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| | {{STRUCTURE_2ppa| PDB=2ppa | SCENE= }} | | {{STRUCTURE_2ppa| PDB=2ppa | SCENE= }} |
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| - | '''Anaerobically manipulated wild type oxidized AfNiR bound to nitrous oxide'''
| + | ===Anaerobically manipulated wild type oxidized AfNiR bound to nitrous oxide=== |
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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 >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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_18358002}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 18358002 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_18358002}} |
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| | ==About this Structure== | | ==About this Structure== |
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| | [[Category: Nitrous oxide]] | | [[Category: Nitrous oxide]] |
| | [[Category: Oxidoreductase]] | | [[Category: Oxidoreductase]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:27:05 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:04:58 2008'' |
Revision as of 10:05, 29 July 2008
Template:STRUCTURE 2ppa
Anaerobically manipulated wild type oxidized AfNiR bound to nitrous oxide
Template:ABSTRACT PUBMED 18358002
About this Structure
2PPA 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 Tue Jul 29 13:04:58 2008
