2ptr: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2ptr.jpg|left|200px]]<br /><applet load="2ptr" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2ptr, resolution 1.85&Aring;" />
-'''Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate'''<br />
-==Overview==
+==Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate==
-Adenylosuccinate lyase (ADL) catalyzes the breakdown of 5-aminoimidazole-, (N-succinylocarboxamide) ribotide (SAICAR) to, 5-aminoimidazole-4-carboxamide ribotide (AICAR) and fumarate, and of, adenylosuccinate (ADS) to adenosine monophosphate (AMP) and fumarate in, the de novo purine biosynthetic pathway. ADL belongs to the, argininosuccinate lyase (ASL)/fumarase C superfamily of enzymes. Members, of this family share several common features including: a mainly, alpha-helical, homotetrameric structure; three regions of highly conserved, amino acid residues; and a general acid-base catalytic mechanism with the, overall beta-elimination of fumarate as a product. The crystal structures, of wild-type Escherichia coli ADL (ec-ADL), and mutant-substrate, (H171A-ADS) and -product (H171N-AMP*FUM) complexes have been determined to, 2.0, 1.85, and 2.0 A resolution, respectively. The H171A-ADS and, H171N-AMP*FUM structures provide the first detailed picture of the ADL, active site, and have enabled the precise identification of substrate, binding and putative catalytic residues. Contrary to previous suggestions, the ec-ADL structures implicate S295 and H171 in base and acid catalysis, respectively. Furthermore, structural alignments of ec-ADL with other, superfamily members suggest for the first time a large conformational, movement of the flexible C3 loop (residues 287-303) in ec-ADL upon, substrate binding and catalysis, resulting in its closure over the active, site. This loop movement has been observed in other superfamily enzymes, and has been proposed to be essential for catalysis. The ADL catalytic, mechanism is re-examined in light of the results presented here.
+<StructureSection load='2ptr' size='340' side='right'caption='[[2ptr]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ptr]] is a 2 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=2PTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PTR 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]] 1.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2SA:2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC+ACID'>2SA</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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [https://pdbe.org/2ptr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [https://www.ebi.ac.uk/pdbsum/2ptr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ptr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PUR8_ECOLI PUR8_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/pt/2ptr_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=2ptr ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-PTR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with 2SA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Adenylosuccinate_lyase Adenylosuccinate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.2 4.3.2.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2PTR OCA].
+*[[Adenylosuccinate lyase 3D structures|Adenylosuccinate lyase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Substrate and Product Complexes of Escherichia coli Adenylosuccinate Lyase Provide New Insights into the Enzymatic Mechanism., Tsai M, Koo J, Yip P, Colman RF, Segall ML, Howell PL, J Mol Biol. 2007 Jul 13;370(3):541-554. Epub 2007 May 4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17531264 17531264]
-[[Category: Adenylosuccinate lyase]]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Howell, P.L.]]
+[[Category: Howell PL]]
-[[Category: Tsai, M.]]
+[[Category: Tsai M]]
-[[Category: 2SA]]
-[[Category: adenylosuccinate lyase]]
-[[Category: mutant-substrate complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:39:51 2007''