2oqx

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[[Image:2oqx.gif|left|200px]]<br /><applet load="2oqx" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2oqx, resolution 1.900&Aring;" />
 
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'''Crystal Structure of the apo form of E. coli tryptophanase at 1.9 A resolution'''<br />
 
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==Overview==
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==Crystal Structure of the apo form of E. coli tryptophanase at 1.9 A resolution==
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The crystal structure of apo tryptophanase from Escherichia coli (space, group F222, unit-cell parameters a = 118.4, b = 120.1, c = 171.2 A) was, determined at 1.9 A resolution using the molecular-replacement method and, refined to an R factor of 20.3% (R(free) = 23.2%). The structure revealed, a significant shift in the relative orientation of the domains compared, with both the holo form of Proteus vulgaris tryptophanase and with another, crystal structure of apo E. coli tryptophanase, reflecting the internal, flexibility of the molecule. Domain shifts were previously observed in, tryptophanase and in the closely related enzyme tyrosine phenol-lyase, with the holo form found in an open conformation and the apo form in, either an open or a closed conformation. Here, a wide-open conformation of, the apo form of tryptophanase is reported. A conformational change is also, observed in loop 297-303. The structure contains a hydrated Mg(2+) at the, cation-binding site and a Cl(-) ion at the subunit interface. The enzyme, activity depends on the nature of the bound cation, with smaller ions, serving as inhibitors. It is hypothesized that this effect arises from, variations of the coordination geometry of the bound cation.
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<StructureSection load='2oqx' size='340' side='right'caption='[[2oqx]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2oqx]] 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=2OQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OQX FirstGlance]. <br>
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2oqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oqx OCA], [https://pdbe.org/2oqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oqx RCSB], [https://www.ebi.ac.uk/pdbsum/2oqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oqx ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q5UES8_ECOLX Q5UES8_ECOLX]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oq/2oqx_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2oqx ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of apo tryptophanase from Escherichia coli (space group F222, unit-cell parameters a = 118.4, b = 120.1, c = 171.2 A) was determined at 1.9 A resolution using the molecular-replacement method and refined to an R factor of 20.3% (R(free) = 23.2%). The structure revealed a significant shift in the relative orientation of the domains compared with both the holo form of Proteus vulgaris tryptophanase and with another crystal structure of apo E. coli tryptophanase, reflecting the internal flexibility of the molecule. Domain shifts were previously observed in tryptophanase and in the closely related enzyme tyrosine phenol-lyase, with the holo form found in an open conformation and the apo form in either an open or a closed conformation. Here, a wide-open conformation of the apo form of tryptophanase is reported. A conformational change is also observed in loop 297-303. The structure contains a hydrated Mg(2+) at the cation-binding site and a Cl(-) ion at the subunit interface. The enzyme activity depends on the nature of the bound cation, with smaller ions serving as inhibitors. It is hypothesized that this effect arises from variations of the coordination geometry of the bound cation.
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==About this Structure==
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The structure of apo tryptophanase from Escherichia coli reveals a wide-open conformation.,Tsesin N, Kogan A, Gdalevsky GY, Himanen JP, Cohen-Luria R, Parola AH, Goldgur Y, Almog O Acta Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):969-74. Epub 2007, Aug 17. PMID:17704565<ref>PMID:17704565</ref>
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2OQX 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 <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=EPE:'>EPE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Tryptophanase Tryptophanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.1 4.1.99.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OQX OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The structure of apo tryptophanase from Escherichia coli reveals a wide-open conformation., Tsesin N, Kogan A, Gdalevsky GY, Himanen JP, Cohen-Luria R, Parola AH, Goldgur Y, Almog O, Acta Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):969-74. Epub 2007, Aug 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17704565 17704565]
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</div>
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<div class="pdbe-citations 2oqx" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Tryptophanase]]
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[[Category: Almog O]]
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[[Category: Almog, O.]]
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[[Category: Cohen-Luria R]]
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[[Category: Cohen-Luria, R.]]
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[[Category: Gdalevsky G]]
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[[Category: Gdalevsky, G.]]
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[[Category: Goldgur Y]]
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[[Category: Goldgur, Y.]]
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[[Category: Kogan A]]
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[[Category: Kogan, A.]]
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[[Category: Parola A]]
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[[Category: Parola, A.]]
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[[Category: CL]]
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[[Category: EPE]]
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[[Category: MG]]
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[[Category: lyase]]
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[[Category: pyridoxal phosphate]]
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[[Category: tryptophan catabolism]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 12:32:30 2008''
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Current revision

Crystal Structure of the apo form of E. coli tryptophanase at 1.9 A resolution

PDB ID 2oqx

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