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| | ==4-Chlorobenzoyl-CoA Ligase/Synthetase in the Thioester-forming Conformation, bound to 4-chlorophenacyl-CoA== | | ==4-Chlorobenzoyl-CoA Ligase/Synthetase in the Thioester-forming Conformation, bound to 4-chlorophenacyl-CoA== |
| - | <StructureSection load='3cw9' size='340' side='right' caption='[[3cw9]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='3cw9' size='340' side='right'caption='[[3cw9]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3cw9]] is a 2 chain structure with 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=3CW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CW9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3cw9]] is a 2 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=3CW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CW9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=01A:4-CHLOROPHENACYL-COENZYME+A'>01A</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1t5d|1t5d]], [[1pg4|1pg4]], [[3cw8|3cw8]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=01A:4-CHLOROPHENACYL-COENZYME+A'>01A</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cw9 OCA], [https://pdbe.org/3cw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cw9 RCSB], [https://www.ebi.ac.uk/pdbsum/3cw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cw9 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3cw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cw9 OCA], [http://pdbe.org/3cw9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cw9 RCSB], [http://www.ebi.ac.uk/pdbsum/3cw9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cw9 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8GN86_9BURK Q8GN86_9BURK] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 4-chlorobenzoate--CoA ligase]] | + | [[Category: Alcaligenes sp. AL3007]] |
| - | [[Category: Alcaligenes sp]] | + | [[Category: Large Structures]] |
| - | [[Category: Cao, J]] | + | [[Category: Cao J]] |
| - | [[Category: Dunaway-Mariano, D]] | + | [[Category: Dunaway-Mariano D]] |
| - | [[Category: Gulick, A M]] | + | [[Category: Gulick AM]] |
| - | [[Category: Reger, A S]] | + | [[Category: Reger AS]] |
| - | [[Category: Wu, R]] | + | [[Category: Wu R]] |
| - | [[Category: Acyl-coa ligase]]
| + | |
| - | [[Category: Adenylate-forming enzyme]]
| + | |
| - | [[Category: Domain alternation]]
| + | |
| - | [[Category: Ligase]]
| + | |
| Structural highlights
3cw9 is a 2 chain structure with sequence from Alcaligenes sp. AL3007. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
Q8GN86_9BURK
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Members of the adenylate-forming family of enzymes play a role in the metabolism of halogenated aromatics and of short, medium, and long chain fatty acids, as well as in the biosynthesis of menaquinone, peptide antibiotics, and peptide siderophores. This family includes a subfamily of acyl- and aryl-CoA ligases that catalyze thioester synthesis through two half-reactions. A carboxylate substrate first reacts with ATP to form an acyl-adenylate. Subsequent to the release of the product PP i, the enzyme binds CoA, which attacks the activated acyl group to displace AMP. Structural and functional studies on different family members suggest that these enzymes alternate between two conformations during catalysis of the two half-reactions. Specifically, after the initial adenylation step, the C-terminal domain rotates by approximately 140 degrees to adopt a second conformation for thioester formation. Previously, we determined the structure of 4-chlorobenzoate:CoA ligase (CBL) in the adenylate forming conformation bound to 4-chlorobenzoate. We have determined two new crystal structures. We have determined the structure of CBL in the original adenylate-forming conformation, bound to the adenylate intermediate. Additionally, we have used a novel product analogue, 4-chlorophenacyl-CoA, to trap the enzyme in the thioester-forming conformation and determined this structure in a new crystal form. This work identifies a novel binding pocket for the CoA nucleotide. The structures presented herein provide the foundation for biochemical analyses presented in the accompanying manuscript in this issue [Wu et al. (2008) Biochemistry 47, 8026-8039]. The complete characterization of this enzyme allows us to provide an explanation for the use of the domain alternation strategy by these enzymes.
Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase.,Reger AS, Wu R, Dunaway-Mariano D, Gulick AM Biochemistry. 2008 Aug 5;47(31):8016-25. Epub 2008 Jul 12. PMID:18620418[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Reger AS, Wu R, Dunaway-Mariano D, Gulick AM. Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase. Biochemistry. 2008 Aug 5;47(31):8016-25. Epub 2008 Jul 12. PMID:18620418 doi:10.1021/bi800696y
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