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2pp8

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(New page: 200px {{Structure |PDB= 2pp8 |SIZE=350|CAPTION= <scene name='initialview01'>2pp8</scene>, resolution 1.50&Aring; |SITE= <scene name='pdbsite=AC1:Cu1+Binding+Site+...)
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[[Image:2pp8.jpg|left|200px]]
[[Image:2pp8.jpg|left|200px]]
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{{Structure
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<!--
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|PDB= 2pp8 |SIZE=350|CAPTION= <scene name='initialview01'>2pp8</scene>, resolution 1.50&Aring;
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The line below this paragraph, containing "STRUCTURE_2pp8", creates the "Structure Box" on the page.
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|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:Act+Binding+Site+For+Residue+B+1503'>AC7</scene>, <scene name='pdbsite=AC8:Act+Binding+Site+For+Residue+B+1504'>AC8</scene>, <scene name='pdbsite=AC9:Act+Binding+Site+For+Residue+B+1505'>AC9</scene>, <scene name='pdbsite=BC1:Act+Binding+Site+For+Residue+C+1506'>BC1</scene>, <scene name='pdbsite=BC2:Act+Binding+Site+For+Residue+C+1507'>BC2</scene>, <scene name='pdbsite=BC3:Act+Binding+Site+For+Residue+C+1508'>BC3</scene>, <scene name='pdbsite=BC4:Act+Binding+Site+For+Residue+C+1509'>BC4</scene>, <scene name='pdbsite=BC5:Act+Binding+Site+For+Residue+A+1510'>BC5</scene>, <scene name='pdbsite=BC6:Trs+Binding+Site+For+Residue+A+1501'>BC6</scene>, <scene name='pdbsite=BC7:Fmt+Binding+Site+For+Residue+A+401'>BC7</scene>, <scene name='pdbsite=BC8:Fmt+Binding+Site+For+Residue+B+401'>BC8</scene> and <scene name='pdbsite=BC9:Fmt+Binding+Site+For+Residue+C+401'>BC9</scene>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|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>
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or leave the SCENE parameter empty for the default display.
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|GENE= nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis])
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-->
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|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>
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{{STRUCTURE_2pp8| PDB=2pp8 | SCENE= }}
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|RELATEDENTRY=[[1snr|1SNR]], [[1sjm|1SJM]], [[2fjs|2FJS]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp8 OCA], [http://www.ebi.ac.uk/pdbsum/2pp8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pp8 RCSB]</span>
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}}
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'''Formate bound to oxidized wild type AfNiR'''
'''Formate bound to oxidized wild type AfNiR'''
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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]
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: Alcaligenes faecalis]]
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[[Category: Nitrite reductase (NO-forming)]]
 
[[Category: Single protein]]
[[Category: Single protein]]
[[Category: Eltis, L D.]]
[[Category: Eltis, L D.]]
[[Category: Murphy, M E.P.]]
[[Category: Murphy, M E.P.]]
[[Category: Tocheva, E I.]]
[[Category: Tocheva, E I.]]
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[[Category: bacteria]]
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[[Category: Bacteria]]
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[[Category: copper]]
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[[Category: Copper]]
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[[Category: denitrification]]
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[[Category: Denitrification]]
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[[Category: nitrite reductase]]
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[[Category: Nitrite reductase]]
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[[Category: oxidoreductase]]
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[[Category: Oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:26:50 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 2 11:57:51 2008''
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Revision as of 06:26, 24 April 2008

Image:2pp8.jpg

Template:STRUCTURE 2pp8

Formate bound to oxidized wild type AfNiR


Overview

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 Structure

2PP8 is a Single protein structure of sequence from Alcaligenes faecalis. Full crystallographic information is available from OCA.

Reference

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 09:26:50 2008

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