1amq: Difference between revisions

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-[[Image:1amq.jpg|left|200px]]
-<!--
+==X-RAY CRYSTALLOGRAPHIC STUDY OF PYRIDOXAMINE 5'-PHOSPHATE-TYPE ASPARTATE AMINOTRANSFERASES FROM ESCHERICHIA COLI IN THREE FORMS==
-The line below this paragraph, containing "STRUCTURE_1amq", creates the "Structure Box" on the page.
+<StructureSection load='1amq' size='340' side='right'caption='[[1amq]], [[Resolution|resolution]] 2.20&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'>[[1amq]] 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=1AMQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AMQ 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]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene></td></tr>
-{{STRUCTURE_1amq|  PDB=1amq  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1amq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1amq OCA], [https://pdbe.org/1amq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1amq RCSB], [https://www.ebi.ac.uk/pdbsum/1amq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1amq 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/am/1amq_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=1amq ConSurf].
+<div style="clear:both"></div>
-'''X-RAY CRYSTALLOGRAPHIC STUDY OF PYRIDOXAMINE 5'-PHOSPHATE-TYPE ASPARTATE AMINOTRANSFERASES FROM ESCHERICHIA COLI IN THREE FORMS'''
+==See Also==
+*[[Aspartate aminotransferase 3D structures|Aspartate aminotransferase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The three-dimensional structures of pyridoxamine 5'-phosphate-type aspartate aminotransferase from Escherichia coli and its complexes with maleate and glutarate have been determined by X-ray crystallography at 2.2, 2.1, and 2.7 A resolution, respectively. The enzyme is a dimeric form comprising two identical subunits, each of which is divided into one large and one small domain. The complex with maleate showed that substrate (or inhibitor) binding induced a large conformational change from the "open" to the "closed" form, resulting in closure of the active site by the small domain movement, as was observed in the pyridoxal 5'-phosphate-type enzyme. In the open form, three hydrophobic residues (hydrophobic plug) at the entrance of the active site are exposed to solvent. Maleate binding make the active site more hydrophobic by charge compensation and release of water molecules, facilitating the movement of the hydrophobic plug into the active site pocket to induce a large conformational change in the enzyme. Maleate is fixed rigidly in the active site pocket by extensive salt bridges and a hydrogen bonding network, guaranteeing the stereo-specificity of the catalysis and giving a Michaelis complex model. Contrary to our expectation, the glutarate complex was in the open form, suggesting that the equilibrium between the open and closed forms lies far toward the open form in solution. The water molecules located in the active site pocket were almost completely conserved between Escherichia coli and chicken mitochondrial aspartate aminotransferase with the same type of cofactor and the same conformation.
-==About this Structure==
-AMQ 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=1AMQ OCA].
-==Reference==
-X-ray crystallographic study of pyridoxamine 5'-phosphate-type aspartate aminotransferases from Escherichia coli in three forms., Miyahara I, Hirotsu K, Hayashi H, Kagamiyama H, J Biochem. 1994 Nov;116(5):1001-12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7896726 7896726]
-[[Category: Aspartate transaminase]]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Hayashi, H.]]
+[[Category: Hayashi H]]
-[[Category: Hirotsu, K.]]
+[[Category: Hirotsu K]]
-[[Category: Kagamiyama, H.]]
+[[Category: Kagamiyama H]]
-[[Category: Miyahara, I.]]
+[[Category: Miyahara I]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 10:27:34 2008''