1wls: Difference between revisions

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OCA

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-[[Image:1wls.gif|left|200px]]<br /><applet load="1wls" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1wls, resolution 2.16&Aring;" />
-'''Crystal structure of L-asparaginase I homologue protein from Pyrococcus horikoshii'''<br />
-==Overview==
+==Crystal structure of L-asparaginase I homologue protein from Pyrococcus horikoshii==
-The crystal structure of the L-asparaginase from the hyperthermophilic, archaeon Pyrococcus horikoshii (PhA) was determined by the multiwavelength, anomalous diffraction (MAD) method and was refined to a resolution of 2.16, angstroms with a crystallographic R factor and free R factor of 21.1 and, 25.3%, respectively. This is the first report of the three-dimensional, structure of a type I L-asparaginase. These enyzmes are known as cytosolic, L-asparaginases with lower affinities for substrate than the type II, L-asparaginases. Although the overall fold of PhA was closely related to, the structure of the well characterized type II L-asparaginase, structural, differences were also detected. PhA forms a homodimer that corresponds to, half the homotetramer of type II L-asparaginases. Structure comparison at, the active site reveals that most catalytic residues are conserved except, for two residues that recognize the amino group of the substrate., Additionally, a remarkable structural difference is found in the so-called, 'active-site flexible loop'. In PhA this loop is stabilized by, beta-hairpin formation and by elaborate interactions with the, type-I-specific alpha-helical region derived from the other subunit, forming the PhA dimer. The flexible loop of the type II enzyme is, considered to serve as a mobile gate to the active site. Therefore, the, loop stabilization observed in the PhA structure may cause limitation of, the access of the substrate to the active site.
+<StructureSection load='1wls' size='340' side='right'caption='[[1wls]], [[Resolution|resolution]] 2.16&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1wls]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WLS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WLS 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]] 2.16&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1wls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wls OCA], [https://pdbe.org/1wls PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wls RCSB], [https://www.ebi.ac.uk/pdbsum/1wls PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wls ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O57797_PYRHO O57797_PYRHO]
+== 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/wl/1wls_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=1wls ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of the L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii (PhA) was determined by the multiwavelength anomalous diffraction (MAD) method and was refined to a resolution of 2.16 angstroms with a crystallographic R factor and free R factor of 21.1 and 25.3%, respectively. This is the first report of the three-dimensional structure of a type I L-asparaginase. These enyzmes are known as cytosolic L-asparaginases with lower affinities for substrate than the type II L-asparaginases. Although the overall fold of PhA was closely related to the structure of the well characterized type II L-asparaginase, structural differences were also detected. PhA forms a homodimer that corresponds to half the homotetramer of type II L-asparaginases. Structure comparison at the active site reveals that most catalytic residues are conserved except for two residues that recognize the amino group of the substrate. Additionally, a remarkable structural difference is found in the so-called 'active-site flexible loop'. In PhA this loop is stabilized by beta-hairpin formation and by elaborate interactions with the type-I-specific alpha-helical region derived from the other subunit forming the PhA dimer. The flexible loop of the type II enzyme is considered to serve as a mobile gate to the active site. Therefore, the loop stabilization observed in the PhA structure may cause limitation of the access of the substrate to the active site.
-==About this Structure==
+Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution.,Yao M, Yasutake Y, Morita H, Tanaka I Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):294-301. Epub 2005, Feb 24. PMID:15735339<ref>PMID:15735339</ref>
-WLS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Active as [http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WLS OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution., Yao M, Yasutake Y, Morita H, Tanaka I, Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):294-301. Epub 2005, Feb 24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15735339 15735339]
+</div>
-[[Category: Asparaginase]]
+<div class="pdbe-citations 1wls" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Asparaginase 3D structures|Asparaginase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Pyrococcus horikoshii]]
-[[Category: Single protein]]
+[[Category: Morita H]]
-[[Category: Morita, H.]]
+[[Category: Tanaka I]]
-[[Category: Tanaka, I.]]
+[[Category: Yao M]]
-[[Category: Yao, M.]]
+[[Category: Yasutake Y]]
-[[Category: Yasutake, Y.]]
-[[Category: structural genomics]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 00:11:49 2007''