2pp9: Difference between revisions

Revision as of 09:26, 24 April 2008

Nitrate bound wild type oxidized AfNiR

OverviewOverview

The interaction of copper-containing dissimilatory nitrite reductase from Alcaligenes faecalis S-6 ( AfNiR) with each of five small molecules was studied using crystallography and steady-state kinetics. Structural studies revealed that each small molecule interacted with the oxidized catalytic type 2 copper of AfNiR. Three small molecules (formate, acetate and nitrate) mimic the substrate by having at least two oxygen atoms for bidentate coordination to the type 2 copper atom. These three anions bound to the copper ion in the same asymmetric, bidentate manner as nitrite. Consistent with their weak inhibition of the enzyme ( K i >50 mM), the Cu-O distances in these AfNiR-inhibitor complexes were approximately 0.15 A longer than that observed in the AfNiR-nitrite complex. The binding mode of each inhibitor is determined in part by steric interactions with the side chain of active site residue Ile257. Moreover, the side chain of Asp98, a conserved residue that hydrogen bonds to type 2 copper-bound nitrite and nitric oxide, was either disordered or pointed away from the inhibitors. Acetate and formate inhibited AfNiR in a mixed fashion, consistent with the occurrence of second acetate binding site in the AfNiR-acetate complex that occludes access to the type 2 copper. A fourth small molecule, nitrous oxide, bound to the oxidized metal in a side-on fashion reminiscent of nitric oxide to the reduced copper. Nevertheless, nitrous oxide bound at a farther distance from the metal. The fifth small molecule, azide, inhibited the reduction of nitrite by AfNiR most strongly ( K ic = 2.0 +/- 0.1 mM). This ligand bound to the type 2 copper center end-on with a Cu-N c distance of approximately 2 A, and was the only inhibitor to form a hydrogen bond with Asp98. Overall, the data substantiate the roles of Asp98 and Ile257 in discriminating substrate from other small anions.

About this StructureAbout this Structure

2PP9 is a Single protein structure of sequence from Alcaligenes faecalis. Full crystallographic information is available from OCA.

ReferenceReference

Conserved Active Site Residues Limit Inhibition of a Copper-Containing Nitrite Reductase by Small Molecules., Tocheva EI, Eltis LD, Murphy ME, Biochemistry. 2008 Mar 22;. PMID:18358002 Page seeded by OCA on Thu Apr 24 09:26:58 2008

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OCA

@@ Line 1: / Line 1: @@
 [[Image:2pp9.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 2pp9 |SIZE=350|CAPTION= <scene name='initialview01'>2pp9</scene>, resolution 1.80&Aring;
+The line below this paragraph, containing "STRUCTURE_2pp9", creates the "Structure Box" on the page.
-|SITE= <scene name='pdbsite=AC1:Cu1+Binding+Site+For+Residue+A+501'>AC1</scene>, <scene name='pdbsite=AC2:Cu+Binding+Site+For+Residue+A+502'>AC2</scene>, <scene name='pdbsite=AC3:Cu1+Binding+Site+For+Residue+B+501'>AC3</scene>, <scene name='pdbsite=AC4:Cu+Binding+Site+For+Residue+B+502'>AC4</scene>, <scene name='pdbsite=AC5:Cu1+Binding+Site+For+Residue+C+501'>AC5</scene>, <scene name='pdbsite=AC6:Cu+Binding+Site+For+Residue+C+502'>AC6</scene>, <scene name='pdbsite=AC7:No3+Binding+Site+For+Residue+A+503'>AC7</scene>, <scene name='pdbsite=AC8:No3+Binding+Site+For+Residue+B+503'>AC8</scene>, <scene name='pdbsite=AC9:No3+Binding+Site+For+Residue+C+503'>AC9</scene>, <scene name='pdbsite=BC1:Act+Binding+Site+For+Residue+B+2003'>BC1</scene>, <scene name='pdbsite=BC2:Act+Binding+Site+For+Residue+B+2004'>BC2</scene>, <scene name='pdbsite=BC3:Act+Binding+Site+For+Residue+B+2005'>BC3</scene>, <scene name='pdbsite=BC4:Act+Binding+Site+For+Residue+C+2006'>BC4</scene>, <scene name='pdbsite=BC5:Act+Binding+Site+For+Residue+C+2007'>BC5</scene>, <scene name='pdbsite=BC6:Act+Binding+Site+For+Residue+C+2008'>BC6</scene>, <scene name='pdbsite=BC7:Act+Binding+Site+For+Residue+C+2009'>BC7</scene>, <scene name='pdbsite=BC8:Act+Binding+Site+For+Residue+A+2010'>BC8</scene> and <scene name='pdbsite=BC9:Trs+Binding+Site+For+Residue+A+2001'>BC9</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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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_(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] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis])
+-->
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam07732 Cu-oxidase_3], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00394 Cu-oxidase]</span>
+{{STRUCTURE_2pp9|  PDB=2pp9  |  SCENE=  }}
-|RELATEDENTRY=[[1snr|1SNR]], [[1sjm|1SJM]], [[2fjs|2FJS]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp9 OCA], [http://www.ebi.ac.uk/pdbsum/2pp9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pp9 RCSB]</span>
-}}
 '''Nitrate bound wild type oxidized AfNiR'''
@@ Line 24: / Line 21: @@
 Conserved Active Site Residues Limit Inhibition of a Copper-Containing Nitrite Reductase by Small Molecules., Tocheva EI, Eltis LD, Murphy ME, Biochemistry. 2008 Mar 22;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18358002 18358002]
 [[Category: Alcaligenes faecalis]]
-[[Category: Nitrite reductase (NO-forming)]]
 [[Category: Single protein]]
 [[Category: Murphy, M E.P.]]
 [[Category: Tocheva, E I.]]
-[[Category: bacteria]]
+[[Category: Bacteria]]
-[[Category: copper]]
+[[Category: Copper]]
-[[Category: denitrification]]
+[[Category: Denitrification]]
-[[Category: nitrate]]
+[[Category: Nitrate]]
-[[Category: nitrite reductase]]
+[[Category: Nitrite reductase]]
-[[Category: oxidoreductase]]
+[[Category: Oxidoreductase]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:26:58 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  2 11:57:53 2008''