2qb3: Difference between revisions

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-[[Image:2qb3.jpg|left|200px]]
- {{Structure
+==Structural Studies Reveal the Inactivation of E. coli L-Aspartate Aminotransferase by (s)-4,5-dihydro-2-thiophenecarboxylic acid (SADTA) via Two Mechanisms (at pH 7.5)==
-|PDB= 2qb3 |SIZE=350|CAPTION= <scene name='initialview01'>2qb3</scene>, resolution 1.45&Aring;
+<StructureSection load='2qb3' size='340' side='right'caption='[[2qb3]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <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&#39;-DEOXY-4&#39;-AMINOPYRIDOXAL-5&#39;-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>
+<table><tr><td colspan='2'>[[2qb3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QB3 FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_transaminase Aspartate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.1 2.6.1.1] </span>
+</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=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>
-|GENE= aspC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KST:N~6~-(5-CARBOXY-3-THIENYL)-L-LYSINE'>KST</scene></td></tr>
-|DOMAIN=
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2q7w|2q7w]], [[2qa3|2qa3]], [[2qb2|2qb2]]</div></td></tr>
-|RELATEDENTRY=[[2q7w|2Q7W]], [[2qa3|2QA3]], [[2qb2|2QB2]]
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aspC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qb3 OCA], [http://www.ebi.ac.uk/pdbsum/2qb3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2qb3 RCSB]</span>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aspartate_transaminase Aspartate transaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.1 2.6.1.1] </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=2qb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qb3 OCA], [https://pdbe.org/2qb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qb3 RCSB], [https://www.ebi.ac.uk/pdbsum/2qb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qb3 ProSAT]</span></td></tr>
+</table>
+== 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/2qb3_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=2qb3 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-2-thiophenecarboxylic acid (SADTA) via Two Mechanisms (at pH 7.5)'''
+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 2qb3" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-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.
+*[[Aspartate aminotransferase 3D structures|Aspartate aminotransferase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-QB3 is a [[Single protein]] 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=2QB3 OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Bacillus coli migula 1895]]
-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:[http://www.ncbi.nlm.nih.gov/pubmed/17713924 17713924]
 [[Category: Aspartate transaminase]]
-[[Category: Escherichia coli]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Fu, M]]
-[[Category: Fu, M.]]
+[[Category: Lepore, B]]
-[[Category: Lepore, B.]]
+[[Category: Liu, D]]
-[[Category: Liu, D.]]
+[[Category: Petsko, G A]]
-[[Category: Petsko, G A.]]
+[[Category: Pozharski, E]]
-[[Category: Pozharski, E.]]
+[[Category: Ringe, D]]
-[[Category: Ringe, D.]]
+[[Category: Silverman, R B]]
-[[Category: Silverman, R B.]]
+[[Category: Aspartate aminotransferase]]
-[[Category: aspartate aminotransferase]]
+[[Category: Mechanism-based inactivator]]
-[[Category: mechanism-based inactivator]]
+[[Category: Ph dependence]]
-[[Category: ph dependence]]
+[[Category: Plp]]
-[[Category: plp]]
+[[Category: Sadta]]
-[[Category: sadta]]
+[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:47:05 2008''