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| | ==Reduced and acetaldoxime-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment== | | ==Reduced and acetaldoxime-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment== |
| - | <StructureSection load='3wfd' size='340' side='right' caption='[[3wfd]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='3wfd' size='340' side='right'caption='[[3wfd]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wfd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WFD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wfd]] 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=3WFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WFD 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=AXO:(1E)-N-HYDROXYETHANIMINE'>AXO</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></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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3o0r|3o0r]], [[3wfb|3wfb]], [[3wfc|3wfc]], [[3wfe|3wfe]]</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=AXO:(1E)-N-HYDROXYETHANIMINE'>AXO</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></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric-oxide_reductase_(cytochrome_c) Nitric-oxide reductase (cytochrome c)], with EC number [http://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=3wfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wfd OCA], [https://pdbe.org/3wfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wfd RCSB], [https://www.ebi.ac.uk/pdbsum/3wfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wfd ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wfd OCA], [http://pdbe.org/3wfd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wfd RCSB], [http://www.ebi.ac.uk/pdbsum/3wfd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wfd ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NORC_PSEAE NORC_PSEAE]] Component of the anaerobic respiratory chain that transforms nitrate to dinitrogen (denitrification). [[http://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). | + | [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 == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Mus musculus]] | | [[Category: Mus musculus]] |
| - | [[Category: Pseudomonas aeruginosa]] | + | [[Category: Pseudomonas aeruginosa PAO1]] |
| - | [[Category: Fukumori, Y]] | + | [[Category: Fukumori Y]] |
| - | [[Category: Hino, T]] | + | [[Category: Hino T]] |
| - | [[Category: Ishii, S]] | + | [[Category: Ishii S]] |
| - | [[Category: Sato, N]] | + | [[Category: Sato N]] |
| - | [[Category: Shiro, Y]] | + | [[Category: Shiro Y]] |
| - | [[Category: Sugimoto, H]] | + | [[Category: Sugimoto H]] |
| - | [[Category: Tosha, T]] | + | [[Category: Tosha T]] |
| - | [[Category: Immune system-oxidoreductase complex]]
| + | |
| - | [[Category: Membrane protein]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| Structural highlights
3wfd is a 4 chain structure with sequence from Mus musculus and Pseudomonas aeruginosa PAO1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.3Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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).
Publication Abstract from PubMed
Nitric oxide reductase (NOR) catalyzes the generation of nitrous oxide (N2 O) via the reductive coupling of two nitric oxide (NO) molecules at a heme/non-heme Fe center. We report herein on the structures of the reduced and ligand-bound forms of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa at a resolution of 2.3-2.7 A, to elucidate structure-function relationships in NOR, and compare them to those of cytochrome c oxidase (CCO) that is evolutionarily related to NOR. Comprehensive crystallographic refinement of the CO-bound form of cNOR suggested that a total of four atoms can be accommodated at the binuclear center. Consistent with this, binding of bulky acetaldoxime (CH3 -CH=N-OH) to the binuclear center of cNOR was confirmed by the structural analysis. Active site reduction and ligand binding in cNOR induced only ~0.5 A increase in the heme/non-heme Fe distance, but no significant structural change in the protein. The highly localized structural change is consistent with the lack of proton-pumping activity in cNOR, because redox-coupled conformational changes are thought to be crucial for proton pumping in CCO. It also permits the rapid decomposition of cytotoxic NO in denitrification. In addition, the shorter heme/non-heme Fe distance even in the bulky ligand-bound form of cNOR (~4.5 A) than the heme/Cu distance in CCO (~5 A) suggests the ability of NOR to maintain two NO molecules within a short distance in the confined space of the active site, thereby facilitating N-N coupling to produce a hyponitrite intermediate for the generation of N2 O. (c) Proteins 2013;. (c) 2013 Wiley Periodicals, Inc.
Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes.,Sato N, Ishii S, Sugimoto H, Hino T, Fukumori Y, Sako Y, Shiro Y, Tosha T Proteins. 2013 Dec 13. doi: 10.1002/prot.24492. PMID:24338896[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Sato N, Ishii S, Sugimoto H, Hino T, Fukumori Y, Sako Y, Shiro Y, Tosha T. Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes. Proteins. 2013 Dec 13. doi: 10.1002/prot.24492. PMID:24338896 doi:http://dx.doi.org/10.1002/prot.24492
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