1rk5: Difference between revisions

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-[[Image:1rk5.png|left|200px]]
-{{STRUCTURE_1rk5|  PDB=1rk5  |  SCENE=  }}
+==The D-aminoacylase mutant D366A in complex with 100mM CuCl2==
+<StructureSection load='1rk5' size='340' side='right'caption='[[1rk5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1rk5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RK5 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rk5 OCA], [https://pdbe.org/1rk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rk5 RCSB], [https://www.ebi.ac.uk/pdbsum/1rk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rk5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9AGH8_ALCFA Q9AGH8_ALCFA]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rk/1rk5_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1rk5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===The D-aminoacylase mutant D366A in complex with 100mM CuCl2===
+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<ref>PMID:14736882</ref>
-{{ABSTRACT_PUBMED_14736882}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1rk5" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[1rk5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RK5 OCA].
+*[[Aminoacylase 3D structures|Aminoacylase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:014736882</ref><ref group="xtra">PMID:012454005</ref><ref group="xtra">PMID:012381838</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Alcaligenes faecalis]]
-[[Category: N-acyl-D-amino-acid deacylase]]
+[[Category: Large Structures]]
-[[Category: Chou, L Y.]]
+[[Category: Chou LY]]
-[[Category: Lai, W L.]]
+[[Category: Lai WL]]
-[[Category: Liaw, S H.]]
+[[Category: Liaw SH]]
-[[Category: Ting, C Y.]]
+[[Category: Ting CY]]
-[[Category: Tsai, Y C.]]
+[[Category: Tsai YC]]
-[[Category: Beta barrel]]
-[[Category: Hydrolase]]
-[[Category: Insertion]]
-[[Category: Tim barrel]]