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1fdk

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(New page: 200px<br /><applet load="1fdk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fdk, resolution 1.91&Aring;" /> '''CARBOXYLIC ESTER HYD...)
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[[Image:1fdk.gif|left|200px]]<br /><applet load="1fdk" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1fdk, resolution 1.91&Aring;" />
 
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'''CARBOXYLIC ESTER HYDROLASE (PLA2-MJ33 INHIBITOR COMPLEX)'''<br />
 
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==Overview==
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==CARBOXYLIC ESTER HYDROLASE (PLA2-MJ33 INHIBITOR COMPLEX)==
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The structure of recombinant bovine pancreatic phospholipase A2 (PLA2), complexed with the competitive inhibitor, 1-hexadecyl-3-(trifluoroethyl)-sn-glycero -2-phosphomethanol (hereafter, MJ33), a phospholipid analogue without the sn-3 phosphodiester group, has, been determined. The crystals are trigonal, space group P3121, a = b =, 46.36 A and c = 102.56 A, and isomorphous to the recombinant PLA2 with one, molecule in the asymmetric unit. The structure was refined using 8082, reflections between 8.0 and 1.91 A resolution to a final R-value of 18.4%, [Rfree = 28.0%]. The model includes 957 protein atoms, 86 water molecules, one calcium ion, and 26 non-hydrogen atoms of the inhibitor MJ33. The, overall tertiary fold of the complex is very similar to that of the, inhibitor-free recombinant PLA2 with a root mean square deviation of 0.32, A for all the backbone atoms. The electron density of the surface loop, residues 62-66 is clear and ordered, unlike the other trigonal bovine PLA2, structures done to date. This structural change could be responsible for, the interfacial allosteric activation, which thermodynamically relates the, enhanced binding of the substrate mimic to the active site of the enzyme., MJ33 is tightly bound in the active-site cleft, dislodging the equatorial, coordinated calcium water (W5), the putative catalytic water W6, and the, neighboring water W7. The axial coordinated calcium water is missing; thus, the hexacoordinated calcium is a monocapped pentagonal pyramid. Although, MJ33 is a sn-2 tetrahedral mimic, its phosphate binds to PLA2 differently, from the sn-2 phosphonate analogue of phospholipids, another tetrahedral, mimic. The knowledge of the active-site geometry of MJ33 would be useful, in the design of more useful therapeutic agents for PLA2.
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<StructureSection load='1fdk' size='340' side='right'caption='[[1fdk]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1fdk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FDK FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.91&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLE:1-DECYL-3-TRIFLUORO+ETHYL-SN-GLYCERO-2-PHOSPHOMETHANOL'>GLE</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fdk OCA], [https://pdbe.org/1fdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fdk RCSB], [https://www.ebi.ac.uk/pdbsum/1fdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fdk ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PA21B_BOVIN PA21B_BOVIN] PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/1fdk_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1fdk ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1FDK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with CA and GLE 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=1FDK OCA].
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*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of the complex of bovine pancreatic phospholipase A2 with the inhibitor 1-hexadecyl-3-(trifluoroethyl)-sn-glycero-2-phosphomethanol,., Sekar K, Eswaramoorthy S, Jain MK, Sundaralingam M, Biochemistry. 1997 Nov 18;36(46):14186-91. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9369492 9369492]
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[[Category: Bos taurus]]
[[Category: Bos taurus]]
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[[Category: Phospholipase A(2)]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Sundaralingam M]]
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[[Category: Sundaralingam, M.]]
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[[Category: CA]]
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[[Category: GLE]]
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[[Category: carboxylic ester hydrolase]]
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[[Category: enzyme]]
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[[Category: lipid degradation]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:50:25 2007''
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Current revision

CARBOXYLIC ESTER HYDROLASE (PLA2-MJ33 INHIBITOR COMPLEX)

PDB ID 1fdk

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