1yaz: Difference between revisions

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AZIDE-BOUND YEAST CU(II)/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE

OverviewOverview

A reaction cycle is proposed for the mechanism of copper-zinc superoxide dismutase (CuZnSOD) that involves inner sphere electron transfer from superoxide to Cu(II) in one portion of the cycle and outer sphere electron transfer from Cu(I) to superoxide in the other portion of the cycle. This mechanism is based on three yeast CuZnSOD structures determined by X-ray crystallography together with many other observations. The new structures reported here are (1) wild type under 15 atm of oxygen pressure, (2) wild type in the presence of azide, and (3) the His48Cys mutant. Final R-values for the three structures are respectively 20.0%, 17.3%, and 20.9%. Comparison of these three new structures to the wild-type yeast Cu(I)ZnSOD model, which has a broken imidazolate bridge, reveals the following: (i) The protein backbones (the "SOD rack") remain essentially unchanged. (ii) A pressure of 15 atm of oxygen causes a displacement of the copper ion 0.37 A from its Cu(I) position in the trigonal plane formed by His46, His48, and His120. The displacement is perpendicular to this plane and toward the NE2 atom of His63 and is accompanied by elongated copper electron density in the direction of the displacement suggestive of two copper positions in the crystal. The copper geometry remains three coordinate, but the His48-Cu bond distance increases by 0.18 A. (iii) Azide binding also causes a displacement of the copper toward His63 such that it moves 1.28 A from the wild-type Cu(I) position, but unlike the effect of 15 atm of oxygen, there is no two-state character. The geometry becomes five-coordinate square pyramidal, and the His63 imidazolate bridge re-forms. The His48-Cu distance increases by 0.70 A, suggesting that His48 becomes an axial ligand. (iv) The His63 imidazole ring tilts upon 15 atm of oxygen treatment and azide binding. Its NE2 atom moves toward the trigonal plane by 0.28 and 0.66 A, respectively, in these structures. (v) The replacement of His48 by Cys, which does not bind copper, results in a five-coordinate square pyramidal, bridge-intact copper geometry with a novel chloride ligand. Combining results from these and other CuZnSOD crystal structures, we offer the outlines of a structure-based cyclic mechanism.

About this StructureAbout this Structure

1YAZ is a Single protein structure of sequence from Saccharomyces cerevisiae with , and as ligands. Active as Superoxide dismutase, with EC number 1.15.1.1 Full crystallographic information is available from OCA.

ReferenceReference

A structure-based mechanism for copper-zinc superoxide dismutase., Hart PJ, Balbirnie MM, Ogihara NL, Nersissian AM, Weiss MS, Valentine JS, Eisenberg D, Biochemistry. 1999 Feb 16;38(7):2167-78. PMID:10026301

