1cqw: Difference between revisions

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-[[Image:1cqw.jpg|left|200px]]
-<!--
+==NAI COCRYSTALLISED WITH HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES==
-The line below this paragraph, containing "STRUCTURE_1cqw", creates the "Structure Box" on the page.
+<StructureSection load='1cqw' size='340' side='right'caption='[[1cqw]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
-{{STRUCTURE_1cqw|  PDB=1cqw  |  SCENE=  }}
+<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>
-'''NAI COCRYSTALLISED WITH HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES'''
+==See Also==
+*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-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.
+[[Category: Large Structures]]
+[[Category: Rhodococcus sp]]
-==About this Structure==
+[[Category: Affholter JA]]
-CQW is a [[Single protein]] structure of sequence from [http://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].
+[[Category: Holmes IH]]
+[[Category: Kan L]]
-==Reference==
+[[Category: Newman J]]
-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://www.ncbi.nlm.nih.gov/pubmed/10587433 10587433]
+[[Category: Peat TS]]
-[[Category: Haloalkane dehalogenase]]
+[[Category: Richard R]]
-[[Category: Rhodococcus sp.]]
+[[Category: Schindler JF]]
-[[Category: Single protein]]
+[[Category: Swanson PE]]
-[[Category: Affholter, J A.]]
+[[Category: Terwilliger TC]]
-[[Category: Holmes, I H.]]
+[[Category: Unkefer CJ]]
-[[Category: Kan, L.]]
-[[Category: Newman, J.]]
-[[Category: Peat, T S.]]
-[[Category: Richard, R.]]
-[[Category: Schindler, J F.]]
-[[Category: Swanson, P E.]]
-[[Category: Terwilliger, T C.]]
-[[Category: Unkefer, C J.]]
-[[Category: A/b hydrolase fold]]
-[[Category: Dehalogenase i-s bond]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:01:26 2008''