2j9x: Difference between revisions

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-[[Image:2j9x.gif|left|200px]]
-<!--
+==Tryptophan Synthase in complex with GP, alpha-D,L-glycerol-phosphate, Cs, pH6.5 - alpha aminoacrylate form - (GP)E(A-A)==
-The line below this paragraph, containing "STRUCTURE_2j9x", creates the "Structure Box" on the page.
+<StructureSection load='2j9x' size='340' side='right'caption='[[2j9x]], [[Resolution|resolution]] 1.90&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'>[[2j9x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J9X 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene>, <scene name='pdbligand=P1T:2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC+ACID'>P1T</scene></td></tr>
-{{STRUCTURE_2j9x|  PDB=2j9x  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2j9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j9x OCA], [https://pdbe.org/2j9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j9x RCSB], [https://www.ebi.ac.uk/pdbsum/2j9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j9x ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRPA_SALTY TRPA_SALTY] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate.
+== 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/j9/2j9x_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=2j9x ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In the tryptophan synthase bienzyme complex, indole produced by substrate cleavage at the alpha-site is channeled to the beta-site via a 25 A long tunnel. Within the beta-site, indole and l-Ser react with pyridoxal 5'-phosphate in a two-stage reaction to give l-Trp. In stage I, l-Ser forms an external aldimine, E(Aex1), which converts to the alpha-aminoacrylate aldimine, E(A-A). Formation of E(A-A) at the beta-site activates the alpha-site &gt;30-fold. In stage II, indole reacts with E(A-A) to give l-Trp. The binding of alpha-site ligands (ASLs) exerts strong allosteric effects on the reaction of substrates at the beta-site: the distribution of intermediates formed in stage I is shifted in favor of E(A-A), and the binding of ASLs triggers a conformational change in the beta-site to a state with an increased affinity for l-Ser. Here, we compare the behavior of new ASLs as allosteric effectors of stage I with the behavior of the natural product, d-glyceraldehyde 3-phosphate. Rapid kinetics and kinetic isotope effects show these ASLs bind with affinities ranging from micro- to millimolar, and the rate-determining step for conversion of E(Aex1) to E(A-A) is increased by 8-10-fold. To derive a structure-based mechanism for stage I, X-ray structures of both the E(Aex1) and E(A-A) states complexed with the different ASLs were determined and compared with structures of the ASL complexes with the internal aldimine [Ngo, H., Harris, R., Kimmich, N., Casino, P., Niks, D., Blumenstein, L., Barends, T. R., Kulik, V., Weyand, M., Schlichting, I., and Dunn, M. F. (2007) Biochemistry 46, 7713-7727].
-'''TRYPTOPHAN SYNTHASE IN COMPLEX WITH GP, ALPHA-D,L-GLYCEROL-PHOSPHATE, CS, PH6.5- ALPHA AMINOACRYLATE FORM- (GP)E(A-A)'''
+Allosteric regulation of substrate channeling in tryptophan synthase: modulation of the L-serine reaction in stage I of the beta-reaction by alpha-site ligands.,Ngo H, Kimmich N, Harris R, Niks D, Blumenstein L, Kulik V, Barends TR, Schlichting I, Dunn MF Biochemistry. 2007 Jul 3;46(26):7740-53. Epub 2007 Jun 9. PMID:17559232<ref>PMID:17559232</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2j9x" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-J9X is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J9X OCA].
+*[[Tryptophan synthase 3D structures|Tryptophan synthase 3D structures]]
-[[Category: Protein complex]]
+== References ==
-[[Category: Salmonella typhimurium]]
+<references/>
-[[Category: Tryptophan synthase]]
+__TOC__
-[[Category: Barends, T R.]]
+</StructureSection>
-[[Category: Blumenstein, L.]]
+[[Category: Large Structures]]
-[[Category: Dunn, M F.]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-[[Category: Harris, R.]]
+[[Category: Barends TR]]
-[[Category: Kimmich, N.]]
+[[Category: Blumenstein L]]
-[[Category: Kulik, V.]]
+[[Category: Dunn MF]]
-[[Category: Ngo, H.]]
+[[Category: Harris R]]
-[[Category: Niks, D.]]
+[[Category: Kimmich N]]
-[[Category: Schlichting, I.]]
+[[Category: Kulik V]]
-[[Category: Allosteric enzyme]]
+[[Category: Ngo H]]
-[[Category: Amino-acid biosynthesis]]
+[[Category: Niks D]]
-[[Category: Aromatic amino acid biosynthesis]]
+[[Category: Schlichting I]]
-[[Category: Crbon- oxygen lyase]]
-[[Category: Lyase]]
-[[Category: Pyridoxal phosphate]]
-[[Category: Synthase]]
-[[Category: Tryptophan biosynthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 08:34:31 2008''