1mks: Difference between revisions

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OCA

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-[[Image:1mks.gif|left|200px]]<br /><applet load="1mks" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1mks, resolution 1.9&Aring;" />
-'''CARBOXYLIC ESTER HYDROLASE, TRIGONAL FORM OF THE TRIPLE MUTANT'''<br />
-==Overview==
+==CARBOXYLIC ESTER HYDROLASE, TRIGONAL FORM OF THE TRIPLE MUTANT==
-The aspartate-99 of secreted phospholipase A2 (PLA2) has been proposed to, be critical for the catalytic mechanism and interfacial activation of, PLA2. Aspartate-99 connects the catalytic machinery (including the, catalytic diad, the putative catalytic waters W5 and W6, and the calcium, cofactor) to the hydrogen-bonding network. The latter involves Y52, Y73, the structural water, and the N-terminal region putatively required for, the interfacial activation. A triple mutant of bovine pancreatic PLA2 with, substitutions aspartate plus adjacent tyrosine residues (Y52,73F/D99N) was, constructed, its X-ray structure was determined, and kinetic, characteristics were analyzed. The kinetic properties of the D99N mutant, constructed previously were also further analyzed. The X-ray structure of, the Y52,73F/D99N mutant indicated a substantial disruption of the, hydrogen-bonding network including the loss of the structural water, similar to that seen in the structure of the D99N mutant published, previously [Kumar, A., Sekharudu, Y. C., Ramakrishnan, B., Dupureur, C., M., Zhu, H., Tsai, M.-D., &amp; Sundaralingam, M. (1994) Protein Sci. 3, 2082-2088]. Kinetic analysis demonstrated that these mutants possessed, considerable catalytic activity with a k(cat) value of about 5% compared, to WT. The values of the interfacial Michaelis constant were also little, perturbed (ca. 4-fold lower for D99N and marginally higher for, Y52,73F/D99N). The results taken together suggest that the, hydrogen-bonding network is not critically important for interfacial, activation. Instead, it is the chemical step that is perturbed, though, only modestly, in the mutants.
+<StructureSection load='1mks' size='340' side='right'caption='[[1mks]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1mks]] 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=1MKS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MKS 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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=1mks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mks OCA], [https://pdbe.org/1mks PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mks RCSB], [https://www.ebi.ac.uk/pdbsum/1mks PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mks ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PA21B_BOVIN PA21B_BOVIN] 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/mk/1mks_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1mks ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The aspartate-99 of secreted phospholipase A2 (PLA2) has been proposed to be critical for the catalytic mechanism and interfacial activation of PLA2. Aspartate-99 connects the catalytic machinery (including the catalytic diad, the putative catalytic waters W5 and W6, and the calcium cofactor) to the hydrogen-bonding network. The latter involves Y52, Y73, the structural water, and the N-terminal region putatively required for the interfacial activation. A triple mutant of bovine pancreatic PLA2 with substitutions aspartate plus adjacent tyrosine residues (Y52,73F/D99N) was constructed, its X-ray structure was determined, and kinetic characteristics were analyzed. The kinetic properties of the D99N mutant constructed previously were also further analyzed. The X-ray structure of the Y52,73F/D99N mutant indicated a substantial disruption of the hydrogen-bonding network including the loss of the structural water similar to that seen in the structure of the D99N mutant published previously [Kumar, A., Sekharudu, Y. C., Ramakrishnan, B., Dupureur, C. M., Zhu, H., Tsai, M.-D., &amp; Sundaralingam, M. (1994) Protein Sci. 3, 2082-2088]. Kinetic analysis demonstrated that these mutants possessed considerable catalytic activity with a k(cat) value of about 5% compared to WT. The values of the interfacial Michaelis constant were also little perturbed (ca. 4-fold lower for D99N and marginally higher for Y52,73F/D99N). The results taken together suggest that the hydrogen-bonding network is not critically important for interfacial activation. Instead, it is the chemical step that is perturbed, though only modestly, in the mutants.
-==About this Structure==
+Phospholipase A2 engineering. Structural and functional roles of the highly conserved active site residue aspartate-99.,Sekar K, Yu BZ, Rogers J, Lutton J, Liu X, Chen X, Tsai MD, Jain MK, Sundaralingam M Biochemistry. 1997 Mar 18;36(11):3104-14. PMID:9115986<ref>PMID:9115986</ref>
-MKS 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 as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1MKS OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Phospholipase A2 engineering. Structural and functional roles of the highly conserved active site residue aspartate-99., Sekar K, Yu BZ, Rogers J, Lutton J, Liu X, Chen X, Tsai MD, Jain MK, Sundaralingam M, Biochemistry. 1997 Mar 18;36(11):3104-14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9115986 9115986]
+</div>
+<div class="pdbe-citations 1mks" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Phospholipase A(2)]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Sundaralingam M]]
-[[Category: Sundaralingam, M.]]
-[[Category: CA]]
-[[Category: carboxylic ester hydrolase]]
-[[Category: enzyme]]
-[[Category: hydrolase]]
-[[Category: trigonal form]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:29:00 2007''