1lwb

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[[Image:1lwb.jpg|left|200px]]
 
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==Crystal structure of prokaryotic phospholipase A2 at atomic resolution==
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The line below this paragraph, containing "STRUCTURE_1lwb", creates the "Structure Box" on the page.
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<StructureSection load='1lwb' size='340' side='right'caption='[[1lwb]], [[Resolution|resolution]] 1.05&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'>[[1lwb]] 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=1LWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LWB 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]] 1.05&#8491;</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=1lwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwb OCA], [https://pdbe.org/1lwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lwb RCSB], [https://www.ebi.ac.uk/pdbsum/1lwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwb ProSAT]</span></td></tr>
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{{STRUCTURE_1lwb| PDB=1lwb | SCENE= }}
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</table>
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== Function ==
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'''Crystal structure of prokaryotic phospholipase A2 at atomic resolution'''
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[https://www.uniprot.org/uniprot/Q6UV28_STRVN Q6UV28_STRVN]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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==Overview==
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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/lw/1lwb_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=1lwb 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 ==
We have found a secreted phospholipase A(2) (PLA(2), EC 3.1.1.4) from Streptomyces violaceoruber A-2688, which is the first PLA(2) identified in prokaryote, and determined its tertiary structure by NMR and X-ray analyses. In this study, we collected the X-ray diffraction data of the bacterial PLA(2) at room temperature (297 K) using conventional MoK(alpha) radiation and refined the structure at a 1.05 A resolution. The atomic resolution analysis led us to introduce disordered conformations and hydrogen atoms into a full anisotropic model. The molecular motion, which is expressed as the sum of rigid-body motion and internal motion of protein, is roughly estimated as the thermal motion when the X-ray diffraction data are collected at room temperature. In this study, we applied a TLS (rigid-body motion in terms of translation, libration, and screw motions) model to analyze the rigid-body motion of the bacterial PLA(2) and calculated the internal motion by subtracting the estimate of the rigid-body motion from the observed anisotropic temperature factor. We also subjected the TLS model to estimate the internal motion of the bovine pancreatic PLA(2) using the anisotropic temperature factor deposited in the Protein Data Bank. Both results indicate that the localization of regions exhibiting larger internal motion in the bacterial PLA(2) is almost the same as that in the bovine pancreatic PLA(2), suggesting that although the tertiary structure of the bacterial PLA(2) is strikingly different from that of the bovine pancreatic PLA(2), the internal motion, which is associated with the calcium(II) ion-binding, phospholipid-binding, and allosteric interfacial activation, is commonly observed in both PLA(2)s.
We have found a secreted phospholipase A(2) (PLA(2), EC 3.1.1.4) from Streptomyces violaceoruber A-2688, which is the first PLA(2) identified in prokaryote, and determined its tertiary structure by NMR and X-ray analyses. In this study, we collected the X-ray diffraction data of the bacterial PLA(2) at room temperature (297 K) using conventional MoK(alpha) radiation and refined the structure at a 1.05 A resolution. The atomic resolution analysis led us to introduce disordered conformations and hydrogen atoms into a full anisotropic model. The molecular motion, which is expressed as the sum of rigid-body motion and internal motion of protein, is roughly estimated as the thermal motion when the X-ray diffraction data are collected at room temperature. In this study, we applied a TLS (rigid-body motion in terms of translation, libration, and screw motions) model to analyze the rigid-body motion of the bacterial PLA(2) and calculated the internal motion by subtracting the estimate of the rigid-body motion from the observed anisotropic temperature factor. We also subjected the TLS model to estimate the internal motion of the bovine pancreatic PLA(2) using the anisotropic temperature factor deposited in the Protein Data Bank. Both results indicate that the localization of regions exhibiting larger internal motion in the bacterial PLA(2) is almost the same as that in the bovine pancreatic PLA(2), suggesting that although the tertiary structure of the bacterial PLA(2) is strikingly different from that of the bovine pancreatic PLA(2), the internal motion, which is associated with the calcium(II) ion-binding, phospholipid-binding, and allosteric interfacial activation, is commonly observed in both PLA(2)s.
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==About this Structure==
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Atomic resolution structure of prokaryotic phospholipase A2: analysis of internal motion and implication for a catalytic mechanism.,Matoba Y, Sugiyama M Proteins. 2003 May 15;51(3):453-69. PMID:12696056<ref>PMID:12696056</ref>
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1LWB 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=1LWB OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Atomic resolution structure of prokaryotic phospholipase A2: analysis of internal motion and implication for a catalytic mechanism., Matoba Y, Sugiyama M, Proteins. 2003 May 15;51(3):453-69. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12696056 12696056]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 1lwb" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Streptomyces violaceoruber]]
[[Category: Streptomyces violaceoruber]]
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[[Category: Matoba, Y.]]
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[[Category: Matoba Y]]
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[[Category: Sugiyama, M.]]
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[[Category: Sugiyama M]]
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[[Category: Atomic resolution]]
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[[Category: Internal motion]]
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[[Category: Phospholipase a2]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 00:21:48 2008''
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Current revision

Crystal structure of prokaryotic phospholipase A2 at atomic resolution

PDB ID 1lwb

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