6l1x: Difference between revisions

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<StructureSection load='6l1x' size='340' side='right'caption='[[6l1x]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
<StructureSection load='6l1x' size='340' side='right'caption='[[6l1x]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6l1x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Neiml Neiml]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L1X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L1X FirstGlance]. <br>
<table><tr><td colspan='2'>[[6l1x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis_alpha14 Neisseria meningitidis alpha14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L1X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L1X FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.15&#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;'>[[6fwf|6fwf]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">norB, NMO_1451 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=662598 NEIML])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitric-oxide_reductase_(cytochrome_c) Nitric-oxide reductase (cytochrome c)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.5 1.7.2.5] </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=6l1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l1x OCA], [https://pdbe.org/6l1x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l1x RCSB], [https://www.ebi.ac.uk/pdbsum/6l1x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l1x 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=6l1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l1x OCA], [https://pdbe.org/6l1x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l1x RCSB], [https://www.ebi.ac.uk/pdbsum/6l1x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l1x ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/C6S880_NEIML C6S880_NEIML]
Neisseria meningitidis is carried by nearly a billion humans, causing developmental impairment and over 100 000 deaths a year. A quinol-dependent nitric oxide reductase (qNOR) plays a critical role in the survival of the bacterium in the human host. X-ray crystallographic analyses of qNOR, including that from N. meningitidis (NmqNOR) reported here at 3.15 A resolution, show monomeric assemblies, despite the more active dimeric sample being used for crystallization. Cryo-electron microscopic analysis of the same chromatographic fraction of NmqNOR, however, revealed a dimeric assembly at 3.06 A resolution. It is shown that zinc (which is used in crystallization) binding near the dimer-stabilizing TMII region contributes to the disruption of the dimer. A similar destabilization is observed in the monomeric ( approximately 85 kDa) cryo-EM structure of a mutant (Glu494Ala) qNOR from the opportunistic pathogen Alcaligenes (Achromobacter) xylosoxidans, which primarily migrates as a monomer. The monomer-dimer transition of qNORs seen in the cryo-EM and crystallographic structures has wider implications for structural studies of multimeric membrane proteins. X-ray crystallographic and cryo-EM structural analyses have been performed on the same chromatographic fraction of NmqNOR to high resolution. This represents one of the first examples in which the two approaches have been used to reveal a monomeric assembly in crystallo and a dimeric assembly in vitrified cryo-EM grids. A number of factors have been identified that may trigger the destabilization of helices that are necessary to preserve the integrity of the dimer. These include zinc binding near the entry of the putative proton-transfer channel and the preservation of the conformational integrity of the active site. The mutation near the active site results in disruption of the active site, causing an additional destabilization of helices (TMIX and TMX) that flank the proton-transfer channel helices, creating an inert monomeric enzyme.
 
The active form of quinol-dependent nitric oxide reductase from Neisseria meningitidis is a dimer.,Jamali MAM, Gopalasingam CC, Johnson RM, Tosha T, Muramoto K, Muench SP, Antonyuk SV, Shiro Y, Hasnain SS IUCrJ. 2020 Mar 21;7(Pt 3):404-415. doi: 10.1107/S2052252520003656. eCollection, 2020 May 1. PMID:32431824<ref>PMID:32431824</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6l1x" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Neiml]]
[[Category: Neisseria meningitidis alpha14]]
[[Category: Antonyuk, S V]]
[[Category: Antonyuk SV]]
[[Category: Hasnain, S S]]
[[Category: Hasnain SS]]
[[Category: Jamali, M M.A]]
[[Category: Jamali MMA]]
[[Category: Muramoto, K]]
[[Category: Muramoto K]]
[[Category: Shiro, Y]]
[[Category: Shiro Y]]
[[Category: Tosha, T]]
[[Category: Tosha T]]
[[Category: Membrane-bound]]
[[Category: Nitric oxide]]
[[Category: Oxidoreductase]]
[[Category: Reductase]]

Latest revision as of 13:45, 27 March 2024

Quinol-dependent nitric oxide reductase (qNOR) from Neisseria meningitidis in the monomeric oxidized state with zinc complex.Quinol-dependent nitric oxide reductase (qNOR) from Neisseria meningitidis in the monomeric oxidized state with zinc complex.

Structural highlights

6l1x is a 1 chain structure with sequence from Neisseria meningitidis alpha14. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.15Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

C6S880_NEIML

6l1x, resolution 3.15Å

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OCA
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