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-[[Image:1yaz.gif|left|200px]]<br /><applet load="1yaz" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1yaz.gif|left|200px]]<br /><applet load="1yaz" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1yaz, resolution 1.7&Aring;" />
 '''AZIDE-BOUND YEAST CU(II)/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE'''<br />
 ==Overview==
-A reaction cycle is proposed for the mechanism of copper-zinc superoxide, dismutase (CuZnSOD) that involves inner sphere electron transfer from, superoxide to Cu(II) in one portion of the cycle and outer sphere electron, transfer from Cu(I) to superoxide in the other portion of the cycle. This, mechanism is based on three yeast CuZnSOD structures determined by X-ray, crystallography together with many other observations. The new structures, reported here are (1) wild type under 15 atm of oxygen pressure, (2) wild, type in the presence of azide, and (3) the His48Cys mutant. Final R-values, for the three structures are respectively 20.0%, 17.3%, and 20.9%., Comparison of these three new structures to the wild-type yeast Cu(I)ZnSOD, model, which has a broken imidazolate bridge, reveals the following: (i), The protein backbones (the "SOD rack") remain essentially unchanged. (ii), A pressure of 15 atm of oxygen causes a displacement of the copper ion, 0.37 A from its Cu(I) position in the trigonal plane formed by His46, His48, and His120. The displacement is perpendicular to this plane and, toward the NE2 atom of His63 and is accompanied by elongated copper, electron density in the direction of the displacement suggestive of two, copper positions in the crystal. The copper geometry remains three, coordinate, but the His48-Cu bond distance increases by 0.18 A. (iii), Azide binding also causes a displacement of the copper toward His63 such, that it moves 1.28 A from the wild-type Cu(I) position, but unlike the, effect of 15 atm of oxygen, there is no two-state character. The geometry, becomes five-coordinate square pyramidal, and the His63 imidazolate bridge, re-forms. The His48-Cu distance increases by 0.70 A, suggesting that His48, becomes an axial ligand. (iv) The His63 imidazole ring tilts upon 15 atm, of oxygen treatment and azide binding. Its NE2 atom moves toward the, trigonal plane by 0.28 and 0.66 A, respectively, in these structures. (v), The replacement of His48 by Cys, which does not bind copper, results in a, five-coordinate square pyramidal, bridge-intact copper geometry with a, novel chloride ligand. Combining results from these and other CuZnSOD, crystal structures, we offer the outlines of a structure-based cyclic, mechanism.
+A reaction cycle is proposed for the mechanism of copper-zinc superoxide dismutase (CuZnSOD) that involves inner sphere electron transfer from superoxide to Cu(II) in one portion of the cycle and outer sphere electron transfer from Cu(I) to superoxide in the other portion of the cycle. This mechanism is based on three yeast CuZnSOD structures determined by X-ray crystallography together with many other observations. The new structures reported here are (1) wild type under 15 atm of oxygen pressure, (2) wild type in the presence of azide, and (3) the His48Cys mutant. Final R-values for the three structures are respectively 20.0%, 17.3%, and 20.9%. Comparison of these three new structures to the wild-type yeast Cu(I)ZnSOD model, which has a broken imidazolate bridge, reveals the following: (i) The protein backbones (the "SOD rack") remain essentially unchanged. (ii) A pressure of 15 atm of oxygen causes a displacement of the copper ion 0.37 A from its Cu(I) position in the trigonal plane formed by His46, His48, and His120. The displacement is perpendicular to this plane and toward the NE2 atom of His63 and is accompanied by elongated copper electron density in the direction of the displacement suggestive of two copper positions in the crystal. The copper geometry remains three coordinate, but the His48-Cu bond distance increases by 0.18 A. (iii) Azide binding also causes a displacement of the copper toward His63 such that it moves 1.28 A from the wild-type Cu(I) position, but unlike the effect of 15 atm of oxygen, there is no two-state character. The geometry becomes five-coordinate square pyramidal, and the His63 imidazolate bridge re-forms. The His48-Cu distance increases by 0.70 A, suggesting that His48 becomes an axial ligand. (iv) The His63 imidazole ring tilts upon 15 atm of oxygen treatment and azide binding. Its NE2 atom moves toward the trigonal plane by 0.28 and 0.66 A, respectively, in these structures. (v) The replacement of His48 by Cys, which does not bind copper, results in a five-coordinate square pyramidal, bridge-intact copper geometry with a novel chloride ligand. Combining results from these and other CuZnSOD crystal structures, we offer the outlines of a structure-based cyclic mechanism.
 ==About this Structure==
-YAZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with CU, ZN and AZI as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YAZ OCA].
+YAZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=CU:'>CU</scene>, <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=AZI:'>AZI</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YAZ OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Single protein]]
 [[Category: Superoxide dismutase]]
-[[Category: Balbirnie, M.M.]]
+[[Category: Balbirnie, M M.]]
 [[Category: Eisenberg, D.]]
-[[Category: Hart, P.J.]]
+[[Category: Hart, P J.]]
-[[Category: Nersissian, A.M.]]
+[[Category: Nersissian, A M.]]
-[[Category: Ogihara, N.L.]]
+[[Category: Ogihara, N L.]]
-[[Category: Valentine, J.S.]]
+[[Category: Valentine, J S.]]
-[[Category: Weiss, M.S.]]
+[[Category: Weiss, M S.]]
 [[Category: AZI]]
 [[Category: CU]]
@@ Line 28: / Line 28: @@
 [[Category: zinc]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:39:44 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:03:28 2008''