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| - | [[Image:3bng.jpg|left|200px]] | |
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| - | {{Structure
| + | ==W. succinogenes NrfA Y218F== |
| - | |PDB= 3bng |SIZE=350|CAPTION= <scene name='initialview01'>3bng</scene>, resolution 1.50Å
| + | <StructureSection load='3bng' size='340' side='right'caption='[[3bng]], [[Resolution|resolution]] 1.50Å' scene=''> |
| - | |SITE= <scene name='pdbsite=AC1:Act+Binding+Site+For+Residue+A+3'>AC1</scene>, <scene name='pdbsite=AC2:Act+Binding+Site+For+Residue+A+4'>AC2</scene>, <scene name='pdbsite=AC3:Act+Binding+Site+For+Residue+A+5'>AC3</scene>, <scene name='pdbsite=AC4:So4+Binding+Site+For+Residue+A+1'>AC4</scene>, <scene name='pdbsite=AC5:So4+Binding+Site+For+Residue+A+2'>AC5</scene>, <scene name='pdbsite=AC6:Ca+Binding+Site+For+Residue+A+508'>AC6</scene>, <scene name='pdbsite=AC7:Y1+Binding+Site+For+Residue+A+509'>AC7</scene>, <scene name='pdbsite=AC8:Y1+Binding+Site+For+Residue+A+510'>AC8</scene>, <scene name='pdbsite=AC9:Y1+Binding+Site+For+Residue+A+511'>AC9</scene>, <scene name='pdbsite=BC1:Y1+Binding+Site+For+Residue+A+512'>BC1</scene>, <scene name='pdbsite=BC2:Hem+Binding+Site+For+Residue+A+513'>BC2</scene>, <scene name='pdbsite=BC3:Hem+Binding+Site+For+Residue+A+514'>BC3</scene>, <scene name='pdbsite=BC4:Hem+Binding+Site+For+Residue+A+515'>BC4</scene>, <scene name='pdbsite=BC5:Hem+Binding+Site+For+Residue+A+516'>BC5</scene> and <scene name='pdbsite=BC6:Hem+Binding+Site+For+Residue+A+517'>BC6</scene>
| + | == Structural highlights == |
| - | |LIGAND= <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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y1:YTTRIUM+ION'>Y1</scene>
| + | <table><tr><td colspan='2'>[[3bng]] 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=3BNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BNG FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(cytochrome;_ammonia-forming) Nitrite reductase (cytochrome; ammonia-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.2 1.7.2.2] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</td></tr> |
| - | |GENE= nrfA Y218F ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=844 Wolinella succinogenes])
| + | <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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y1:YTTRIUM+ION'>Y1</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bng OCA], [https://pdbe.org/3bng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bng RCSB], [https://www.ebi.ac.uk/pdbsum/3bng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bng ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1fs7|1FS7]], [[3bnf|3BNF]], [[3bnh|3BNH]], [[3bnj|3BNJ]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bng OCA], [http://www.ebi.ac.uk/pdbsum/3bng PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bng RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/NRFA_WOLSU NRFA_WOLSU] Plays a role in nitrite reduction.<ref>PMID:10672190</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/bn/3bng_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=3bng ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | '''W. succinogenes NrfA Y218F'''
| + | ==See Also== |
| - | | + | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] |
| - | | + | == References == |
| - | ==Overview== | + | <references/> |
| - | 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.
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==About this Structure== | + | [[Category: Large Structures]] |
| - | 3BNG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Wolinella_succinogenes Wolinella succinogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BNG OCA].
| + | |
| - | | + | |
| - | ==Reference==
| + | |
| - | 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:[http://www.ncbi.nlm.nih.gov/pubmed/18201106 18201106]
| + | |
| - | [[Category: Nitrite reductase (cytochrome; ammonia-forming)]]
| + | |
| - | [[Category: Single protein]] | + | |
| | [[Category: Wolinella succinogenes]] | | [[Category: Wolinella succinogenes]] |
| - | [[Category: Einsle, O.]] | + | [[Category: Einsle O]] |
| - | [[Category: Lukat, P.]] | + | [[Category: Lukat P]] |
| - | [[Category: c-type cytochrome]]
| + | |
| - | [[Category: calcium]]
| + | |
| - | [[Category: electron transport]]
| + | |
| - | [[Category: heme]]
| + | |
| - | [[Category: iron]]
| + | |
| - | [[Category: metal-binding]]
| + | |
| - | [[Category: nitrite reductase]]
| + | |
| - | [[Category: oxidoreductase]]
| + | |
| - | [[Category: periplasm]]
| + | |
| - | [[Category: transport]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:27:38 2008''
| + | |
