3bnh: Difference between revisions
New page: left|200px<br /><applet load="3bnh" size="350" color="white" frame="true" align="right" spinBox="true" caption="3bnh, resolution 1.75Å" /> '''W. succinogenes NrfA... |
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[[Image:3bnh.jpg|left|200px]] | [[Image:3bnh.jpg|left|200px]] | ||
'''W. succinogenes NrfA Y218F Nitrite Complex''' | {{Structure | ||
|PDB= 3bnh |SIZE=350|CAPTION= <scene name='initialview01'>3bnh</scene>, resolution 1.75Å | |||
|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> | |||
|LIGAND= <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y1:YTTRIUM+ION'>Y1</scene> and <scene name='pdbligand=HEM:PROTOPORPHYRIN IX CONTAINING FE'>HEM</scene> | |||
|ACTIVITY= [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] | |||
|GENE= nrfA Y218F ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=844 Wolinella succinogenes]) | |||
}} | |||
'''W. succinogenes NrfA Y218F Nitrite Complex''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
3BNH is a [ | 3BNH 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=3BNH OCA]. | ||
==Reference== | ==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:// | 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: Nitrite reductase (cytochrome; ammonia-forming)]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: transport]] | [[Category: transport]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:00:10 2008'' | ||
Revision as of 20:00, 20 March 2008
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| , resolution 1.75Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , , , , , , and | ||||||
| Ligands: | , , , , and | ||||||
| Gene: | nrfA Y218F (Wolinella succinogenes) | ||||||
| Activity: | Nitrite reductase (cytochrome; ammonia-forming), with EC number 1.7.2.2 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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 Thu Mar 20 19:00:10 2008