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2dh5
From Proteopedia
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| - | [[Image:2dh5.gif|left|200px]]<br /><applet load="2dh5" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2dh5, resolution 2.90Å" /> | ||
| - | '''Crystal structure of E. coli Holo-TrpB'''<br /> | ||
| - | == | + | ==Crystal structure of E. coli Holo-TrpB== |
| - | + | <StructureSection load='2dh5' size='340' side='right'caption='[[2dh5]], [[Resolution|resolution]] 2.90Å' scene=''> | |
| - | [ | + | == Structural highlights == |
| - | + | <table><tr><td colspan='2'>[[2dh5]] 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=2DH5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DH5 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]] 2.9Å</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=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=2dh5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dh5 OCA], [https://pdbe.org/2dh5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dh5 RCSB], [https://www.ebi.ac.uk/pdbsum/2dh5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dh5 ProSAT], [https://www.topsan.org/Proteins/RSGI/2dh5 TOPSAN]</span></td></tr> |
| - | + | </table> | |
| - | [ | + | == Function == |
| - | [ | + | [https://www.uniprot.org/uniprot/TRPB_ECOLI TRPB_ECOLI] The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine.[HAMAP-Rule:MF_00133] |
| - | [ | + | == 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/dh/2dh5_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=2dh5 ConSurf]. |
| - | + | <div style="clear:both"></div> | |
| - | + | <div style="background-color:#fffaf0;"> | |
| - | + | == Publication Abstract from PubMed == | |
| - | + | To understand the basis for the lower activity of the tryptophan synthase beta(2) subunit in comparison to the alpha(2)beta(2) complex, we determined the crystal structures of apo-beta(2) and holo-beta(2) from Escherichia coli at 3.0 and 2.9 A resolutions, respectively. To our knowledge, this is the first report of both beta(2) subunit structures with and without pyridoxal-5'-phosphate. The apo-type molecule retained a dimeric form in solution, as in the case of the holo-beta(2) subunit. The subunit structures of both the apo-beta(2) and the holo-beta(2) forms consisted of two domains, namely the N domain and the C domain. Although there were significant structural differences between the apo- and holo-structures, they could be easily superimposed with a 22 degrees rigid body rotation of the C domain. The pyridoxal-5'-phosphate-bound holo-form had multiple interactions between the two domains and a long loop (residues 260-310), which were missing in the apo-form. Comparison of the structures of holo-Ecbeta(2) and Stbeta(2) in the alpha(2)beta(2) complex from Salmonella typhimurium (Stalpha(2)beta(2)) identified the cause of the lower enzymatic activity of holo-Ecbeta(2) in comparison with Stalpha(2)beta(2). The substrate (indole) gate residues, Tyr279 and Phe280, block entry of the substrate into the beta(2) subunit, although the indole can directly access the active site as a result of a wider cleft between the N and C domains in the holo-Ecbeta(2) subunit. In addition, the structure around betaAsp305 of the holo-Ecbeta(2) subunit was similar to the open state of Stalpha(2)beta(2) with low activity, resulting in lower activity of holo-Ecbeta(2). | |
| - | ' | + | Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding.,Nishio K, Ogasahara K, Morimoto Y, Tsukihara T, Lee SJ, Yutani K FEBS J. 2010 May;277(9):2157-70. Epub 2010 Mar 27. PMID:20370823<ref>PMID:20370823</ref> |
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 2dh5" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Tryptophan synthase 3D structures|Tryptophan synthase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Escherichia coli]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Morimoto Y]] | ||
| + | [[Category: Nishio K]] | ||
| + | [[Category: Ogasahara K]] | ||
| + | [[Category: Tsukihara T]] | ||
| + | [[Category: Yutani K]] | ||
Current revision
Crystal structure of E. coli Holo-TrpB
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