1cqw: Difference between revisions

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-[[Image:1cqw.jpg|left|200px]]<br /><applet load="1cqw" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1cqw, resolution 1.50&Aring;" />
-'''NAI COCRYSTALLISED WITH HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES'''<br />
-==Overview==
+==NAI COCRYSTALLISED WITH HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES==
-The hydrolytic haloalkane dehalogenases are promising bioremediation and, biocatalytic agents. Two general classes of dehalogenases have been, reported from Xanthobacter and Rhodococcus. While these enzymes share 30%, amino acid sequence identity, they have significantly different substrate, specificities and halide-binding properties. We report the 1.5 A, resolution crystal structure of the Rhodococcus dehalogenase at pH 5.5, pH, 7.0, and pH 5.5 in the presence of NaI. The Rhodococcus and Xanthobacter, enzymes have significant structural homology in the alpha/beta hydrolase, core, but differ considerably in the cap domain. Consistent with its broad, specificity for primary, secondary, and cyclic haloalkanes, the, Rhodococcus enzyme has a substantially larger active site cavity., Significantly, the Rhodococcus dehalogenase has a different catalytic, triad topology than the Xanthobacter enzyme. In the Xanthobacter, dehalogenase, the third carboxylate functionality in the triad is provided, by D260, which is positioned on the loop between beta7 and the penultimate, helix. The carboxylate functionality in the Rhodococcus catalytic triad is, donated from E141. A model of the enzyme cocrystallized with sodium iodide, shows two iodide binding sites; one that defines the normal substrate and, product-binding site and a second within the active site region. In the, substrate and product complexes, the halogen binds to the Xanthobacter, enzyme via hydrogen bonds with the N(eta)H of both W125 and W175. The, Rhodococcusenzyme does not have a tryptophan analogous to W175. Instead, bound halide is stabilized with hydrogen bonds to the N(eta)H of W118 and, to N(delta)H of N52. It appears that when cocrystallized with NaI the, Rhodococcus enzyme has a rare stable S-I covalent bond to S(gamma) of, C187.
+<StructureSection load='1cqw' size='340' side='right'caption='[[1cqw]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1cqw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CQW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CQW 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]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</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=1cqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cqw OCA], [https://pdbe.org/1cqw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cqw RCSB], [https://www.ebi.ac.uk/pdbsum/1cqw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cqw ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DHAA_RHOSD DHAA_RHOSD]
+== 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/cq/1cqw_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=1cqw ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-CQW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.] with IOD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Haloalkane_dehalogenase Haloalkane dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.5 3.8.1.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1CQW OCA].
+*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Haloalkane dehalogenases: structure of a Rhodococcus enzyme., Newman J, Peat TS, Richard R, Kan L, Swanson PE, Affholter JA, Holmes IH, Schindler JF, Unkefer CJ, Terwilliger TC, Biochemistry. 1999 Dec 7;38(49):16105-14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10587433 10587433]
+[[Category: Large Structures]]
-[[Category: Haloalkane dehalogenase]]
+[[Category: Rhodococcus sp]]
-[[Category: Rhodococcus sp.]]
+[[Category: Affholter JA]]
-[[Category: Single protein]]
+[[Category: Holmes IH]]
-[[Category: Affholter, J.A.]]
+[[Category: Kan L]]
-[[Category: Holmes, I.H.]]
+[[Category: Newman J]]
-[[Category: Kan, L.]]
+[[Category: Peat TS]]
-[[Category: Newman, J.]]
+[[Category: Richard R]]
-[[Category: Peat, T.S.]]
+[[Category: Schindler JF]]
-[[Category: Richard, R.]]
+[[Category: Swanson PE]]
-[[Category: Schindler, J.F.]]
+[[Category: Terwilliger TC]]
-[[Category: Swanson, P.E.]]
+[[Category: Unkefer CJ]]
-[[Category: Terwilliger, T.C.]]
-[[Category: Unkefer, C.J.]]
-[[Category: IOD]]
-[[Category: a/b hydrolase fold]]
-[[Category: dehalogenase i-s bond]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:41:12 2007''