2qb2: Difference between revisions

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-{{Seed}}
-[[Image:2qb2.png|left|200px]]
-<!--
+==Structural Studies Reveal the Inactivation of E. coli L-aspartate aminotransferase by (s)-4,5-dihydro-2thiophenecarboylic acid (SADTA) via two mechanisms (at pH 7.0).==
-The line below this paragraph, containing "STRUCTURE_2qb2", creates the "Structure Box" on the page.
+<StructureSection load='2qb2' size='340' side='right'caption='[[2qb2]], [[Resolution|resolution]] 1.70&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'>[[2qb2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QB2 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KST:N~6~-(5-CARBOXY-3-THIENYL)-L-LYSINE'>KST</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene>, <scene name='pdbligand=PSZ:4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]THIOPHENE-2-CARBOXYLIC+ACID'>PSZ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2qb2|  PDB=2qb2  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qb2 OCA], [https://pdbe.org/2qb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qb2 RCSB], [https://www.ebi.ac.uk/pdbsum/2qb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qb2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AAT_ECOLI AAT_ECOLI]
+== 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/qb/2qb2_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=2qb2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+As a mechanism-based inactivator of PLP-enzymes, (S)-4-amino-4,5-dihydro-2-thiophenecarboxylic acid (SADTA) was cocrystallized with Escherichia coli aspartate aminotransferase (l-AspAT) at a series of pH values ranging from 6 to 8. Five structural models with high resolution (1.4-1.85 A) were obtained for l-AspAT-SADTA complexes at pH 6.0, 6.5, 7.0, 7.5, and 8.0. Electron densities of the models showed that two different adducts had formed in the active sites. One adduct was formed from SADTA covalently linked to pyridoxal 5'-phosphate (PLP) while the other adduct was formed with the inhibitor covalently linked to Lysine246,1 the active site lysine. Moreover, there is a strong indication based on the electron densities that the occurrence of the two adducts is pH dependent. We conclude that SADTA inactivates l-AspAT via two different mechanisms based on the binding direction of the inactivator. Additionally, the structural models also show pH dependence of the protein structure itself, which provided detailed mechanistic implications for l-AspAT.
-===Structural Studies Reveal the Inactivation of E. coli L-aspartate aminotransferase by (s)-4,5-dihydro-2thiophenecarboylic acid (SADTA) via two mechanisms (at pH 7.0).===
+Inactivation of Escherichia coli L-aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-thiophenecarboxylic acid reveals "a tale of two mechanisms".,Liu D, Pozharski E, Lepore BW, Fu M, Silverman RB, Petsko GA, Ringe D Biochemistry. 2007 Sep 18;46(37):10517-27. Epub 2007 Aug 22. PMID:17713924<ref>PMID:17713924</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2qb2" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17713924}}, adds the Publication Abstract to the page
+*[[Aspartate aminotransferase 3D structures|Aspartate aminotransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17713924 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17713924}}
+__TOC__
+</StructureSection>
-==About this Structure==
-QB2 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB2 OCA].
-==Reference==
-<ref group="xtra">PMID:17713924</ref><references group="xtra"/>
-[[Category: Aspartate transaminase]]
 [[Category: Escherichia coli]]
-[[Category: Fu, M.]]
+[[Category: Large Structures]]
-[[Category: Lepore, B.]]
+[[Category: Fu M]]
-[[Category: Liu, D.]]
+[[Category: Lepore B]]
-[[Category: Petsko, G A.]]
+[[Category: Liu D]]
-[[Category: Pozharski, E.]]
+[[Category: Petsko GA]]
-[[Category: Ringe, D.]]
+[[Category: Pozharski E]]
-[[Category: Silverman, R B.]]
+[[Category: Ringe D]]
-[[Category: Aspartate aminotransferase]]
+[[Category: Silverman RB]]
-[[Category: Mechanism-based inactivator]]
-[[Category: Ph dependence]]
-[[Category: Plp]]
-[[Category: Sadta]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:58:51 2009''