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| | <StructureSection load='3bnj' size='340' side='right'caption='[[3bnj]], [[Resolution|resolution]] 1.30Å' scene=''> | | <StructureSection load='3bnj' size='340' side='right'caption='[[3bnj]], [[Resolution|resolution]] 1.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3bnj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_29543 Atcc 29543]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BNJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3bnj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Wolinella_succinogenes Wolinella succinogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BNJ FirstGlance]. <br> |
| - | </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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y1:YTTRIUM+ION'>Y1</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]] 1.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fs7|1fs7]], [[3bnf|3bnf]], [[3bng|3bng]], [[3bnh|3bnh]]</div></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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y1:YTTRIUM+ION'>Y1</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nrfA Y218F ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=844 ATCC 29543])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(cytochrome;_ammonia-forming) Nitrite reductase (cytochrome; ammonia-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.2 1.7.2.2] </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=3bnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnj OCA], [https://pdbe.org/3bnj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bnj RCSB], [https://www.ebi.ac.uk/pdbsum/3bnj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bnj 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=3bnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnj OCA], [https://pdbe.org/3bnj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bnj RCSB], [https://www.ebi.ac.uk/pdbsum/3bnj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bnj ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/NRFA_WOLSU NRFA_WOLSU]] Plays a role in nitrite reduction.<ref>PMID:10672190</ref>
| + | [https://www.uniprot.org/uniprot/NRFA_WOLSU NRFA_WOLSU] Plays a role in nitrite reduction.<ref>PMID:10672190</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/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 29543]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Einsle, O]] | + | [[Category: Wolinella succinogenes]] |
| - | [[Category: Lukat, P]] | + | [[Category: Einsle O]] |
| - | [[Category: C-type cytochrome]] | + | [[Category: Lukat P]] |
| - | [[Category: Calcium]]
| + | |
| - | [[Category: Electron transport]]
| + | |
| - | [[Category: Heme]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Nitrite reductase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Periplasm]]
| + | |
| - | [[Category: Sulfite complex]]
| + | |
| - | [[Category: Transport]]
| + | |
| Structural highlights
3bnj is a 1 chain structure with sequence from Wolinella succinogenes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.3Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
NRFA_WOLSU Plays a role in nitrite reduction.[1]
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
Pentaheme cytochrome c nitrite reductase (ccNiR) catalyzes the six-electron reduction of nitrite to ammonia as the final step in the dissimilatory pathway of nitrate ammonification. It has also been shown to reduce sulfite to sulfide, thus forming the only known link between the biogeochemical cycles of nitrogen and of sulfur. We have found the sulfite reductase activity of ccNiR from Wolinella succinogenes to be significantly smaller than its nitrite reductase activity but still several times higher than the one described for dissimilatory, siroheme-containing sulfite reductases. To compare the sulfite reductase activity of ccNiR with our previous data on nitrite reduction, we determined the binding mode of sulfite to the catalytic heme center of ccNiR from W. succinogenes at a resolution of 1.7 A. Sulfite and nitrite both provide a pair of electrons to form the coordinative bond to the Fe(III) active site of the enzyme, and the oxygen atoms of sulfite are found to interact with the three active site protein residues conserved within the enzyme family. Furthermore, we have characterized the active site variant Y218F of ccNiR that exhibited an almost complete loss of nitrite reductase activity, while sulfite reduction remained unaffected. These data provide a first direct insight into the role of the first sphere of protein ligands at the active site in ccNiR catalysis.
Binding and Reduction of Sulfite by Cytochrome c Nitrite Reductase(,).,Lukat P, Rudolf M, Stach P, Messerschmidt A, Kroneck PM, Simon J, Einsle O Biochemistry. 2008 Feb 19;47(7):2080-2086. Epub 2008 Jan 18. PMID:18201106[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Simon J, Gross R, Einsle O, Kroneck PM, Kroger A, Klimmek O. A NapC/NirT-type cytochrome c (NrfH) is the mediator between the quinone pool and the cytochrome c nitrite reductase of Wolinella succinogenes. Mol Microbiol. 2000 Feb;35(3):686-96. PMID:10672190
- ↑ Lukat P, Rudolf M, Stach P, Messerschmidt A, Kroneck PM, Simon J, Einsle O. Binding and Reduction of Sulfite by Cytochrome c Nitrite Reductase(,). Biochemistry. 2008 Feb 19;47(7):2080-2086. Epub 2008 Jan 18. PMID:18201106 doi:10.1021/bi7021415
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