2q7w: Difference between revisions

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-[[Image:2q7w.jpg|left|200px]]
- {{Structure
+==Structural Studies Reveals the Inactivation of E. coli L-aspartate aminotransferase (S)-4,5-amino-dihydro-2-thiophenecarboxylic acid (SADTA) via two mechanisms at pH 6.0==
-|PDB= 2q7w |SIZE=350|CAPTION= <scene name='initialview01'>2q7w</scene>, resolution 1.40&Aring;
+<StructureSection load='2q7w' size='340' side='right'caption='[[2q7w]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=PMP:4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE'>PMP</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
+<table><tr><td colspan='2'>[[2q7w]] 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=2Q7W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q7W FirstGlance]. <br>
-|ACTIVITY= [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]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
-|GENE= aspC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+<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>
-}}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q7w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q7w OCA], [https://pdbe.org/2q7w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q7w RCSB], [https://www.ebi.ac.uk/pdbsum/2q7w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q7w 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/q7/2q7w_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=2q7w 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 Reveals the Inactivation of E. coli L-aspartate aminotransferase (S)-4,5-amino-dihydro-2-thiophenecarboxylic acid (SADTA) via two mechanisms at pH 6.0'''
+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 2q7w" 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/>
-Q7W 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=2Q7W OCA].
+__TOC__
+</StructureSection>
-==Reference==
-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: Single protein]]
+[[Category: Large Structures]]
-[[Category: Fu, M.]]
+[[Category: Fu M]]
-[[Category: Lepore, B.]]
+[[Category: Lepore B]]
-[[Category: Liu, D.]]
+[[Category: Liu D]]
-[[Category: Petsko, G A.]]
+[[Category: Petsko GA]]
-[[Category: Pozharski, E.]]
+[[Category: Pozharski E]]
-[[Category: Ringe, D.]]
+[[Category: Ringe D]]
-[[Category: Silverman, R B.]]
+[[Category: Silverman RB]]
-[[Category: GOL]]
-[[Category: PMP]]
-[[Category: PSZ]]
-[[Category: SO4]]
-[[Category: mechanism-based inhibitor]]
-[[Category: ph dependence]]
-[[Category: plp]]
-[[Category: sadta]]
-[[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:22:55 2008''