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1l8s

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CARBOXYLIC ESTER HYDROLASE COMPLEX (DIMERIC PLA2 + LPC-ether + ACETATE + PHOSPHATE IONS)

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OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1l8s"

Categories: Large Structures | Sus scrofa | Bahnson BJ | Pan YH

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-[[Image:1l8s.gif|left|200px]]<br /><applet load="1l8s" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1l8s, resolution 1.55&Aring;" />
-'''CARBOXYLIC ESTER HYDROLASE COMPLEX (DIMERIC PLA2 + LPC-ether + ACETATE + PHOSPHATE IONS)'''<br />
-==Overview==
+==CARBOXYLIC ESTER HYDROLASE COMPLEX (DIMERIC PLA2 + LPC-ether + ACETATE + PHOSPHATE IONS)==
-We have solved the 1.55 A crystal structure of the anion-assisted dimer of, porcine pancreatic group IB phospholipase A2 (PLA2), complexed with the, products of hydrolysis of the substrate platelet activating factor. The, dimer contains five coplanar phosphate anions bound at the contact surface, between the two PLA2 subunits. This structure parallels a previously, reported anion-assisted dimer that mimics the tetrahedral intermediate of, PLA2 bound to a substrate interface [Pan, Y. H., et al. (2001), Biochemistry 40, 609-617]. The dimer structure has a molecule of the, product acetate bound in subunit A and the other product, 1-octadecyl-sn-glycero-3-phosphocholine (LPC-ether) to subunit B., Therefore, this structure is of the two individual product binary, complexes and not of a ternary complex with both products in one active, site of PLA2. Protein crystals with bound products were only obtained by, cocrystallization starting from the initial substrate. In contrast, an, alternate crystal form was obtained when PLA2 was cocrystallized with, LPC-ether and succinate, and this crystal form did not contain bound, products. The product bound structure has acetate positioned in the, catalytic site of subunit A such that one of its oxygen atoms is located, 3.5 A from the catalytic calcium. Likewise, a longer than typical, Ca-to-Gly(32) carbonyl distance of 3.4 A results in a final Ca, coordination that is four-coordinate and has distorted geometry. The other, oxygen of acetate makes hydrogen bonds with N(delta)(1)-His(48), O(delta)(1)-Asp(49), and the catalytic assisting water (w7). In contrast, the glycerophosphocholine headgroup of LPC-ether in subunit B makes no, contacts with calcium or with the catalytic residues His(48) or Asp(49)., The tail of the LPC-ether is located near the active site pocket with the, last nine carbons of the sn-1- acyl chain refined in two alternate, conformations. The remaining atoms of the LPC-ether product have been, modeled into the solvent channel but have their occupancies set to zero in, the refined model due to disorder. Together, the crystallographic and, equilibrium binding results with the two products show that the, simultaneous binding of both the products in a single active site is not, favored.
+<StructureSection load='1l8s' size='340' side='right'caption='[[1l8s]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1l8s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L8S FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LPE:1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>LPE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=1l8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l8s OCA], [https://pdbe.org/1l8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l8s RCSB], [https://www.ebi.ac.uk/pdbsum/1l8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l8s ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PA21B_PIG PA21B_PIG] PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
+== 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/l8/1l8s_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1l8s ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-L8S is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with CA, NA, PO4, ACT and LPE as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1L8S OCA].
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Crystal structure of phospholipase A2 complex with the hydrolysis products of platelet activating factor: equilibrium binding of fatty acid and lysophospholipid-ether at the active site may be mutually exclusive., Pan YH, Yu BZ, Berg OG, Jain MK, Bahnson BJ, Biochemistry. 2002 Dec 17;41(50):14790-800. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12475227 12475227]
+[[Category: Large Structures]]
-[[Category: Phospholipase A(2)]]
-[[Category: Single protein]]
 [[Category: Sus scrofa]]
-[[Category: Bahnson, B.J.]]
+[[Category: Bahnson BJ]]
-[[Category: Pan, Y.H.]]
+[[Category: Pan YH]]
-[[Category: ACT]]
-[[Category: CA]]
-[[Category: LPE]]
-[[Category: NA]]
-[[Category: PO4]]
-[[Category: carboxylic ester hydrolase]]
-[[Category: dimer]]
-[[Category: enzyme]]
-[[Category: hydrolase]]
-[[Category: paf hydrolysis products binding]]
-[[Category: phosphate binding]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:22:43 2007''

1l8s

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CARBOXYLIC ESTER HYDROLASE COMPLEX (DIMERIC PLA2 + LPC-ether + ACETATE + PHOSPHATE IONS)

Structural highlights

Function

Evolutionary Conservation

See Also

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