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| | <StructureSection load='3mmo' size='340' side='right'caption='[[3mmo]], [[Resolution|resolution]] 1.55Å' scene=''> | | <StructureSection load='3mmo' size='340' side='right'caption='[[3mmo]], [[Resolution|resolution]] 1.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3mmo]] is a 2 chain structure with sequence from [http://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 [http://proteopedia.org/fgij/fg.htm?mol=3MMO FirstGlance]. <br> | + | <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='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> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ot4|2ot4]], [[3f29|3f29]]</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'>[http://proteopedia.org/fgij/fg.htm?mol=3mmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mmo OCA], [http://pdbe.org/3mmo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mmo RCSB], [http://www.ebi.ac.uk/pdbsum/3mmo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3mmo ProSAT]</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=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> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q5F2I3_9GAMM Q5F2I3_9GAMM]] Plays a role in nitrite reduction (By similarity).[SAAS:SAAS003321_004_001592] | + | [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]] |
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| | ==See Also== | | ==See Also== |
| | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] | | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] |
| - | *[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]] | |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| | [[Category: Thioalkalivibrio nitratireducens]] | | [[Category: Thioalkalivibrio nitratireducens]] |
| - | [[Category: Bourenkov, G P]] | + | [[Category: Bourenkov GP]] |
| - | [[Category: Boyko, K M]] | + | [[Category: Boyko KM]] |
| - | [[Category: Lamzin, V S]] | + | [[Category: Lamzin VS]] |
| - | [[Category: Polyakov, K M]] | + | [[Category: Polyakov KM]] |
| - | [[Category: Popov, V O]] | + | [[Category: Popov VO]] |
| - | [[Category: Tikhonova, T V]] | + | [[Category: Tikhonova TV]] |
| - | [[Category: Trofimov, A A]] | + | [[Category: Trofimov AA]] |
| - | [[Category: Alpha protein]]
| + | |
| - | [[Category: Eight hemes c]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
3mmo is a 2 chain structure with sequence from Thioalkalivibrio nitratireducens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.55Å |
| Ligands: | , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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).[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 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[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tikhonova TV, Slutsky A, Antipov AN, Boyko KM, Polyakov KM, Sorokin DY, Zvyagilskaya RA, Popov VO. Molecular and catalytic properties of a novel cytochrome c nitrite reductase from nitrate-reducing haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio nitratireducens. Biochim Biophys Acta. 2006 Apr;1764(4):715-23. Epub 2006 Feb 9. PMID:16500161 doi:http://dx.doi.org/10.1016/j.bbapap.2005.12.021
- ↑ Trofimov AA, Polyakov KM, Boyko KM, Tikhonova TV, Safonova TN, Tikhonov AV, Popov AN, Popov VO. Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide. Acta Crystallogr D Biol Crystallogr. 2010 Oct;66(Pt 10):1043-7. Epub 2010, Sep 18. PMID:20944237 doi:10.1107/S0907444910031665
- ↑ Trofimov AA, Polyakov KM, Tikhonova TV, Tikhonov AV, Safonova TN, Boyko KM, Dorovatovskii PV, Popov VO. Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity. Acta Crystallogr D Biol Crystallogr. 2012 Feb;68(Pt 2):144-53. Epub 2012, Jan 13. PMID:22281743 doi:10.1107/S0907444911052632
- ↑ Trofimov AA, Polyakov KM, Boyko KM, Tikhonova TV, Safonova TN, Tikhonov AV, Popov AN, Popov VO. Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide. Acta Crystallogr D Biol Crystallogr. 2010 Oct;66(Pt 10):1043-7. Epub 2010, Sep 18. PMID:20944237 doi:10.1107/S0907444910031665
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