Newman, J]]
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[[Category: Newman J]]
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[[Category: Shapiro, A]]
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[[Category: Shapiro A]]
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[[Category: Stokes, S]]
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[[Category: Stokes S]]
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[[Category: Walkup, G]]
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[[Category: Walkup G]]
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[[Category: Wei, Y]]
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[[Category: Wei Y]]
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[[Category: Atp grasp fold]]
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[[Category: Bacteria]]
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[[Category: Dna]]
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[[Category: Ligase]]
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[[Category: Ligase-ligase inhibitor complex]]
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Current revision

Novel Bacterial NAD+-dependent DNA Ligase Inhibitors with Broad Spectrum Potency and Antibacterial Efficacy In Vivo

PDB ID 3pn1

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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