2y27

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:01, 1 February 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2y27.jpg|left|200px]]
 
-
<!--
+
==crystal structure of PaaK1 in complex with ATP from Burkholderia cenocepacia==
-
The line below this paragraph, containing "STRUCTURE_2y27", creates the "Structure Box" on the page.
+
<StructureSection load='2y27' size='340' side='right'caption='[[2y27]], [[Resolution|resolution]] 1.60&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'>[[2y27]] 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=2Y27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y27 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]] 1.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
-
{{STRUCTURE_2y27| PDB=2y27 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2y27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y27 OCA], [https://pdbe.org/2y27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y27 RCSB], [https://www.ebi.ac.uk/pdbsum/2y27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y27 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/B4E7B5_BURCJ B4E7B5_BURCJ] Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).[PIRNR:PIRNR006444]
 +
<div style="background-color:#fffaf0;">
 +
== 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.
-
===CRYSTAL STRUCTURE OF PAAK1 IN COMPLEX WITH ATP FROM BURKHOLDERIA 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<ref>PMID:21388965</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
==About this Structure==
+
</div>
-
[[2y27]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cenocepacia Burkholderia cenocepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y27 OCA].
+
<div class="pdbe-citations 2y27" style="background-color:#fffaf0;"></div>
-
[[Category: Burkholderia cenocepacia]]
+
== References ==
-
[[Category: Phenylacetate--CoA ligase]]
+
<references/>
-
[[Category: Boulanger, M J.]]
+
__TOC__
-
[[Category: Law, A.]]
+
</StructureSection>
 +
[[Category: Burkholderia cenocepacia J2315]]
 +
[[Category: Large Structures]]
 +
[[Category: Boulanger MJ]]
 +
[[Category: Law A]]

Current revision

crystal structure of PaaK1 in complex with ATP from Burkholderia cenocepacia

PDB ID 2y27

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2y27"
Personal tools