2gn2

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[[Image:2gn2.png|left|200px]]
 
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==Crystal structure of tetrameric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium in complex with CMP at 2.5A resolution (Hexagonal form)==
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The line below this paragraph, containing "STRUCTURE_2gn2", creates the "Structure Box" on the page.
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<StructureSection load='2gn2' size='340' side='right'caption='[[2gn2]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2gn2]] is a 1 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=2GN2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GN2 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.5&#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=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_2gn2| PDB=2gn2 | SCENE= }}
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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=2gn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gn2 OCA], [https://pdbe.org/2gn2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gn2 RCSB], [https://www.ebi.ac.uk/pdbsum/2gn2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gn2 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TDCB_SALTY TDCB_SALTY] Catalyzes the anaerobic formation of alpha-ketobutyrate and ammonia from threonine in a two-step reaction. The first step involved a dehydration of threonine and a production of enamine intermediates (aminocrotonate), which tautomerizes to its imine form (iminobutyrate). Both intermediates are unstable and short-lived. The second step is the nonenzymatic hydrolysis of the enamine/imine intermediates to form 2-ketobutyrate and free ammonia. In the low water environment of the cell, the second step is accelerated by RidA. TdcB also dehydrates serine to yield pyruvate via analogous enamine/imine intermediates.<ref>PMID:17046821</ref>
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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/gn/2gn2_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=2gn2 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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Two different pyridoxal 5'-phosphate-containing l-threonine deaminases (EC 4.3.1.19), biosynthetic and biodegradative, which catalyze the deamination of l-threonine to alpha-ketobutyrate, are present in Escherichia coli and Salmonella typhimurium. Biodegradative threonine deaminase (TdcB) catalyzes the first reaction in the anaerobic breakdown of l-threonine to propionate. TdcB, unlike the biosynthetic threonine deaminase, is insensitive to l-isoleucine and is activated by AMP. In the present study, TdcB from S. typhimurium was cloned and overexpressed in E. coli. In the presence of AMP or CMP, the recombinant enzyme was converted to the tetrameric form accompanied by significant enzyme activation. To provide insights into ligand-mediated oligomerization and enzyme activation, crystal structures of S. typhimurium TdcB and its complex with CMP were determined. In the native structure, TdcB is in a dimeric form, whereas in the TdcB.CMP complex, it exists in a tetrameric form with 222 symmetry and appears as a dimer of dimers. Tetrameric TdcB binds to four molecules of CMP, two at each of the dimer interfaces. Comparison of the dimer structure in the ligand (CMP)-free and -bound forms suggests that the changes induced by ligand binding at the dimer interface are essential for tetramerization. The differences observed in the tertiary and quaternary structures of TdcB in the absence and presence of CMP appear to account for enzyme activation and increased binding affinity for l-threonine. Comparison of TdcB with related pyridoxal 5'-phosphate-dependent enzymes points to structural and mechanistic similarities.
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===Crystal structure of tetrameric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium in complex with CMP at 2.5A resolution (Hexagonal form)===
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Crystal structures of Salmonella typhimurium biodegradative threonine deaminase and its complex with CMP provide structural insights into ligand-induced oligomerization and enzyme activation.,Simanshu DK, Savithri HS, Murthy MR J Biol Chem. 2006 Dec 22;281(51):39630-41. Epub 2006 Oct 17. PMID:17046821<ref>PMID:17046821</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 2gn2" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17046821}}, adds the Publication Abstract to the page
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*[[Deaminase 3D structures|Deaminase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 17046821 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17046821}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[2gn2]] is a 1 chain structure with sequence from [http://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=2GN2 OCA].
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[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
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[[Category: Murthy MRN]]
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==Reference==
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[[Category: Savithri HS]]
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<ref group="xtra">PMID:17046821</ref><ref group="xtra">PMID:16511321</ref><references group="xtra"/>
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[[Category: Simanshu DK]]
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[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
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[[Category: Threonine ammonia-lyase]]
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[[Category: Murthy, M R.N.]]
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[[Category: Savithri, H S.]]
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[[Category: Simanshu, D K.]]
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[[Category: Biodegradative threonine deaminase]]
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[[Category: Cmp]]
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[[Category: L-threonine metabolism]]
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[[Category: Lyase]]
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[[Category: Plp]]
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[[Category: Tdcb]]
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[[Category: Threonine dehydratase]]
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Current revision

Crystal structure of tetrameric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium in complex with CMP at 2.5A resolution (Hexagonal form)

PDB ID 2gn2

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