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==Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)== | ==Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)== | ||
<StructureSection load='3fo3' size='340' side='right' caption='[[3fo3]], [[Resolution|resolution]] 1.40Å' scene=''> | <StructureSection load='3fo3' size='340' side='right'caption='[[3fo3]], [[Resolution|resolution]] 1.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3fo3]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3fo3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thioalkalivibrio_nitratireducens Thioalkalivibrio nitratireducens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FO3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FO3 FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=THJ:THIOSULFATE'>THJ</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.4Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=THJ:THIOSULFATE'>THJ</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3fo3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fo3 OCA], [https://pdbe.org/3fo3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fo3 RCSB], [https://www.ebi.ac.uk/pdbsum/3fo3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fo3 ProSAT]</span></td></tr> | ||
<table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/NIR_THIND NIR_THIND] Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process (PubMed:16500161, PubMed:22281743). Has very low activity toward hydroxylamine (PubMed:16500161). Has even lower activity toward sulfite (PubMed:16500161, PubMed:22281743). Sulfite reductase activity is maximal at neutral pH (PubMed:20944237).<ref>PMID:16500161</ref> <ref>PMID:20944237</ref> <ref>PMID:22281743</ref> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fo/3fo3_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fo/3fo3_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/ | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3fo3 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3fo3" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[ | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Thioalkalivibrio nitratireducens]] | [[Category: Thioalkalivibrio nitratireducens]] | ||
[[Category: Antipov | [[Category: Antipov AN]] | ||
[[Category: Bourenkov | [[Category: Bourenkov GP]] | ||
[[Category: Boyko | [[Category: Boyko KM]] | ||
[[Category: Lamzin | [[Category: Lamzin VS]] | ||
[[Category: Polyakov | [[Category: Polyakov KM]] | ||
[[Category: Popov | [[Category: Popov AN]] | ||
[[Category: Popov | [[Category: Popov VO]] | ||
[[Category: Slutsky | [[Category: Slutsky A]] | ||
[[Category: Tikhonova | [[Category: Tikhonova TV]] | ||
[[Category: Trofimov | [[Category: Trofimov AA]] | ||
[[Category: Zvyagilskaya | [[Category: Zvyagilskaya RA]] | ||
Latest revision as of 10:57, 9 October 2024
Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)
Structural highlights
FunctionNIR_THIND Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process (PubMed:16500161, PubMed:22281743). Has very low activity toward hydroxylamine (PubMed:16500161). Has even lower activity toward sulfite (PubMed:16500161, PubMed:22281743). Sulfite reductase activity is maximal at neutral pH (PubMed:20944237).[1] [2] [3] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe structures of complexes of octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR) with the substrate sulfite (1.4 A resolution; R(cryst) = 0.126) and the inhibitor cyanide (1.55 A resolution; R(cryst) = 0.148) have been established. The complex with sulfite was prepared by the reduction of the protein crystal with sodium dithionite. The sulfite ion is bound to the iron ion of the catalytic haem through the S atom. The Fe-S distance is 2.24 A. The structure of the cyanide complex with full occupancy of the ligand site was established for the first time for cytochrome c nitrite reductases. The cyanide ion is bound to the catalytic haem iron through the C atom. The Fe-C distance is 1.91 A and the Fe-C-N angle is 171 degrees . The sulfite reductase activity of TvNiR was measured at different pH values. The activity is 0.02 micromol of HS(-) per minute per milligram at pH 7.0; it decreases with increasing pH and is absent at pH 9.0. Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide.,Trofimov AA, Polyakov KM, Boyko KM, Tikhonova TV, Safonova TN, Tikhonov AV, Popov AN, Popov VO Acta Crystallogr D Biol Crystallogr. 2010 Oct;66(Pt 10):1043-7. Epub 2010, Sep 18. PMID:20944237[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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