3qdl: Difference between revisions

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<StructureSection load='3qdl' size='340' side='right'caption='[[3qdl]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3qdl' size='340' side='right'caption='[[3qdl]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3qdl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QDL FirstGlance]. <br>
<table><tr><td colspan='2'>[[3qdl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QDL FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rdxA, HP_0954 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=3qdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdl OCA], [https://pdbe.org/3qdl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qdl RCSB], [https://www.ebi.ac.uk/pdbsum/3qdl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qdl 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=3qdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdl OCA], [https://pdbe.org/3qdl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qdl RCSB], [https://www.ebi.ac.uk/pdbsum/3qdl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qdl ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RDXA_HELPY RDXA_HELPY]] Reduction of a variety of nitroaromatic compounds using NADPH as source of reducing equivalents; two electrons are transferred (By similarity). Capable of reducing metronidazole; inactive RdxA renders the bacterium resistant to this compound. The reduction of metronidazole generates hydroxylamine, a potent mutagen and bactericide.<ref>PMID:9622362</ref> 
[https://www.uniprot.org/uniprot/RDXA_HELPY RDXA_HELPY] Reduction of a variety of nitroaromatic compounds using NADPH as source of reducing equivalents; two electrons are transferred (By similarity). Capable of reducing metronidazole; inactive RdxA renders the bacterium resistant to this compound. The reduction of metronidazole generates hydroxylamine, a potent mutagen and bactericide.<ref>PMID:9622362</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The RdxA oxygen insensitive nitroreductase of the human gastric pathogen Helicobacter pylori is responsible for the susceptibility of this organism to the redox active prodrug metronidazole (MTZ). Loss-of-function mutations in rdxA are primarily responsible for resistance to this therapeutic. RdxA exhibits potent NADPH oxidase activity under aerobic conditions and metronidazole reductase activity under strictly anaerobic conditions. Here we report the crystal structure of RdxA, which is a homodimer exhibiting domain swapping and containing two molecules of FMN bound at the dimer interface. We have found a gap between the side chain of Tyr47 and the isoalloxazine ring of FMN that seems appropriate for substrate binding. The structure does not include residues 97-128, which corresponds to a locally unstable part of the NTR from E. coli, and might be involved in cofactor binding. Comparison of H pylori RdxA to other oxidoreductases of known structure suggests RdxA may belong to a new subgroup of oxidoreductases in which a cysteine sidechain close to the FMN cofactor could be involved in the reductive activity. In this respect, mutation of C159 to A or S (C159A/S) has resulted in loss of MTZ reductase activity, but not NADPH oxidase activity. The RdxA structure allows interpretation of the many loss-of-function mutations previously described, including those affecting C159, a residue whose interaction with FMN is required for nitroreduction of MTZ. Our studies provide unique insights into the redox behavior of the flavin in this key enzyme for metronidazole activation, and with potential use in gene therapy. (c) 2012 The Authors Journal compilation (c) 2012 FEBS.
 
Structure of RdxA: an oxygen insensitive nitroreductase essential for metronidazole activation in Helicobacter pylori.,Martinez-Julvez M, Rojas AL, Olekhnovich I, Angarica VE, Hoffman PS, Sancho J FEBS J. 2012 Oct 8. doi: 10.1111/febs.12020. PMID:23039228<ref>PMID:23039228</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3qdl" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Nitroreductase|Nitroreductase]]
*[[Nitroreductase 3D structures|Nitroreductase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 43504]]
[[Category: Helicobacter pylori]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Hoffman, P S]]
[[Category: Hoffman PS]]
[[Category: Martinez-Julvez, M]]
[[Category: Martinez-Julvez M]]
[[Category: Olekhnovich, I N]]
[[Category: Olekhnovich IN]]
[[Category: Rojas, A L]]
[[Category: Rojas AL]]
[[Category: Sancho, J]]
[[Category: Sancho J]]
[[Category: Oxidoreductase]]

Latest revision as of 14:41, 14 March 2024

Crystal structure of RdxA from Helicobacter pyroliCrystal structure of RdxA from Helicobacter pyroli

Structural highlights

3qdl is a 4 chain structure with sequence from Helicobacter pylori. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RDXA_HELPY Reduction of a variety of nitroaromatic compounds using NADPH as source of reducing equivalents; two electrons are transferred (By similarity). Capable of reducing metronidazole; inactive RdxA renders the bacterium resistant to this compound. The reduction of metronidazole generates hydroxylamine, a potent mutagen and bactericide.[1]

See Also

References

  1. ↑ Goodwin A, Kersulyte D, Sisson G, Veldhuyzen van Zanten SJ, Berg DE, Hoffman PS. Metronidazole resistance in Helicobacter pylori is due to null mutations in a gene (rdxA) that encodes an oxygen-insensitive NADPH nitroreductase. Mol Microbiol. 1998 Apr;28(2):383-93. PMID:9622362

3qdl, resolution 2.00Å

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