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2pp9

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[[Image:2pp9.jpg|left|200px]]
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{{STRUCTURE_2pp9| PDB=2pp9 | SCENE= }}
{{STRUCTURE_2pp9| PDB=2pp9 | SCENE= }}
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'''Nitrate bound wild type oxidized AfNiR'''
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===Nitrate bound wild type oxidized AfNiR===
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==Overview==
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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 &gt;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.
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(as it appears on PubMed at http://www.pubmed.gov), where 18358002 is the PubMed ID number.
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{{ABSTRACT_PUBMED_18358002}}
==About this Structure==
==About this Structure==
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[[Category: Nitrite reductase]]
[[Category: Nitrite reductase]]
[[Category: Oxidoreductase]]
[[Category: Oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:26:58 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 19:58:27 2008''

Revision as of 16:58, 28 July 2008

Image:2pp9.png

Template:STRUCTURE 2pp9

Nitrate bound wild type oxidized AfNiR

Template:ABSTRACT PUBMED 18358002

About this Structure

2PP9 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 Mon Jul 28 19:58:27 2008

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