1j9r: Difference between revisions

Revision as of 14:20, 21 February 2008

Crystal structure of nitrite soaked reduced D98N AFNIR

OverviewOverview

High-resolution nitrite soaked oxidized and reduced crystal structures of two active site mutants, D98N and H255N, of nitrite reductase (NIR) from Alcaligenes faecalis S-6 were determined to better than 2.0 A resolution. In the oxidized D98N nitrite-soaked structures, nitrite is coordinated to the type II copper via its oxygen atoms in an asymmetric bidentate manner; however, elevated B-factors and weak electron density indicate that both nitrite and Asn98 are less ordered than in the native enzyme. This disorder likely results from the inability of the N delta 2 atom of Asn98 to form a hydrogen bond with the bound protonated nitrite, indicating that the hydrogen bond between Asp98 and nitrite in the native NIR structure is essential in anchoring nitrite in the active site for catalysis. In the oxidized nitrite soaked H255N crystal structure, nitrite does not displace the ligand water and is instead coordinated in an alternative mode via a single oxygen to the type II copper. His255 is clearly essential in defining the nitrite binding site despite the lack of direct interaction with the substrate in the native enzyme. The resulting pentacoordinate copper site in the H255N structure also serves as a model for a proposed transient intermediate in the catalytic mechanism consisting of a hydroxyl and nitric oxide molecule coordinated to the copper. The formation of an unusual dinuclear type I copper site in the reduced nitrite soaked D98N and H255N crystal structures may represent an evolutionary link between the mononuclear type I copper centers and dinuclear Cu(A) sites.

About this StructureAbout this Structure

1J9R is a Single protein structure of sequence from Alcaligenes faecalis with and as ligands. Active as Nitrite reductase (NO-forming), with EC number 1.7.2.1 Full crystallographic information is available from OCA.

ReferenceReference

Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate., Boulanger MJ, Murphy ME, Biochemistry. 2001 Aug 7;40(31):9132-41. PMID:11478880

Page seeded by OCA on Thu Feb 21 13:20:14 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1j9r.gif|left|200px]]<br /><applet load="1j9r" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1j9r.gif|left|200px]]<br /><applet load="1j9r" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1j9r, resolution 2.00&Aring;" />
 '''Crystal structure of nitrite soaked reduced D98N AFNIR'''<br />
 ==Overview==
-High-resolution nitrite soaked oxidized and reduced crystal structures of, two active site mutants, D98N and H255N, of nitrite reductase (NIR) from, Alcaligenes faecalis S-6 were determined to better than 2.0 A resolution., In the oxidized D98N nitrite-soaked structures, nitrite is coordinated to, the type II copper via its oxygen atoms in an asymmetric bidentate manner;, however, elevated B-factors and weak electron density indicate that both, nitrite and Asn98 are less ordered than in the native enzyme. This, disorder likely results from the inability of the N delta 2 atom of Asn98, to form a hydrogen bond with the bound protonated nitrite, indicating that, the hydrogen bond between Asp98 and nitrite in the native NIR structure is, essential in anchoring nitrite in the active site for catalysis. In the, oxidized nitrite soaked H255N crystal structure, nitrite does not displace, the ligand water and is instead coordinated in an alternative mode via a, single oxygen to the type II copper. His255 is clearly essential in, defining the nitrite binding site despite the lack of direct interaction, with the substrate in the native enzyme. The resulting pentacoordinate, copper site in the H255N structure also serves as a model for a proposed, transient intermediate in the catalytic mechanism consisting of a hydroxyl, and nitric oxide molecule coordinated to the copper. The formation of an, unusual dinuclear type I copper site in the reduced nitrite soaked D98N, and H255N crystal structures may represent an evolutionary link between, the mononuclear type I copper centers and dinuclear Cu(A) sites.
+High-resolution nitrite soaked oxidized and reduced crystal structures of two active site mutants, D98N and H255N, of nitrite reductase (NIR) from Alcaligenes faecalis S-6 were determined to better than 2.0 A resolution. In the oxidized D98N nitrite-soaked structures, nitrite is coordinated to the type II copper via its oxygen atoms in an asymmetric bidentate manner; however, elevated B-factors and weak electron density indicate that both nitrite and Asn98 are less ordered than in the native enzyme. This disorder likely results from the inability of the N delta 2 atom of Asn98 to form a hydrogen bond with the bound protonated nitrite, indicating that the hydrogen bond between Asp98 and nitrite in the native NIR structure is essential in anchoring nitrite in the active site for catalysis. In the oxidized nitrite soaked H255N crystal structure, nitrite does not displace the ligand water and is instead coordinated in an alternative mode via a single oxygen to the type II copper. His255 is clearly essential in defining the nitrite binding site despite the lack of direct interaction with the substrate in the native enzyme. The resulting pentacoordinate copper site in the H255N structure also serves as a model for a proposed transient intermediate in the catalytic mechanism consisting of a hydroxyl and nitric oxide molecule coordinated to the copper. The formation of an unusual dinuclear type I copper site in the reduced nitrite soaked D98N and H255N crystal structures may represent an evolutionary link between the mononuclear type I copper centers and dinuclear Cu(A) sites.
 ==About this Structure==
-J9R 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 CU and NO2 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1J9R OCA].
+J9R 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=CU:'>CU</scene> and <scene name='pdbligand=NO2:'>NO2</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=1J9R OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Nitrite reductase (NO-forming)]]
 [[Category: Single protein]]
-[[Category: Boulanger, M.J.]]
+[[Category: Boulanger, M J.]]
-[[Category: Murphy, M.E.]]
+[[Category: Murphy, M E.]]
 [[Category: CU]]
 [[Category: NO2]]
 [[Category: curpredoxin fold copper nitrite]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:02:10 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:20:14 2008''