2at1: Difference between revisions

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-[[Image:2at1.jpg|left|200px]]
-<!--
+==CRYSTAL STRUCTURES OF PHOSPHONOACETAMIDE LIGATED T AND PHOSPHONOACETAMIDE AND MALONATE LIGATED R STATES OF ASPARTATE CARBAMOYLTRANSFERASE AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL PH==
-The line below this paragraph, containing "STRUCTURE_2at1", creates the "Structure Box" on the page.
+<StructureSection load='2at1' size='340' side='right'caption='[[2at1]], [[Resolution|resolution]] 2.80&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'>[[2at1]] is a 4 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=2AT1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AT1 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]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PCT:PHOSPHONOACETAMIDE'>PCT</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2at1|  PDB=2at1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2at1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2at1 OCA], [https://pdbe.org/2at1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2at1 RCSB], [https://www.ebi.ac.uk/pdbsum/2at1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2at1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYRB_ECOLI PYRB_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/at/2at1_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=2at1 ConSurf].
+<div style="clear:both"></div>
-'''CRYSTAL STRUCTURES OF PHOSPHONOACETAMIDE LIGATED T AND PHOSPHONOACETAMIDE AND MALONATE LIGATED R STATES OF ASPARTATE CARBAMOYLTRANSFERASE AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL PH'''
+==See Also==
+*[[Aspartate carbamoyltransferase 3D structures|Aspartate carbamoyltransferase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The T----R transition of the cooperative enzyme aspartate carbamoyltransferase occurs at pH 7 in single crystals without visibly cracking many of the crystals and leaving those uncracked suitable for single-crystal X-ray analysis. To promote the T----R transition, we employ the competitive inhibitors of carbamoyl phosphate and aspartate, which are phosphonoacetamide (PAM) and malonate, respectively. In response to PAM binding to the T-state crystals, residues Thr 53-Thr 55 and Pro 266-Pro 268 move to their R-state positions to bind to the phosphonate and amino group of PAM. These changes induce a conformation that can bind tightly the aspartate analogue malonate, which thereby effects the allosteric transition. We prove this by showing that PAM-ligated T-state crystals (Tpam), space group P321 (a = 122.2 A, c = 142.2 A), when transferred to a solution containing 20 mM PAM and 8 mM malonate at pH 7, isomerize to R-state crystals (Rpam,mal,soak), space group also P321 (a = 122.2 A, c = 156.4 A). The R-state structure in which the T----R transition occurs within the crystal at pH 7 compares very well (rms = 0.19 A for all atoms) with an R-state structure determined at pH 7 in which the crystals were initially grown in a solution of PAM and malonate at pH 5.9 and subsequently transferred to a buffer containing the ligands at pH 7 (Rpam,mal,crys). In fact, both of the PAM and malonate ligated R-state structures are very similar to both the carbamoyl phosphate and succinate or the N-(phosphonoacetyl)-L-aspartate ligated structures, even though the R-state structures reported here were determined at pH 7. Crystallographic residuals refined to 0.16-0.18 at 2.8-A resolution for the three structures.
-==About this Structure==
-AT1 is a [[Protein complex]] structure of sequences 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=2AT1 OCA].
-==Reference==
-Crystal structures of phosphonoacetamide ligated T and phosphonoacetamide and malonate ligated R states of aspartate carbamoyltransferase at 2.8-A resolution and neutral pH., Gouaux JE, Lipscomb WN, Biochemistry. 1990 Jan 16;29(2):389-402. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2405902 2405902]
-[[Category: Aspartate carbamoyltransferase]]
 [[Category: Escherichia coli]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Gouaux, J E.]]
+[[Category: Gouaux JE]]
-[[Category: Lipscomb, W N.]]
+[[Category: Lipscomb WN]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 19:26:46 2008''