2gez: Difference between revisions

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-{{Seed}}
-[[Image:2gez.png|left|200px]]
-<!--
+==Crystal structure of potassium-independent plant asparaginase==
-The line below this paragraph, containing "STRUCTURE_2gez", creates the "Structure Box" on the page.
+<StructureSection load='2gez' size='340' side='right'caption='[[2gez]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2gez]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Lupinus_luteus Lupinus luteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GEZ FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_2gez|  PDB=2gez  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gez OCA], [https://pdbe.org/2gez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gez RCSB], [https://www.ebi.ac.uk/pdbsum/2gez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gez ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ASPG_LUPLU ASPG_LUPLU] Degrades proteins damaged by L-isoaspartyl residue formation (also known as beta-Asp residues). Also has L-asparaginase activity, which is used to liberate stored nitrogen during seed development.
+== 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/ge/2gez_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2gez ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In plants, specialized enzymes are required to catalyze the release of ammonia from asparagine, which is the main nitrogen-relocation molecule in these organisms. In addition, K+-independent plant asparaginases are also active in splitting the aberrant isoaspartyl peptide bonds, which makes these proteins important for seed viability and germination. Here, we present the crystal structure of potassium-independent L-asparaginase from yellow lupine (LlA) and confirm the classification of this group of enzymes in the family of Ntn-hydrolases. The alpha- and beta-subunits that form the mature (alphabeta)2 enzyme arise from autoproteolytic cleavage of two copies of a precursor protein. In common with other Ntn-hydrolases, the (alphabeta) heterodimer has a sandwich-like fold with two beta-sheets flanked by two layers of alpha-helices (alphabetabetaalpha). The nucleophilic Thr193 residue, which is liberated in the autocatalytic event at the N terminus of subunit beta, is part of an active site that is similar to that observed in a homologous bacterial enzyme. An unusual sodium-binding loop of the bacterial protein, necessary for proper positioning of all components of the active site, shows strictly conserved conformation and metal coordination in the plant enzyme. A chloride anion complexed in the LlA structure marks the position of the alpha-carboxylate group of the L-aspartyl substrate/product moiety. Detailed analysis of the active site suggests why the plant enzyme hydrolyzes asparagine and its beta-peptides but is inactive towards substrates accepted by similar Ntn-hydrolases, such as taspase1, an enzyme implicated in some human leukemias. Structural comparisons of LlA and taspase1 provide interesting insights into the role of small inorganic ions in the latter enzyme.
-===Crystal structure of potassium-independent plant asparaginase===
+Crystal structure of plant asparaginase.,Michalska K, Bujacz G, Jaskolski M J Mol Biol. 2006 Jun 30;360(1):105-16. Epub 2006 May 15. PMID:16725155<ref>PMID:16725155</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2gez" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16725155}}, adds the Publication Abstract to the page
+*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16725155 is the PubMed ID number.
+*[[Asparaginase 3D structures|Asparaginase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_16725155}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-GEZ is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Lupinus_luteus Lupinus luteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEZ OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:16725155</ref><references group="xtra"/>
-[[Category: Asparaginase]]
 [[Category: Lupinus luteus]]
-[[Category: Bujacz, G.]]
+[[Category: Bujacz G]]
-[[Category: Jaskolski, M.]]
+[[Category: Jaskolski M]]
-[[Category: Michalska, K.]]
+[[Category: Michalska K]]
-[[Category: Autoproteolysis]]
-[[Category: Isoaspartyl aminopeptidase]]
-[[Category: L-asparaginase]]
-[[Category: Ntn-hydrolase]]
-[[Category: Sodium binding]]
-[[Category: Taspase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:50:43 2009''