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| | <StructureSection load='1lwb' size='340' side='right'caption='[[1lwb]], [[Resolution|resolution]] 1.05Å' scene=''> | | <StructureSection load='1lwb' size='340' side='right'caption='[[1lwb]], [[Resolution|resolution]] 1.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1lwb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinomyces_violaceus-ruber"_(sic)_waksman_and_curtis_1916 "actinomyces violaceus-ruber" (sic) waksman and curtis 1916]. 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> | + | <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> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1faz|1faz]], [[1kp4|1kp4]], [[1it4|1it4]], [[1it5|1it5]]</div></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.05Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </span></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=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> | | <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> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q6UV28_STRVN Q6UV28_STRVN] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Matoba, Y]] | + | [[Category: Streptomyces violaceoruber]] |
| - | [[Category: Sugiyama, M]] | + | [[Category: Matoba Y]] |
| - | [[Category: Atomic resolution]] | + | [[Category: Sugiyama M]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Internal motion]]
| + | |
| - | [[Category: Phospholipase a2]]
| + | |
| Structural highlights
Function
Q6UV28_STRVN
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Matoba Y, Sugiyama M. Atomic resolution structure of prokaryotic phospholipase A2: analysis of internal motion and implication for a catalytic mechanism. Proteins. 2003 May 15;51(3):453-69. PMID:12696056 doi:10.1002/prot.10360
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