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| - | [[Image:2qvx.jpg|left|200px]] | |
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| - | {{Structure
| + | ==4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3-Chlorobenzoate== |
| - | |PDB= 2qvx |SIZE=350|CAPTION= <scene name='initialview01'>2qvx</scene>, resolution 2.70Å
| + | <StructureSection load='2qvx' size='340' side='right'caption='[[2qvx]], [[Resolution|resolution]] 2.70Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=3BZ:3-CHLOROBENZOATE'>3BZ</scene>
| + | <table><tr><td colspan='2'>[[2qvx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_sp._AL3007 Alcaligenes sp. AL3007]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QVX FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3BZ:3-CHLOROBENZOATE'>3BZ</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvx OCA], [https://pdbe.org/2qvx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qvx RCSB], [https://www.ebi.ac.uk/pdbsum/2qvx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qvx ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1t5d|1T5D]], [[1pg4|1PG4]], [[2qvy|2QVY]], [[2qvz|2QVZ]], [[2qw0|2QW0]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvx OCA], [http://www.ebi.ac.uk/pdbsum/2qvx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2qvx RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/Q8GN86_9BURK Q8GN86_9BURK] |
| - | | + | == Evolutionary Conservation == |
| - | '''4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3-Chlorobenzoate'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qv/2qvx_consurf.spt"</scriptWhenChecked> |
| - | Environmental aromatic acids are transformed to chemical energy in bacteria that possess the requisite secondary pathways. Some of these pathways rely on the activation of the aromatic acid by coenzyme A (CoA) thioesterification catalyzed by an aromatic acid: CoA ligase. Adaptation of such pathways to the bioremediation of man-made pollutants such as polychlorinated biphenyl (PCB) and dichlorodiphenyltrichloroethane (DDT) requires that the chlorinated benzoic acid byproduct that is formed be able to be eliminated by further degradation. To take advantage of natural benzoic acid degrading pathways requiring initial ring activation by thioesterification, the pathway aromatic acid:CoA ligase must be an effective catalyst with the chlorinated benzoic acid. This study, which focuses on the 4-chlorobenzoate:CoA ligase (CBL) of the 4-monochlorobiphenyl degrading bacterium Alcaligenes sp. strain ALP83, was carried out to determine if the 4-chlorobenzoate binding site of this enzyme can be transformed by rational design to recognize the chlorobenzoic acids formed in the course of breakdown of other environmental PCB congeners. The fundamental question addressed in this study is whether it is possible to add or subtract space from the substrate-binding pocket of this ligase (to complement the topology of the unnatural aromatic substrate) without causing disruption of the ligase catalytic machinery. Herein, we report the results of a substrate specificity analysis that, when interpreted within the context of the X-ray crystal structures, set the stage for the rational design of the ligase for thioesterification of two PCB-derived chlorobenzoic acids. The ligase was first optimized to catalyze CoA thioesterification of 3,4-dichlorobenzoic acid, a poor substrate, by truncating Ile303, a large hydrophobic residue that packs against the ring meta-C(H) group. The structural basis for the approximately 100-fold enhancement in the rate of 3,4-dichlorobenzoate thioesterification catalyzed by the I303A and I303G CBL mutants was validated by determination of the crystal structure of the 3,4-dichlorobenzoate-bound enzymes. Determinations of the structures of I303 mutant complexes of 3-chlorobenzoate, a very poor substrate, revealed nonproductive binding as a result of the inability of the substrate ring C(4)H group to fill the pocket that binds the C(4)Cl group of the native substrate. The C(4)Cl pocket of the CBL I303A mutant was then reduced in size by strategic amino acid replacement. A 54-fold improvement in catalytic efficiency was observed for the CBL F184W/I303A/V209T triple mutant. The results of this investigation are interpreted as evidence that the plasticity of the ligase catalytic scaffold is sufficient to allow expansion of substrate range by rational design. The combination of structural and kinetic analyses of the constructed mutants proved to be an effective approach to engineering the ligase for novel substrates.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 2QVX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_sp. Alcaligenes sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVX OCA].
| + | </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=2qvx ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference==
| + | __TOC__ |
| - | Rational redesign of the 4-chlorobenzoate binding site of 4-chlorobenzoate: coenzyme a ligase for expanded substrate range., Wu R, Reger AS, Cao J, Gulick AM, Dunaway-Mariano D, Biochemistry. 2007 Dec 18;46(50):14487-99. Epub 2007 Nov 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18027984 18027984]
| + | </StructureSection> |
| - | [[Category: 4-chlorobenzoate--CoA ligase]]
| + | [[Category: Alcaligenes sp. AL3007]] |
| - | [[Category: Alcaligenes sp.]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]] | + | [[Category: Cao J]] |
| - | [[Category: Cao, J.]] | + | [[Category: Dunaway-Mariano D]] |
| - | [[Category: Dunaway-Mariano, D.]] | + | [[Category: Gulick AM]] |
| - | [[Category: Gulick, A M.]] | + | [[Category: Reger AS]] |
| - | [[Category: Reger, A S.]] | + | [[Category: Wu R]] |
| - | [[Category: Wu, R.]] | + | |
| - | [[Category: acyl-coa ligase]]
| + | |
| - | [[Category: adenylate-forming enzyme]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:53:55 2008''
| + | |
