2flt: Difference between revisions

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-{{Seed}}
-[[Image:2flt.png|left|200px]]
-<!--
+==The X-ray structure of the cis-3-chloroacrylic acid dehalogenase cis-CaaD inactivated with (R)-Oxirane-2-carboxylate==
-The line below this paragraph, containing "STRUCTURE_2flt", creates the "Structure Box" on the page.
+<StructureSection load='2flt' size='340' side='right'caption='[[2flt]], [[Resolution|resolution]] 2.10&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'>[[2flt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Coryneform_bacterium Coryneform bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FLT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FLT 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]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LAC:LACTIC+ACID'>LAC</scene></td></tr>
-{{STRUCTURE_2flt|  PDB=2flt  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2flt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2flt OCA], [https://pdbe.org/2flt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2flt RCSB], [https://www.ebi.ac.uk/pdbsum/2flt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2flt ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q6VPE5_9CORY Q6VPE5_9CORY]
+== 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/fl/2flt_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2flt ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The bacterial degradation pathways for the nematocide 1,3-dichloropropene rely on hydrolytic dehalogenation reactions catalyzed by cis- and trans-3-chloroacrylic acid dehalogenases (cis-CaaD and CaaD, respectively). X-ray crystal structures of native cis-CaaD and cis-CaaD inactivated by (R)-oxirane-2-carboxylate were elucidated. They locate four known catalytic residues (Pro-1, Arg-70, Arg-73, and Glu-114) and two previously unknown, potential catalytic residues (His-28 and Tyr-103'). The Y103F and H28A mutants of these latter two residues displayed reductions in cis-CaaD activity confirming their importance in catalysis. The structure of the inactivated enzyme shows covalent modification of the Pro-1 nitrogen atom by (R)-2-hydroxypropanoate at the C3 position. The interactions in the complex implicate Arg-70 or a water molecule bound to Arg-70 as the proton donor for the epoxide ring-opening reaction and Arg-73 and His-28 as primary binding contacts for the carboxylate group. This proposed binding mode places the (R)-enantiomer, but not the (S)-enantiomer, in position to covalently modify Pro-1. The absence of His-28 (or an equivalent) in CaaD could account for the fact that CaaD is not inactivated by either enantiomer. The cis-CaaD structures support a mechanism in which Glu-114 and Tyr-103' activate a water molecule for addition to C3 of the substrate and His-28, Arg-70, and Arg-73 interact with the C1 carboxylate group to assist in substrate binding and polarization. Pro-1 provides a proton at C2. The involvement of His-28 and Tyr-103' distinguishes the cis-CaaD mechanism from the otherwise parallel CaaD mechanism. The two mechanisms probably evolved independently as the result of an early gene duplication of a common ancestor.
-===The X-ray structure of the cis-3-chloroacrylic acid dehalogenase cis-CaaD inactivated with (R)-Oxirane-2-carboxylate===
+Crystal structures of native and inactivated cis-3-chloroacrylic acid dehalogenase. Structural basis for substrate specificity and inactivation by (R)-oxirane-2-carboxylate.,de Jong RM, Bazzacco P, Poelarends GJ, Johnson WH Jr, Kim YJ, Burks EA, Serrano H, Thunnissen AM, Whitman CP, Dijkstra BW J Biol Chem. 2007 Jan 26;282(4):2440-9. Epub 2006 Nov 22. PMID:17121835<ref>PMID:17121835</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2flt" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17121835}}, adds the Publication Abstract to the page
+*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17121835 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17121835}}
+__TOC__
+</StructureSection>
-==About this Structure==
-FLT is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Coryneform_bacterium Coryneform bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FLT OCA].
-==Reference==
-<ref group="xtra">PMID:17121835</ref><references group="xtra"/>
 [[Category: Coryneform bacterium]]
-[[Category: Jong, R M.de.]]
+[[Category: Large Structures]]
-[[Category: 3-chloroacrylic acid dehalogenase]]
+[[Category: De Jong RM]]
-[[Category: 4-oxalocrotonate tautomerase]]
-[[Category: 4ot family]]
-[[Category: Covalent inhibitor]]
-[[Category: Hydratase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:32:23 2009''