2qb3

From Proteopedia

(Difference between revisions)

Current revision

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)

Structural highlights

2qb3 is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.45Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AAT_ECOLI

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Liu D, Pozharski E, Lepore BW, Fu M, Silverman RB, Petsko GA, Ringe D. Inactivation of Escherichia coli L-aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-thiophenecarboxylic acid reveals "a tale of two mechanisms". Biochemistry. 2007 Sep 18;46(37):10517-27. Epub 2007 Aug 22. PMID:17713924 doi:http://dx.doi.org/10.1021/bi700663n

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2qb3"

@@ Line 3: / Line 3: @@
 <StructureSection load='2qb3' size='340' side='right'caption='[[2qb3]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<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>
+<table><tr><td colspan='2'>[[2qb3]] 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=2QB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QB3 FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
-<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>
+<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='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>
-<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>
-<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>
+== Function ==
+[https://www.uniprot.org/uniprot/AAT_ECOLI AAT_ECOLI]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 16: / Line 15: @@
   <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>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Aspartate transaminase]]
 [[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: Aspartate aminotransferase]]
-[[Category: Mechanism-based inactivator]]
-[[Category: Ph dependence]]
-[[Category: Plp]]
-[[Category: Sadta]]
-[[Category: Transferase]]

2qb3

From Proteopedia

Current revision

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)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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