3d1i: Difference between revisions
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==Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite== | ==Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite== | ||
<StructureSection load='3d1i' size='340' side='right' caption='[[3d1i]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='3d1i' size='340' side='right'caption='[[3d1i]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3d1i]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3d1i]] 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=3D1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D1I FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=NO2:NITRITE+ION'>NO2</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> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</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=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</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></td></tr> | |||
<tr id='resources'><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=3d1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1i OCA], [https://pdbe.org/3d1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d1i RCSB], [https://www.ebi.ac.uk/pdbsum/3d1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1i ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == 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/d1/3d1i_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/3d1i_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> | ||
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==See Also== | ==See Also== | ||
*[[ | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Antipov | [[Category: Thioalkalivibrio nitratireducens]] | ||
[[Category: Bourenkov | [[Category: Antipov AN]] | ||
[[Category: Boyko | [[Category: Bourenkov GP]] | ||
[[Category: Lamzin | [[Category: Boyko KM]] | ||
[[Category: Polyakov | [[Category: Lamzin VS]] | ||
[[Category: Popov | [[Category: Polyakov KM]] | ||
[[Category: Popov | [[Category: Popov AN]] | ||
[[Category: Slutsky | [[Category: Popov VO]] | ||
[[Category: Tikhonova | [[Category: Slutsky A]] | ||
[[Category: Zvyagilskaya | [[Category: Tikhonova TV]] | ||
[[Category: Zvyagilskaya RA]] | |||
