3r5y: Difference between revisions

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<StructureSection load='3r5y' size='340' side='right'caption='[[3r5y]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='3r5y' size='340' side='right'caption='[[3r5y]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3r5y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinomyces_bovis_farcinicus"_gasperini_1894 "actinomyces bovis farcinicus" gasperini 1894]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R5Y FirstGlance]. <br>
<table><tr><td colspan='2'>[[3r5y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Nocardia_farcinica Nocardia farcinica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R5Y FirstGlance]. <br>
</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.801&#8491;</td></tr>
<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]], [[3r5w|3r5w]], [[3r5z|3r5z]]</div></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>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NFA_33440 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37329 "Actinomyces bovis farcinicus" Gasperini 1894])</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=3r5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5y OCA], [https://pdbe.org/3r5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r5y RCSB], [https://www.ebi.ac.uk/pdbsum/3r5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5y 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=3r5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5y OCA], [https://pdbe.org/3r5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r5y RCSB], [https://www.ebi.ac.uk/pdbsum/3r5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5y ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/Q5YUF0_NOCFA Q5YUF0_NOCFA]
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3r5y" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Actinomyces bovis farcinicus gasperini 1894]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Barry, C E]]
[[Category: Nocardia farcinica]]
[[Category: Boshoff, H I.M]]
[[Category: Barry CE]]
[[Category: Bursulaya, B]]
[[Category: Boshoff HIM]]
[[Category: Cellitti, S E]]
[[Category: Bursulaya B]]
[[Category: Cherian, J]]
[[Category: Cellitti SE]]
[[Category: Choi, I]]
[[Category: Cherian J]]
[[Category: Dick, T]]
[[Category: Choi I]]
[[Category: Geierstanger, B H]]
[[Category: Dick T]]
[[Category: Gurumurthy, M]]
[[Category: Geierstanger BH]]
[[Category: Jones, D H]]
[[Category: Gurumurthy M]]
[[Category: Lee, Y S]]
[[Category: Jones DH]]
[[Category: Manjunatha, U H]]
[[Category: Lee YS]]
[[Category: Mukherjee, T]]
[[Category: Manjunatha UH]]
[[Category: Nayya, A]]
[[Category: Mukherjee T]]
[[Category: Niyomrattanakit, P]]
[[Category: Nayya A]]
[[Category: Shaffer, J]]
[[Category: Niyomrattanakit P]]
[[Category: Spraggon, G]]
[[Category: Shaffer J]]
[[Category: Deazaflavin-dependent nitroreductase]]
[[Category: Spraggon G]]
[[Category: Duf385]]
[[Category: F420]]
[[Category: Nitroimidazole]]
[[Category: Pa-824]]
[[Category: Split barrel-like fold]]
[[Category: Unknown function]]

Latest revision as of 12:11, 14 March 2024

Structure of a Deazaflavin-dependent nitroreductase from Nocardia farcinica, with co-factor F420

3r5y, resolution 1.80Å

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