2zal: Difference between revisions

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-[[Image:2zal.png|left|200px]]
-<!--
+==Crystal structure of E. coli isoaspartyl aminopeptidase/L-asparaginase in complex with L-aspartate==
-The line below this paragraph, containing "STRUCTURE_2zal", creates the "Structure Box" on the page.
+<StructureSection load='2zal' size='340' side='right'caption='[[2zal]], [[Resolution|resolution]] 1.90&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'>[[2zal]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1seo 1seo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZAL 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-{{STRUCTURE_2zal|  PDB=2zal  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zal OCA], [https://pdbe.org/2zal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zal RCSB], [https://www.ebi.ac.uk/pdbsum/2zal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zal ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IAAA_ECOLI IAAA_ECOLI] Degrades proteins damaged by L-isoaspartyl residue formation (also known as beta-Asp residues). Degrades L-isoaspartyl-containing di- and maybe also tripeptides. Also has L-asparaginase activity, although this may not be its principal function.<ref>PMID:11988085</ref>   May be involved in glutathione, and possibly other peptide, transport, although these results could also be due to polar effects of disruption.<ref>PMID:11988085</ref>
+== 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/za/2zal_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=2zal ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of Escherichia coli isoaspartyl aminopeptidase/asparaginase (EcAIII), an enzyme belonging to the N-terminal nucleophile (Ntn)-hydrolases family, has been determined at 1.9-A resolution for a complex obtained by cocrystallization with l-aspartate, which is a product of both enzymatic reactions catalyzed by EcAIII. The enzyme is a dimer of heterodimers, (alphabeta)(2). The (alphabeta) heterodimer, which arises by autoproteolytic cleavage of the immature protein, exhibits an alphabetabetaalpha-sandwich fold, typical for Ntn-hydrolases. The asymmetric unit contains one copy of the EcAIII.Asp complex, with clearly visible l-aspartate ligands, one bound in each of the two active sites of the enzyme. The l-aspartate ligand is located near Thr(179), the N-terminal residue of subunit beta liberated in the autoproteolytic event. Structural comparisons with the free form of EcAIII reveal that there are no major rearrangements of the active site upon aspartate binding. Although the ligand binding mode is similar to that observed in an l-aspartate complex of the related enzyme human aspartylglucosaminidase, the architecture of the EcAIII active site sheds light on the question of substrate specificity and explains why EcAIII is not able to hydrolyze glycosylated asparagine substrates.
-===Crystal structure of E. coli isoaspartyl aminopeptidase/L-asparaginase in complex with L-aspartate===
+Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate.,Michalska K, Brzezinski K, Jaskolski M J Biol Chem. 2005 Aug 5;280(31):28484-91. Epub 2005 Jun 9. PMID:15946951<ref>PMID:15946951</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15946951}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2zal" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15946951 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_15946951}}
-==About this Structure==
-[[2zal]] is a 4 chain structure of [[Aminopeptidase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1seo 1seo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZAL OCA].
 ==See Also==
-*[[Aminopeptidase]]
+*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
+*[[Asparaginase 3D structures|Asparaginase 3D structures]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:15946951</ref><ref group="xtra">PMID:11053866</ref><ref group="xtra">PMID:7477383</ref><ref group="xtra">PMID:9541410</ref><ref group="xtra">PMID:8846222</ref><ref group="xtra">PMID:9685368</ref><ref group="xtra">PMID:10490104</ref><ref group="xtra">PMID:14616088</ref><ref group="xtra">PMID:15159592</ref><references group="xtra"/>
+<references/>
-[[Category: Escherichia coli k12]]
+__TOC__
-[[Category: Brzezinski, K.]]
+</StructureSection>
-[[Category: Jaskolski, M.]]
+[[Category: Escherichia coli K-12]]
-[[Category: Michalska, K.]]
+[[Category: Large Structures]]
-[[Category: Asparaginase]]
+[[Category: Brzezinski K]]
-[[Category: Autoproteolysis]]
+[[Category: Jaskolski M]]
-[[Category: Isoaspartyl peptidase]]
+[[Category: Michalska K]]
-[[Category: L-aspartate/calcium cluster]]
-[[Category: Ntn-hydrolase]]