This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2ppe
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:2ppe.jpg|left|200px]] | + | [[Image:2ppe.jpg|left|200px]] |
| - | + | ||
| - | '''Reduced H145A mutant of AfNiR exposed to NO''' | + | {{Structure |
| + | |PDB= 2ppe |SIZE=350|CAPTION= <scene name='initialview01'>2ppe</scene>, resolution 1.75Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NO:NITROGEN+OXIDE'>NO</scene> and <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] | ||
| + | |GENE= nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis]) | ||
| + | }} | ||
| + | |||
| + | '''Reduced H145A mutant of AfNiR exposed to NO''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 2PPE is a [ | + | 2PPE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPE OCA]. |
==Reference== | ==Reference== | ||
| - | Stable copper-nitrosyl formation by nitrite reductase in either oxidation state., Tocheva EI, Rosell FI, Mauk AG, Murphy ME, Biochemistry. 2007 Oct 30;46(43):12366-74. Epub 2007 Oct 9. PMID:[http:// | + | Stable copper-nitrosyl formation by nitrite reductase in either oxidation state., Tocheva EI, Rosell FI, Mauk AG, Murphy ME, Biochemistry. 2007 Oct 30;46(43):12366-74. Epub 2007 Oct 9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17924665 17924665] |
[[Category: Alcaligenes faecalis]] | [[Category: Alcaligenes faecalis]] | ||
[[Category: Nitrite reductase (NO-forming)]] | [[Category: Nitrite reductase (NO-forming)]] | ||
| Line 28: | Line 37: | ||
[[Category: oxidoreductase]] | [[Category: oxidoreductase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:15:53 2008'' |
Revision as of 16:15, 20 March 2008
| |||||||
| , resolution 1.75Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , and | ||||||
| Gene: | nirK, nir (Alcaligenes faecalis) | ||||||
| Activity: | Nitrite reductase (NO-forming), with EC number 1.7.2.1 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Reduced H145A mutant of AfNiR exposed to NO
Overview
Nitrite reductase (NiR) is an enzyme that uses type 1 and type 2 copper sites to reduce nitrite to nitric oxide during bacterial denitrification. A copper-nitrosyl intermediate is a proposed, yet poorly characterized feature of the NiR catalytic cycle. This intermediate is formally described as Cu(I)-NO+ and is proposed to be formed at the type 2 copper site after nitrite binding and electron transfer from the type 1 copper site. In this study, copper-nitrosyl complexes were formed by prolonged exposure of exogenous NO to crystals of wild-type and two variant forms of NiR from Alcaligenes faecalis (AfNiR), and the structures were determined to 1.8 A or better resolution. Exposing oxidized wild-type crystals to NO results in the reverse reaction and formation of nitrite that remains bound at the active site. In a type 1 copper site mutant (H145A) that is incapable of electron transfer to the type 2 site, the reverse reaction is not observed. Instead, in both oxidized and reduced H145A crystals, NO is observed bound in a side-on manner to the type 2 copper. In AfNiR, Asp98 forms hydrogen bonds to both substrate and product bound to the type 2 Cu. In the D98N variant, NO is bound side-on but is more disordered when observed for the wild-type enzyme. The solution EPR spectra of the crystallographically characterized NiR-NO complexes indicate the presence of an oxidized type 2 copper site and thus are interpreted as resulting from stable copper-nitrosyls and formally assigned as Cu(II)-NO-. A reaction scheme in which a second NO molecule is oxidized to nitrite can account for the formation of a Cu(II)-NO- species after exposure of the oxidized H145A variant to NO gas.
About this Structure
2PPE is a Single protein structure of sequence from Alcaligenes faecalis. Full crystallographic information is available from OCA.
Reference
Stable copper-nitrosyl formation by nitrite reductase in either oxidation state., Tocheva EI, Rosell FI, Mauk AG, Murphy ME, Biochemistry. 2007 Oct 30;46(43):12366-74. Epub 2007 Oct 9. PMID:17924665
Page seeded by OCA on Thu Mar 20 18:15:53 2008
