3r5w

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<StructureSection load='3r5w' size='340' side='right'caption='[[3r5w]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
<StructureSection load='3r5w' size='340' side='right'caption='[[3r5w]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3r5w]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R5W FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3r5w]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R5W 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=F42:COENZYME+F420'>F42</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]] 1.786&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3r5l|3r5l]], [[3r5p|3r5p]], [[3r5r|3r5r]], [[3r5y|3r5y]], [[3r5z|3r5z]]</div></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=F42:COENZYME+F420'>F42</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ddn, MT3651, Rv3547 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=3r5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5w OCA], [https://pdbe.org/3r5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r5w RCSB], [https://www.ebi.ac.uk/pdbsum/3r5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5w 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=3r5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5w OCA], [https://pdbe.org/3r5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r5w RCSB], [https://www.ebi.ac.uk/pdbsum/3r5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5w ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/DDN_MYCTU DDN_MYCTU]] Nitroreductase involved in the bioreductive activation of the antitubercular prodrug PA-824 (nitroimidazo-oxazine) developed for anti-tuberculosis therapy against both replicating and persistent bacteria. It converts PA-824 into three primary metabolites; the major one is the des-nitroimidazole (des-nitro) which generated reactive nitrogen species, including nitric oxide (NO). Reactive nitrogen species play a major role in mammalian defense against mycobacterial infections.<ref>PMID:16387854</ref> <ref>PMID:19039139</ref>
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[https://www.uniprot.org/uniprot/DDN_MYCTU DDN_MYCTU] Nitroreductase involved in the bioreductive activation of the antitubercular prodrug PA-824 (nitroimidazo-oxazine) developed for anti-tuberculosis therapy against both replicating and persistent bacteria. It converts PA-824 into three primary metabolites; the major one is the des-nitroimidazole (des-nitro) which generated reactive nitrogen species, including nitric oxide (NO). Reactive nitrogen species play a major role in mammalian defense against mycobacterial infections.<ref>PMID:16387854</ref> <ref>PMID:19039139</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Tuberculosis continues to be a global health threat, making bicyclic nitroimidazoles an important new class of therapeutics. A deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis catalyzes the reduction of nitroimidazoles such as PA-824, resulting in intracellular release of lethal reactive nitrogen species. The N-terminal 30 residues of Ddn are functionally important but are flexible or access multiple conformations, preventing structural characterization of the full-length, enzymatically active enzyme. Several structures were determined of a truncated, inactive Ddn protein core with and without bound F(420) deazaflavin coenzyme as well as of a catalytically competent homolog from Nocardia farcinica. Mutagenesis studies based on these structures identified residues important for binding of F(420) and PA-824. The proposed orientation of the tail of PA-824 toward the N terminus of Ddn is consistent with current structure-activity relationship data.
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Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824.,Cellitti SE, Shaffer J, Jones DH, Mukherjee T, Gurumurthy M, Bursulaya B, Boshoff HI, Choi I, Nayyar A, Lee YS, Cherian J, Niyomrattanakit P, Dick T, Manjunatha UH, Barry CE 3rd, Spraggon G, Geierstanger BH Structure. 2012 Jan 11;20(1):101-12. PMID:22244759<ref>PMID:22244759</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 3r5w" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[Nitroreductase|Nitroreductase]]
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*[[Nitroreductase 3D structures|Nitroreductase 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Barry, C E]]
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[[Category: Mycobacterium tuberculosis]]
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[[Category: Boshoff, H I.M]]
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[[Category: Barry CE]]
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[[Category: Bursulaya, B]]
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[[Category: Boshoff HIM]]
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[[Category: Cellitti, S E]]
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[[Category: Bursulaya B]]
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[[Category: Cherian, J]]
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[[Category: Cellitti SE]]
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[[Category: Choi, I]]
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[[Category: Cherian J]]
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[[Category: Dick, T]]
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[[Category: Choi I]]
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[[Category: Geierstanger, B H]]
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[[Category: Dick T]]
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[[Category: Gurumurthy, M]]
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[[Category: Geierstanger BH]]
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[[Category: Jones, D H]]
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[[Category: Gurumurthy M]]
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[[Category: Lee, Y S]]
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[[Category: Jones DH]]
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[[Category: Manjunatha, U H]]
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[[Category: Lee YS]]
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[[Category: Mukherjee, T]]
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[[Category: Manjunatha UH]]
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[[Category: Nayya, A]]
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[[Category: Mukherjee T]]
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[[Category: Niyomrattanakit, P]]
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[[Category: Nayya A]]
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[[Category: Shaffer, J]]
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[[Category: Niyomrattanakit P]]
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[[Category: Spraggon, G]]
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[[Category: Shaffer J]]
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[[Category: Deazaflavin-dependent nitroreductase]]
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[[Category: Spraggon G]]
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[[Category: Duf385]]
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[[Category: F420]]
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[[Category: Nitroimidazole]]
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[[Category: Opc-67683]]
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[[Category: Oxidoreductase]]
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[[Category: Pa-824]]
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[[Category: Split barrel-like fold]]
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Current revision

Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420

PDB ID 3r5w

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