1kp4: Difference between revisions

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-[[Image:1kp4.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1kp4", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_1kp4|  PDB=1kp4  |  SCENE=  }}
-'''CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2'''
+==CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2==
+<StructureSection load='1kp4' size='340' side='right'caption='[[1kp4]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kp4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_violaceoruber Streptomyces violaceoruber]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KP4 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]] 1.6&#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=1kp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kp4 OCA], [https://pdbe.org/1kp4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kp4 RCSB], [https://www.ebi.ac.uk/pdbsum/1kp4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kp4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q6UV28_STRVN Q6UV28_STRVN]
+== 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/kp/1kp4_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=1kp4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In this study, the x-ray crystal structures of the calcium-free and calcium-bound forms of phospholipase A(2) (PLA(2)), produced extracellularly by Streptomyces violaceoruber, were determined by using the multiple isomorphous replacement and molecular replacement methods, respectively. The former and latter structures were refined to an R-factor of 18.8% at a 1.4-A resolution and an R-factor of 15.0% at a 1.6-A resolution, respectively. The overall structure of the prokaryotic PLA(2) exhibits a novel folding topology that demonstrates that it is completely distinct from those of eukaryotic PLA(2)s, which have been already determined by x-ray and NMR analyses. Furthermore, the coordination geometry of the calcium(II) ion apparently deviated from that of eukaryotic PLA(2)s. Regardless of the evolutionary divergence, the catalytic mechanism including the calcium(II) ion on secreted PLA(2) seems to be conserved between prokaryotic and eukaryotic cells. Demonstrating that the overall structure determined by x-ray analysis is almost the same as that determined by NMR analysis is useful to discuss the catalytic mechanism at the molecular level of the bacterial PLA(2).
-==Overview==
+The crystal structure of prokaryotic phospholipase A2.,Matoba Y, Katsube Y, Sugiyama M J Biol Chem. 2002 May 31;277(22):20059-69. Epub 2002 Mar 15. PMID:11897785<ref>PMID:11897785</ref>
-In this study, the x-ray crystal structures of the calcium-free and calcium-bound forms of phospholipase A(2) (PLA(2)), produced extracellularly by Streptomyces violaceoruber, were determined by using the multiple isomorphous replacement and molecular replacement methods, respectively. The former and latter structures were refined to an R-factor of 18.8% at a 1.4-A resolution and an R-factor of 15.0% at a 1.6-A resolution, respectively. The overall structure of the prokaryotic PLA(2) exhibits a novel folding topology that demonstrates that it is completely distinct from those of eukaryotic PLA(2)s, which have been already determined by x-ray and NMR analyses. Furthermore, the coordination geometry of the calcium(II) ion apparently deviated from that of eukaryotic PLA(2)s. Regardless of the evolutionary divergence, the catalytic mechanism including the calcium(II) ion on secreted PLA(2) seems to be conserved between prokaryotic and eukaryotic cells. Demonstrating that the overall structure determined by x-ray analysis is almost the same as that determined by NMR analysis is useful to discuss the catalytic mechanism at the molecular level of the bacterial PLA(2).
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-KP4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_violaceoruber Streptomyces violaceoruber]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KP4 OCA].
+</div>
+<div class="pdbe-citations 1kp4" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-The crystal structure of prokaryotic phospholipase A2., Matoba Y, Katsube Y, Sugiyama M, J Biol Chem. 2002 May 31;277(22):20059-69. Epub 2002 Mar 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11897785 11897785]
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
-[[Category: Single protein]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptomyces violaceoruber]]
-[[Category: Katsube, Y.]]
+[[Category: Katsube Y]]
-[[Category: Matoba, Y.]]
+[[Category: Matoba Y]]
-[[Category: Sugiyama, M.]]
+[[Category: Sugiyama M]]
-[[Category: Calcium ion]]
-[[Category: Phospholipase a2]]
-[[Category: Prokaryote]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 23:00:14 2008''