1v4y: Difference between revisions

Revision as of 16:31, 21 February 2008

The functional role of the binuclear metal center in D-aminoacylase. One-metal activation and second-metal attenuation

OverviewOverview

Our structural comparison of the TIM barrel metal-dependent hydrolase(-like) superfamily suggests a classification of their divergent active sites into four types: alphabeta-binuclear, alpha-mononuclear, beta-mononuclear, and metal-independent subsets. The d-aminoacylase from Alcaligenes faecalis DA1 belongs to the beta-mononuclear subset due to the fact that the catalytically essential Zn(2+) is tightly bound at the beta site with coordination by Cys(96), His(220), and His(250), even though it possesses a binuclear active site with a weak alpha binding site. Additional Zn(2+), Cd(2+), and Cu(2+), but not Ni(2+), Co(2+), Mg(2+), Mn(2+), and Ca(2+), can inhibit enzyme activity. Crystal structures of these metal derivatives show that Zn(2+) and Cd(2+) bind at the alpha(1) subsite ligated by His(67), His(69), and Asp(366), while Cu(2+) at the alpha(2) subsite is chelated by His(67), His(69) and Cys(96). Unexpectedly, the crystal structure of the inactive H220A mutant displays that the endogenous Zn(2+) shifts to the alpha(3) subsite coordinated by His(67), His(69), Cys(96), and Asp(366), revealing that elimination of the beta site changes the coordination geometry of the alpha ion with an enhanced affinity. Kinetic studies of the metal ligand mutants such as C96D indicate the uniqueness of the unusual bridging cysteine and its involvement in catalysis. Therefore, the two metal-binding sites in the d-aminoacylase are interactive with partially mutual exclusion, thus resulting in widely different affinities for the activation/attenuation mechanism, in which the enzyme is activated by the metal ion at the beta site, but inhibited by the subsequent binding of the second ion at the alpha site.

About this StructureAbout this Structure

1V4Y is a Single protein structure of sequence from Alcaligenes faecalis with and as ligands. Active as N-acyl-D-amino-acid deacylase, with EC number 3.5.1.81 Full crystallographic information is available from OCA.

ReferenceReference

The functional role of the binuclear metal center in D-aminoacylase: one-metal activation and second-metal attenuation., Lai WL, Chou LY, Ting CY, Kirby R, Tsai YC, Wang AH, Liaw SH, J Biol Chem. 2004 Apr 2;279(14):13962-7. Epub 2004 Jan 21. PMID:14736882

Page seeded by OCA on Thu Feb 21 15:31:28 2008

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-[[Image:1v4y.jpg|left|200px]]<br /><applet load="1v4y" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1v4y.jpg|left|200px]]<br /><applet load="1v4y" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1v4y, resolution 1.65&Aring;" />
 '''The functional role of the binuclear metal center in D-aminoacylase. One-metal activation and second-metal attenuation'''<br />
 ==Overview==
-Our structural comparison of the TIM barrel metal-dependent, hydrolase(-like) superfamily suggests a classification of their divergent, active sites into four types: alphabeta-binuclear, alpha-mononuclear, beta-mononuclear, and metal-independent subsets. The d-aminoacylase from, Alcaligenes faecalis DA1 belongs to the beta-mononuclear subset due to the, fact that the catalytically essential Zn(2+) is tightly bound at the beta, site with coordination by Cys(96), His(220), and His(250), even though it, possesses a binuclear active site with a weak alpha binding site., Additional Zn(2+), Cd(2+), and Cu(2+), but not Ni(2+), Co(2+), Mg(2+), Mn(2+), and Ca(2+), can inhibit enzyme activity. Crystal structures of, these metal derivatives show that Zn(2+) and Cd(2+) bind at the alpha(1), subsite ligated by His(67), His(69), and Asp(366), while Cu(2+) at the, alpha(2) subsite is chelated by His(67), His(69) and Cys(96)., Unexpectedly, the crystal structure of the inactive H220A mutant displays, that the endogenous Zn(2+) shifts to the alpha(3) subsite coordinated by, His(67), His(69), Cys(96), and Asp(366), revealing that elimination of the, beta site changes the coordination geometry of the alpha ion with an, enhanced affinity. Kinetic studies of the metal ligand mutants such as, C96D indicate the uniqueness of the unusual bridging cysteine and its, involvement in catalysis. Therefore, the two metal-binding sites in the, d-aminoacylase are interactive with partially mutual exclusion, thus, resulting in widely different affinities for the activation/attenuation, mechanism, in which the enzyme is activated by the metal ion at the beta, site, but inhibited by the subsequent binding of the second ion at the, alpha site.
+Our structural comparison of the TIM barrel metal-dependent hydrolase(-like) superfamily suggests a classification of their divergent active sites into four types: alphabeta-binuclear, alpha-mononuclear, beta-mononuclear, and metal-independent subsets. The d-aminoacylase from Alcaligenes faecalis DA1 belongs to the beta-mononuclear subset due to the fact that the catalytically essential Zn(2+) is tightly bound at the beta site with coordination by Cys(96), His(220), and His(250), even though it possesses a binuclear active site with a weak alpha binding site. Additional Zn(2+), Cd(2+), and Cu(2+), but not Ni(2+), Co(2+), Mg(2+), Mn(2+), and Ca(2+), can inhibit enzyme activity. Crystal structures of these metal derivatives show that Zn(2+) and Cd(2+) bind at the alpha(1) subsite ligated by His(67), His(69), and Asp(366), while Cu(2+) at the alpha(2) subsite is chelated by His(67), His(69) and Cys(96). Unexpectedly, the crystal structure of the inactive H220A mutant displays that the endogenous Zn(2+) shifts to the alpha(3) subsite coordinated by His(67), His(69), Cys(96), and Asp(366), revealing that elimination of the beta site changes the coordination geometry of the alpha ion with an enhanced affinity. Kinetic studies of the metal ligand mutants such as C96D indicate the uniqueness of the unusual bridging cysteine and its involvement in catalysis. Therefore, the two metal-binding sites in the d-aminoacylase are interactive with partially mutual exclusion, thus resulting in widely different affinities for the activation/attenuation mechanism, in which the enzyme is activated by the metal ion at the beta site, but inhibited by the subsequent binding of the second ion at the alpha site.
 ==About this Structure==
-V4Y 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 ACT and ZN as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1V4Y OCA].
+V4Y 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=ACT:'>ACT</scene> and <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V4Y OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: N-acyl-D-amino-acid deacylase]]
 [[Category: Single protein]]
-[[Category: Chou, L.Y.]]
+[[Category: Chou, L Y.]]
-[[Category: Lai, W.L.]]
+[[Category: Lai, W L.]]
-[[Category: Liaw, S.H.]]
+[[Category: Liaw, S H.]]
-[[Category: Ting, C.Y.]]
+[[Category: Ting, C Y.]]
-[[Category: Tsai, Y.C.]]
+[[Category: Tsai, Y C.]]
 [[Category: ACT]]
 [[Category: ZN]]
@@ Line 25: / Line 25: @@
 [[Category: tim barrel]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:36:29 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:31:28 2008''