View source for 7xk3


==Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, state 1==
<StructureSection load='7xk3' size='340' side='right'caption='[[7xk3]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7xk3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae_O395 Vibrio cholerae O395]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XK3 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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PEE:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>PEE</scene>, <scene name='pdbligand=RBF:RIBOFLAVIN'>RBF</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=7xk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xk3 OCA], [https://pdbe.org/7xk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xk3 RCSB], [https://www.ebi.ac.uk/pdbsum/7xk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xk3 ProSAT]</span></td></tr>
</table>
== Function ==
[[https://www.uniprot.org/uniprot/NQRA_VIBC3 NQRA_VIBC3]] NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol.[HAMAP-Rule:MF_00425]
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== Publication Abstract from PubMed ==
The Na(+)-pumping NADH-ubiquinone oxidoreductase (Na(+)-NQR) couples electron transfer from NADH to ubiquinone with Na(+)-pumping, generating an electrochemical Na(+) gradient that is essential for energy-consuming reactions in bacteria. Since Na(+)-NQR is exclusively found in prokaryotes, it is a promising target for highly selective antibiotics. However, the molecular mechanism of inhibition is not well-understood for lack of the atomic structural information about an inhibitor-bound state. Here we present cryo-electron microscopy structures of Na(+)-NQR from Vibrio cholerae with or without a bound inhibitor at 2.5- to 3.1-A resolution. The structures reveal the arrangement of all six redox cofactors including a herein identified 2Fe-2S cluster located between the NqrD and NqrE subunits. A large part of the hydrophilic NqrF is barely visible in the density map, suggesting a high degree of flexibility. This flexibility may be responsible to reducing the long distance between the 2Fe-2S centers in NqrF and NqrD/E. Two different types of specific inhibitors bind to the N-terminal region of NqrB, which is disordered in the absence of inhibitors. The present study provides a foundation for understanding the function of Na(+)-NQR and the binding manner of specific inhibitors.

Cryo-EM structures of Na(+)-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae.,Kishikawa JI, Ishikawa M, Masuya T, Murai M, Kitazumi Y, Butler NL, Kato T, Barquera B, Miyoshi H Nat Commun. 2022 Jul 26;13(1):4082. doi: 10.1038/s41467-022-31718-1. PMID:35882843<ref>PMID:35882843</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 7xk3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Vibrio cholerae O395]]
[[Category: Barquera B]]
[[Category: Ishikawa M]]
[[Category: Kishikawa J]]
[[Category: Masuya T]]
[[Category: Miyoshi H]]
[[Category: Murai M]]