2a88: Difference between revisions

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-[[Image:2a88.gif|left|200px]]<br /><applet load="2a88" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2a88, resolution 1.700&Aring;" />
-'''Crystal structure of A Pantothenate synthetase, apo enzyme in C2 space group'''<br />
-==Overview==
+==Crystal structure of A Pantothenate synthetase, apo enzyme in C2 space group==
-Pantothenate synthetase (PS) from Mycobacterium tuberculosis represents a, potential target for antituberculosis drugs. PS catalyzes the, ATP-dependent condensation of pantoate and beta-alanine to form, pantothenate. Previously, we determined the crystal structure of PS from, M. tuberculosis and its complexes with AMPCPP, pantoate, and pantoyl, adenylate. Here, we describe the crystal structure of this enzyme, complexed with AMP and its last substrate, beta-alanine, and show that the, phosphate group of AMP serves as an anchor for the binding of, beta-alanine. This structure confirms that binding of beta-alanine in the, active site cavity can occur only after formation of the pantoyl adenylate, intermediate. A new crystal form was also obtained; it displays the, flexible wall of the active site cavity in a conformation incapable of, binding pantoate. Soaking of this crystal form with ATP and pantoate gives, a fully occupied complex of PS with ATP. Crystal structures of these, complexes with substrates, the reaction intermediate, and the reaction, product AMP provide a step-by-step view of the PS-catalyzed reaction. A, detailed reaction mechanism and its implications for inhibitor design are, discussed.
+<StructureSection load='2a88' size='340' side='right'caption='[[2a88]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2a88]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A88 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</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=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=2a88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a88 OCA], [https://pdbe.org/2a88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a88 RCSB], [https://www.ebi.ac.uk/pdbsum/2a88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a88 ProSAT], [https://www.topsan.org/Proteins/TBSGC/2a88 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PANC_MYCTU PANC_MYCTU] Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate.<ref>PMID:11669627</ref>
+== 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/a8/2a88_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=2a88 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pantothenate synthetase (PS) from Mycobacterium tuberculosis represents a potential target for antituberculosis drugs. PS catalyzes the ATP-dependent condensation of pantoate and beta-alanine to form pantothenate. Previously, we determined the crystal structure of PS from M. tuberculosis and its complexes with AMPCPP, pantoate, and pantoyl adenylate. Here, we describe the crystal structure of this enzyme complexed with AMP and its last substrate, beta-alanine, and show that the phosphate group of AMP serves as an anchor for the binding of beta-alanine. This structure confirms that binding of beta-alanine in the active site cavity can occur only after formation of the pantoyl adenylate intermediate. A new crystal form was also obtained; it displays the flexible wall of the active site cavity in a conformation incapable of binding pantoate. Soaking of this crystal form with ATP and pantoate gives a fully occupied complex of PS with ATP. Crystal structures of these complexes with substrates, the reaction intermediate, and the reaction product AMP provide a step-by-step view of the PS-catalyzed reaction. A detailed reaction mechanism and its implications for inhibitor design are discussed.
-==About this Structure==
+Crystal structure of the pantothenate synthetase from Mycobacterium tuberculosis, snapshots of the enzyme in action.,Wang S, Eisenberg D Biochemistry. 2006 Feb 14;45(6):1554-61. PMID:16460002<ref>PMID:16460002</ref>
-A88 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with SO4 and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Pantoate--beta-alanine_ligase Pantoate--beta-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.1 6.3.2.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2A88 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of the pantothenate synthetase from Mycobacterium tuberculosis, snapshots of the enzyme in action., Wang S, Eisenberg D, Biochemistry. 2006 Feb 14;45(6):1554-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16460002 16460002]
+</div>
+<div class="pdbe-citations 2a88" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Pantothenate synthetase|Pantothenate synthetase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mycobacterium tuberculosis]]
-[[Category: Pantoate--beta-alanine ligase]]
+[[Category: Eisenberg D]]
-[[Category: Single protein]]
+[[Category: Wang S]]
-[[Category: Eisenberg, D.]]
-[[Category: TBSGC, TB.Structural.Genomics.Consortium.]]
-[[Category: Wang, S.]]
-[[Category: GOL]]
-[[Category: SO4]]
-[[Category: dimer]]
-[[Category: protein structure initiative]]
-[[Category: psi]]
-[[Category: rossmann fold]]
-[[Category: structural genomics]]
-[[Category: tb structural genomics consortium]]
-[[Category: tbsgc]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:58:53 2007''