3bnh: Difference between revisions

Revision as of 20:56, 4 May 2008

W. succinogenes NrfA Y218F Nitrite Complex

OverviewOverview

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.

About this StructureAbout this Structure

3BNH is a Single protein structure of sequence from Wolinella succinogenes. Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Sun May 4 20:56:13 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:3bnh.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 3bnh |SIZE=350|CAPTION= <scene name='initialview01'>3bnh</scene>, resolution 1.75&Aring;
+The line below this paragraph, containing "STRUCTURE_3bnh", creates the "Structure Box" on the page.
-|SITE= <scene name='pdbsite=AC1:No2+Binding+Site+For+Residue+A+1'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Residue+A+508'>AC2</scene>, <scene name='pdbsite=AC3:Act+Binding+Site+For+Residue+A+2'>AC3</scene>, <scene name='pdbsite=AC4:Act+Binding+Site+For+Residue+A+3'>AC4</scene>, <scene name='pdbsite=AC5:So4+Binding+Site+For+Residue+A+509'>AC5</scene>, <scene name='pdbsite=AC6:Y1+Binding+Site+For+Residue+A+515'>AC6</scene>, <scene name='pdbsite=AC7:Y1+Binding+Site+For+Residue+A+516'>AC7</scene>, <scene name='pdbsite=AC8:Y1+Binding+Site+For+Residue+A+517'>AC8</scene>, <scene name='pdbsite=AC9:Hem+Binding+Site+For+Residue+A+510'>AC9</scene>, <scene name='pdbsite=BC1:Hem+Binding+Site+For+Residue+A+511'>BC1</scene>, <scene name='pdbsite=BC2:Hem+Binding+Site+For+Residue+A+512'>BC2</scene>, <scene name='pdbsite=BC3:Hem+Binding+Site+For+Residue+A+513'>BC3</scene> and <scene name='pdbsite=BC4:Hem+Binding+Site+For+Residue+A+514'>BC4</scene>
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|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=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y1:YTTRIUM+ION'>Y1</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|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>
+or leave the SCENE parameter empty for the default display.
-|GENE= nrfA Y218F ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=844 Wolinella succinogenes])
+-->
-|DOMAIN=
+{{STRUCTURE_3bnh|  PDB=3bnh  |  SCENE=  }}
-|RELATEDENTRY=[[1fs7|1FS7]], [[3bnf|3BNF]], [[3bng|3BNG]], [[3bnj|3BNJ]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bnh OCA], [http://www.ebi.ac.uk/pdbsum/3bnh PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bnh RCSB]</span>
-}}
 '''W. succinogenes NrfA Y218F Nitrite Complex'''
@@ Line 23: / Line 20: @@
 ==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: Einsle, O.]]
 [[Category: Lukat, P.]]
-[[Category: c-type cytochrome]]
+[[Category: C-type cytochrome]]
-[[Category: calcium]]
+[[Category: Calcium]]
-[[Category: electron transport]]
+[[Category: Electron transport]]
-[[Category: heme]]
+[[Category: Heme]]
-[[Category: iron]]
+[[Category: Iron]]
-[[Category: metal-binding]]
+[[Category: Metal-binding]]
-[[Category: nitrite complex]]
+[[Category: Nitrite complex]]
-[[Category: nitrite reductase]]
+[[Category: Nitrite reductase]]
-[[Category: oxidoreductase]]
+[[Category: Oxidoreductase]]
-[[Category: periplasm]]
+[[Category: Periplasm]]
-[[Category: transport]]
+[[Category: Transport]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 20:56:13 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:27:39 2008''