2ppf

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:2ppf.jpg|left|200px]]<br /><applet load="2ppf" size="350" color="white" frame="true" align="right" spinBox="true"
+
[[Image:2ppf.jpg|left|200px]]
-
caption="2ppf, resolution 1.65&Aring;" />
+
 
-
'''Reduced mutant D98N of AfNiR exposed to nitric oxide'''<br />
+
{{Structure
 +
|PDB= 2ppf |SIZE=350|CAPTION= <scene name='initialview01'>2ppf</scene>, resolution 1.65&Aring;
 +
|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 mutant D98N of AfNiR exposed to nitric oxide'''
 +
 
==Overview==
==Overview==
Line 7: Line 16:
==About this Structure==
==About this Structure==
-
2PPF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis] with <scene name='pdbligand=CU1:'>CU1</scene>, <scene name='pdbligand=CU:'>CU</scene>, <scene name='pdbligand=ACT:'>ACT</scene>, <scene name='pdbligand=NO:'>NO</scene> and <scene name='pdbligand=TRS:'>TRS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPF OCA].
+
2PPF 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=2PPF 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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17924665 17924665]
+
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 29: Line 38:
[[Category: oxidoreductase]]
[[Category: oxidoreductase]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:31:49 2008''
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:15:57 2008''

Revision as of 16:15, 20 March 2008

Image:2ppf.jpg


PDB ID 2ppf

Drag the structure with the mouse to rotate
, resolution 1.65Å
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 mutant D98N of AfNiR exposed to nitric oxide


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

2PPF 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 18:15:57 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ppf"
Personal tools