|
|
| Line 3: |
Line 3: |
| | <StructureSection load='2y4o' size='340' side='right'caption='[[2y4o]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='2y4o' size='340' side='right'caption='[[2y4o]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2y4o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burcj Burcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y4O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y4O FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2y4o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cenocepacia_J2315 Burkholderia cenocepacia J2315]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y4O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y4O FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=DLL:5-O-[HYDROXY(PHENYLACETYL)PHOSPHORYL]ADENOSINE'>DLL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2y4n|2y4n]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=DLL:5-O-[HYDROXY(PHENYLACETYL)PHOSPHORYL]ADENOSINE'>DLL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phenylacetate--CoA_ligase Phenylacetate--CoA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.30 6.2.1.30] </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=2y4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y4o OCA], [https://pdbe.org/2y4o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y4o RCSB], [https://www.ebi.ac.uk/pdbsum/2y4o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y4o ProSAT]</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=2y4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y4o OCA], [https://pdbe.org/2y4o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y4o RCSB], [https://www.ebi.ac.uk/pdbsum/2y4o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y4o ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/B4EL89_BURCJ B4EL89_BURCJ]] Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).[PIRNR:PIRNR006444]
| + | [https://www.uniprot.org/uniprot/B4EL89_BURCJ B4EL89_BURCJ] Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).[PIRNR:PIRNR006444] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 24: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Burcj]] | + | [[Category: Burkholderia cenocepacia J2315]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Phenylacetate--CoA ligase]]
| + | [[Category: Boulanger MJ]] |
| - | [[Category: Boulanger, M J]] | + | [[Category: Law A]] |
| - | [[Category: Law, A]] | + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Phenylacetic acid degradation pathway]]
| + | |
| Structural highlights
2y4o is a 2 chain structure with sequence from Burkholderia cenocepacia J2315. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.9Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
B4EL89_BURCJ Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).[PIRNR:PIRNR006444]
Publication Abstract from PubMed
The phenylacetic acid (PAA) degradation pathway is the sole aerobic route for phenylacetic acid metabolism in bacteria and facilitates degradation of environmental pollutants such as styrene and ethylbenzene. The PAA pathway also is implicated in promoting Burkholderia cenocepacia infections in cystic fibrosis patients. Intriguingly, the first enzyme in the PAA pathway is present in two copies (paaK1 and paaK2), yet each subsequent enzyme is present in only a single copy. Furthermore, sequence divergence indicates that PaaK1 and PaaK2 form a unique subgroup within the adenylate-forming enzyme (AFE) superfamily. To establish a biochemical rationale for the existence of the PaaK paralogs in B. cenocepacia, we present high resolution x-ray crystal structures of a selenomethionine derivative of PaaK1 in complex with ATP and adenylated phenylacetate intermediate complexes of PaaK1 and PaaK2 in distinct conformations. Structural analysis reveals a novel N-terminal microdomain that may serve to recruit subsequent PAA enzymes, whereas a bifunctional role is proposed for the P-loop in stabilizing the C-terminal domain in conformation 2. The potential for different kinetic profiles was suggested by a structurally divergent extension of the aryl substrate pocket in PaaK1 relative to PaaK2. Functional characterization confirmed this prediction, with PaaK1 possessing a lower K(m) for phenylacetic acid and better able to accommodate 3' and 4' substitutions on the phenyl ring. Collectively, these results offer detailed insight into the reaction mechanism of a novel subgroup of the AFE superfamily and provide a clear biochemical rationale for the presence of paralogous copies of PaaK of B. cenocepacia.
Defining a Structural and Kinetic Rationale for Paralogous Copies of Phenylacetate-CoA Ligases from the Cystic Fibrosis Pathogen Burkholderia cenocepacia J2315.,Law A, Boulanger MJ J Biol Chem. 2011 Apr 29;286(17):15577-85. Epub 2011 Mar 8. PMID:21388965[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Law A, Boulanger MJ. Defining a Structural and Kinetic Rationale for Paralogous Copies of Phenylacetate-CoA Ligases from the Cystic Fibrosis Pathogen Burkholderia cenocepacia J2315. J Biol Chem. 2011 Apr 29;286(17):15577-85. Epub 2011 Mar 8. PMID:21388965 doi:10.1074/jbc.M111.219683
|
