1ppa

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[[Image:1ppa.gif|left|200px]]
 
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==THE CRYSTAL STRUCTURE OF A LYSINE 49 PHOSPHOLIPASE A2 FROM THE VENOM OF THE COTTONMOUTH SNAKE AT 2.0 ANGSTROMS RESOLUTION==
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The line below this paragraph, containing "STRUCTURE_1ppa", creates the "Structure Box" on the page.
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<StructureSection load='1ppa' size='340' side='right'caption='[[1ppa]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1ppa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agkistrodon_piscivorus_piscivorus Agkistrodon piscivorus piscivorus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PPA FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2&#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=ANL:ANILINE'>ANL</scene></td></tr>
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{{STRUCTURE_1ppa| PDB=1ppa | SCENE= }}
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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=1ppa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppa OCA], [https://pdbe.org/1ppa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ppa RCSB], [https://www.ebi.ac.uk/pdbsum/1ppa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppa ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PA2HB_AGKPI PA2HB_AGKPI] Snake venom phospholipase A2 (PLA2) that lacks enzymatic activity, but displays edema-inducing activities.<ref>PMID:1429612</ref>
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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/pp/1ppa_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1ppa ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of a lysine 49 variant phospholipase A2 (K49 PLA2) has been determined at 2.0-A resolution. This particular phospholipase A2, purified from the venom of the eastern cottonmouth (Agkistrodon piscivorus piscivorus), a North American pit viper, differs significantly from others studied crystallographically because of replacement of the aspartate residue at position 49, whose side chain is important in calcium binding, by lysine. The crystallographic analysis of K49 PLA2 was undertaken to assess the structural ramifications of this substitution, particularly as they affect the binding mechanism of both the calcium cofactor and the phospholipid substrate. The protein crystals are tetragonal, space group P4(1)2(1)2, with unit cell dimensions of a = b = 71.7 (1) and c = 57.8 (3) A. Preliminary phases were obtained by molecular replacement techniques with a search model derived from the refined 2.5-A structure of a rattle-snake venom phospholipase A2 (Brunie, S., Bolin, J., Gewirth, D., and Sigler, P. B. (1985) J. Biol. Chem. 260, 9742-9749). The starting model gave an initial crystallographic RF of 0.526 (RF = sigma parallel to Fo /-/ Fc parallel to /sigma/Fo/). The structure was refined against all data to 2.0-A resolution. The final RF is 0.158. The final model includes 150 discrete water molecules. The K49 PLA2 model is composed primarily of alpha-helices joined by loops, some of which are quite extensive. Although dissimilarities are observed in the loop regions, the helical portions are very similar to those in other known phospholipase A2 structures. The proposed catalytic center (His48, Tyr73, and Asp99) is also structurally conserved. The region in K49 PLA2 corresponding to the calcium-binding site in other phospholipases A2 is occupied by the epsilon-amino group of lysine 49.
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'''THE CRYSTAL STRUCTURE OF A LYSINE 49 PHOSPHOLIPASE A2 FROM THE VENOM OF THE COTTONMOUTH SNAKE AT 2.0 ANGSTROMS RESOLUTION'''
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The crystal structure of a lysine 49 phospholipase A2 from the venom of the cottonmouth snake at 2.0-A resolution.,Holland DR, Clancy LL, Muchmore SW, Ryde TJ, Einspahr HM, Finzel BC, Heinrikson RL, Watenpaugh KD J Biol Chem. 1990 Oct 15;265(29):17649-56. PMID:2120215<ref>PMID:2120215</ref>
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==Overview==
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The crystal structure of a lysine 49 variant phospholipase A2 (K49 PLA2) has been determined at 2.0-A resolution. This particular phospholipase A2, purified from the venom of the eastern cottonmouth (Agkistrodon piscivorus piscivorus), a North American pit viper, differs significantly from others studied crystallographically because of replacement of the aspartate residue at position 49, whose side chain is important in calcium binding, by lysine. The crystallographic analysis of K49 PLA2 was undertaken to assess the structural ramifications of this substitution, particularly as they affect the binding mechanism of both the calcium cofactor and the phospholipid substrate. The protein crystals are tetragonal, space group P4(1)2(1)2, with unit cell dimensions of a = b = 71.7 (1) and c = 57.8 (3) A. Preliminary phases were obtained by molecular replacement techniques with a search model derived from the refined 2.5-A structure of a rattle-snake venom phospholipase A2 (Brunie, S., Bolin, J., Gewirth, D., and Sigler, P. B. (1985) J. Biol. Chem. 260, 9742-9749). The starting model gave an initial crystallographic RF of 0.526 (RF = sigma parallel to Fo /-/ Fc parallel to /sigma/Fo/). The structure was refined against all data to 2.0-A resolution. The final RF is 0.158. The final model includes 150 discrete water molecules. The K49 PLA2 model is composed primarily of alpha-helices joined by loops, some of which are quite extensive. Although dissimilarities are observed in the loop regions, the helical portions are very similar to those in other known phospholipase A2 structures. The proposed catalytic center (His48, Tyr73, and Asp99) is also structurally conserved. The region in K49 PLA2 corresponding to the calcium-binding site in other phospholipases A2 is occupied by the epsilon-amino group of lysine 49.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1PPA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Agkistrodon_piscivorus_piscivorus Agkistrodon piscivorus piscivorus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPA OCA].
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</div>
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<div class="pdbe-citations 1ppa" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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The crystal structure of a lysine 49 phospholipase A2 from the venom of the cottonmouth snake at 2.0-A resolution., Holland DR, Clancy LL, Muchmore SW, Ryde TJ, Einspahr HM, Finzel BC, Heinrikson RL, Watenpaugh KD, J Biol Chem. 1990 Oct 15;265(29):17649-56. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2120215 2120215]
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*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Agkistrodon piscivorus piscivorus]]
[[Category: Agkistrodon piscivorus piscivorus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Clancy, L L.]]
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[[Category: Clancy LL]]
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[[Category: Einspahr, H M.]]
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[[Category: Einspahr HM]]
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[[Category: Finzel, B C.]]
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[[Category: Finzel BC]]
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[[Category: Heinrikson, R L.]]
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[[Category: Heinrikson RL]]
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[[Category: Holland, D R.]]
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[[Category: Holland DR]]
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[[Category: Muchmore, S W.]]
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[[Category: Muchmore SW]]
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[[Category: Rydel, T J.]]
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[[Category: Rydel TJ]]
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[[Category: Watenpaugh, K D.]]
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[[Category: Watenpaugh KD]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 05:19:59 2008''
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Current revision

THE CRYSTAL STRUCTURE OF A LYSINE 49 PHOSPHOLIPASE A2 FROM THE VENOM OF THE COTTONMOUTH SNAKE AT 2.0 ANGSTROMS RESOLUTION

PDB ID 1ppa

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