2dh6

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[[Image:2dh6.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of E. coli Apo-TrpB==
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|PDB= 2dh6 |SIZE=350|CAPTION= <scene name='initialview01'>2dh6</scene>, resolution 3.00&Aring;
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<StructureSection load='2dh6' size='340' side='right'caption='[[2dh6]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=X:2&#39;-DEOXY-N7-(8,9-DIHYDRO-9-HYDROXY-10-DEHYDROXY-AFLATOXIN)GUANOSINE+MONOPHOSPHATE'>X</scene>
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<table><tr><td colspan='2'>[[2dh6]] 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=2DH6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DH6 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </span>
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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]] 3&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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|DOMAIN=
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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=2dh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dh6 OCA], [https://pdbe.org/2dh6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dh6 RCSB], [https://www.ebi.ac.uk/pdbsum/2dh6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dh6 ProSAT], [https://www.topsan.org/Proteins/RSGI/2dh6 TOPSAN]</span></td></tr>
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|RELATEDENTRY=[[2dh5|2dh5]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dh6 OCA], [http://www.ebi.ac.uk/pdbsum/2dh6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dh6 RCSB]</span>
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== Function ==
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}}
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[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]
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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/dh/2dh6_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2dh6 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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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).
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'''Crystal structure of E. coli Apo-TrpB'''
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2dh6" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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2DH6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DH6 OCA].
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*[[Tryptophan synthase 3D structures|Tryptophan synthase 3D structures]]
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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: Tryptophan synthase]]
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[[Category: Morimoto Y]]
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[[Category: Morimoto, Y.]]
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[[Category: Nishio K]]
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[[Category: Nishio, K.]]
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[[Category: Ogasahara K]]
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[[Category: Ogasahara, K.]]
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[[Category: Tsukihara T]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Yasuoka N]]
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[[Category: Tsukihara, T.]]
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[[Category: Yutani K]]
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[[Category: Yasuoka, N.]]
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[[Category: Yutani, K.]]
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[[Category: beta-chain]]
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[[Category: lyase]]
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[[Category: national project on protein structural and functional analyse]]
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[[Category: nppsfa]]
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[[Category: plp]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rsgi]]
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[[Category: structural genomic]]
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[[Category: tryptophan synthase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:34:37 2008''
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Current revision

Crystal structure of E. coli Apo-TrpB

PDB ID 2dh6

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