5gux: Difference between revisions
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==Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon== | ==Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon== | ||
<StructureSection load='5gux' size='340' side='right' caption='[[5gux]], [[Resolution|resolution]] 3.30Å' scene=''> | <StructureSection load='5gux' size='340' side='right'caption='[[5gux]], [[Resolution|resolution]] 3.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5gux]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5gux]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GUX FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=10M:DECYL+4-O-ALPHA-D-GLUCOPYRANOSYL-1-THIO-BETA-D-GLUCOPYRANOSIDE'>10M</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=XE:XENON'>XE</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=10M:DECYL+4-O-ALPHA-D-GLUCOPYRANOSYL-1-THIO-BETA-D-GLUCOPYRANOSIDE'>10M</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=XE:XENON'>XE</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=5gux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gux OCA], [https://pdbe.org/5gux PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gux RCSB], [https://www.ebi.ac.uk/pdbsum/5gux PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gux ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/NORB_PSEAE NORB_PSEAE] Component of the anaerobic respiratory chain that transforms nitrate to dinitrogen (denitrification). NorB is the catalytic subunit of the enzyme complex. Shows proton pump activity across the membrane in denitrifying bacterial cells. The mononitrogen reduction is probably coupled to electron transport phosphorylation (By similarity). | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 20: | Line 19: | ||
</div> | </div> | ||
<div class="pdbe-citations 5gux" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5gux" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Antibody 3D structures|Antibody 3D structures]] | |||
*[[3D structures of non-human antibody|3D structures of non-human antibody]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Mus musculus]] | [[Category: Mus musculus]] | ||
[[Category: Pseudomonas aeruginosa | [[Category: Pseudomonas aeruginosa PAO1]] | ||
[[Category: Ishii | [[Category: Ishii S]] | ||
[[Category: Shiro | [[Category: Shiro Y]] | ||
[[Category: Sugimoto | [[Category: Sugimoto H]] | ||
[[Category: Terasaka | [[Category: Terasaka E]] | ||
[[Category: Tosha | [[Category: Tosha T]] | ||
Latest revision as of 14:43, 2 August 2023
Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenonCytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon
Structural highlights
FunctionNORB_PSEAE Component of the anaerobic respiratory chain that transforms nitrate to dinitrogen (denitrification). NorB is the catalytic subunit of the enzyme complex. Shows proton pump activity across the membrane in denitrifying bacterial cells. The mononitrogen reduction is probably coupled to electron transport phosphorylation (By similarity). Publication Abstract from PubMedNitric oxide (NO) plays diverse and significant roles in biological processes despite its cytotoxicity, raising the question of how biological systems control the action of NO to minimize its cytotoxicity in cells. As a great example of such a system, we found a possibility that NO-generating nitrite reductase (NiR) forms a complex with NO-decomposing membrane-integrated NO reductase (NOR) to efficiently capture NO immediately after its production by NiR in anaerobic nitrate respiration called denitrification. The 3.2-A resolution structure of the complex of one NiR functional homodimer and two NOR molecules provides an idea of how these enzymes interact in cells, while the structure may not reflect the one in cells due to the membrane topology. Subsequent all-atom molecular dynamics (MD) simulations of the enzyme complex model in a membrane and structure-guided mutagenesis suggested that a few interenzyme salt bridges and coulombic interactions of NiR with the membrane could stabilize the complex of one NiR homodimer and one NOR molecule and contribute to rapid NO decomposition in cells. The MD trajectories of the NO diffusion in the NiR:NOR complex with the membrane showed that, as a plausible NO transfer mechanism, NO released from NiR rapidly migrates into the membrane, then binds to NOR. These results help us understand the mechanism of the cellular control of the action of cytotoxic NO. Dynamics of nitric oxide controlled by protein complex in bacterial system.,Terasaka E, Yamada K, Wang PH, Hosokawa K, Yamagiwa R, Matsumoto K, Ishii S, Mori T, Yagi K, Sawai H, Arai H, Sugimoto H, Sugita Y, Shiro Y, Tosha T Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9888-9893. doi:, 10.1073/pnas.1621301114. Epub 2017 Aug 28. PMID:28847930[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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