3mmo
From Proteopedia
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| - | {{Seed}} | ||
| - | [[Image:3mmo.png|left|200px]] | ||
| - | < | + | ==Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with cyanide== |
| - | + | <StructureSection load='3mmo' size='340' side='right'caption='[[3mmo]], [[Resolution|resolution]] 1.55Å' scene=''> | |
| - | You may | + | == Structural highlights == |
| - | + | <table><tr><td colspan='2'>[[3mmo]] 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=3MMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MMO FirstGlance]. <br> | |
| - | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55Å</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=CYN:CYANIDE+ION'>CYN</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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=3mmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mmo OCA], [https://pdbe.org/3mmo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mmo RCSB], [https://www.ebi.ac.uk/pdbsum/3mmo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mmo ProSAT]</span></td></tr> | |
| + | </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 == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mm/3mmo_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </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/main_output.php?pdb_ID=3mmo ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The 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<ref>PMID:20944237</ref> | |
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 3mmo" style="background-color:#fffaf0;"></div> | ||
| - | == | + | ==See Also== |
| - | + | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] | |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Thioalkalivibrio nitratireducens]] | [[Category: Thioalkalivibrio nitratireducens]] | ||
| - | [[Category: Bourenkov | + | [[Category: Bourenkov GP]] |
| - | [[Category: Boyko | + | [[Category: Boyko KM]] |
| - | [[Category: Lamzin | + | [[Category: Lamzin VS]] |
| - | [[Category: Polyakov | + | [[Category: Polyakov KM]] |
| - | [[Category: Popov | + | [[Category: Popov VO]] |
| - | [[Category: Tikhonova | + | [[Category: Tikhonova TV]] |
| - | [[Category: Trofimov | + | [[Category: Trofimov AA]] |
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Current revision
Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with cyanide
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