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2o0t

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[[Image:2o0t.gif|left|200px]]
 
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{{Structure
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==The three dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation==
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|PDB= 2o0t |SIZE=350|CAPTION= <scene name='initialview01'>2o0t</scene>, resolution 2.33&Aring;
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<StructureSection load='2o0t' size='340' side='right'caption='[[2o0t]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[2o0t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O0T FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </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]] 2.33&#8491;</td></tr>
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|GENE= lysA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=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=2o0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o0t OCA], [https://pdbe.org/2o0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o0t RCSB], [https://www.ebi.ac.uk/pdbsum/2o0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o0t ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1hkv|1HKV]], [[1hkw|1HKW]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2o0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o0t OCA], [http://www.ebi.ac.uk/pdbsum/2o0t PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2o0t RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/DCDA_MYCTU DCDA_MYCTU] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine (Probable). Is essential for the viability of M.tuberculosis in the host.<ref>PMID:12637582</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/o0/2o0t_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=2o0t 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 three-dimensional structure of the enzyme diaminopimelate decarboxylase from Mycobacterium tuberculosis has been determined in a new crystal form and refined to a resolution of 2.33 A. The monoclinic crystals contain one tetramer exhibiting D(2)-symmetry in the asymmetric unit. The tetramer exhibits a donut-like structure with a hollow interior. All four active sites are accessible only from the interior of the tetrameric assembly. Small-angle X-ray scattering indicates that in solution the predominant oligomeric species of the protein is a dimer, but also that higher oligomers exist at higher protein concentrations. The observed scattering data are best explained by assuming a dimer-tetramer equilibrium with about 7% tetramers present in solution. Consequently, at the elevated protein concentrations in the crowded environment inside the cell the observed tetramer may constitute the biologically relevant functional unit of the enzyme.
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'''The three dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation'''
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The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation.,Weyand S, Kefala G, Svergun DI, Weiss MS J Struct Funct Genomics. 2009 Jun 19. PMID:19543810<ref>PMID:19543810</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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==Overview==
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</div>
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Diaminopimelate decarboxylase from Mycobacterium tuberculosis (LysA, DAPDC, Rv1293) has been cloned and heterologously expressed in Escherichia coli, purified using standard chromatographic techniques and crystallized. Preliminary diffraction data analysis suggests the presence of a homotetramer in the asymmetric unit.
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<div class="pdbe-citations 2o0t" style="background-color:#fffaf0;"></div>
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== References ==
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==About this Structure==
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<references/>
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2O0T is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O0T OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of LysA (Rv1293) from Mycobacterium tuberculosis., Kefala G, Perry LJ, Weiss MS, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Aug 1;61(Pt, 8):782-4. Epub 2005 Jul 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16511157 16511157]
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[[Category: Mycobacterium tuberculosis H37Rv]]
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[[Category: Diaminopimelate decarboxylase]]
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[[Category: Kefala G]]
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[[Category: Mycobacterium tuberculosis]]
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[[Category: Weiss MS]]
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[[Category: Single protein]]
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[[Category: Weyand S]]
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[[Category: Kefala, G.]]
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[[Category: TBSGC, TB Structural Genomics Consortium.]]
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[[Category: Weiss, M S.]]
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[[Category: Weyand, S.]]
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[[Category: decarboxylase]]
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[[Category: lysine biosynthesis]]
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[[Category: plp binding enzyme]]
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[[Category: structural genomic]]
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[[Category: tb structural genomics consortium]]
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[[Category: tbsgc]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:11:04 2008''
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Current revision

The three dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation

PDB ID 2o0t

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