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1kgq

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[[Image:1kgq.gif|left|200px]]
 
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{{Structure
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==Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with L-2-aminopimelate and Succinamide-CoA==
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|PDB= 1kgq |SIZE=350|CAPTION= <scene name='initialview01'>1kgq</scene>, resolution 2.0&Aring;
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<StructureSection load='1kgq' size='340' side='right'caption='[[1kgq]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NPI:2-AMINOPIMELIC+ACID'>NPI</scene> and <scene name='pdbligand=SCO:SUCCINAMIDE-COA'>SCO</scene>
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<table><tr><td colspan='2'>[[1kgq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_variant_bovis Mycobacterium tuberculosis variant bovis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KGQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KGQ FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117]
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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&#8491;</td></tr>
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|GENE= dapD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1765 Mycobacterium bovis])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NPI:(2S)-2-AMINOHEPTANEDIOIC+ACID'>NPI</scene>, <scene name='pdbligand=SCO:SUCCINAMIDE-COA'>SCO</scene></td></tr>
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}}
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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=1kgq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kgq OCA], [https://pdbe.org/1kgq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kgq RCSB], [https://www.ebi.ac.uk/pdbsum/1kgq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kgq ProSAT]</span></td></tr>
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</table>
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'''Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with L-2-aminopimelate and Succinamide-CoA'''
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== Function ==
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[https://www.uniprot.org/uniprot/DAPD_UNKP DAPD_UNKP]
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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Tetrahydrodipicolinate N-succinyltransferase (DapD) catalyzes the succinyl-CoA-dependent acylation of L-2-amino-6-oxopimelate to 2-N-succinyl-6-oxopimelate as part of the succinylase branch of the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants. This pathway provides meso-diaminopimelate as a building block for cell wall peptidoglycan in most bacteria, and is regarded as a target pathway for antibacterial agents. We have solved the X-ray crystal structures of DapD in ternary complexes with pimelate/succinyl-CoA and L-2-aminopimelate with the nonreactive cofactor analog, succinamide-CoA. These structures define the binding conformation of the cofactor succinyl group and its interactions with the enzyme and place its thioester carbonyl carbon in close proximity to the nucleophilic 2-amino group of the acceptor, in support of a direct attack ternary complex mechanism. The acyl group specificity differences between homologous tetrahydrodipicolinate N-acetyl- and N-succinyltransferases can be rationalized with reference to at least three amino acids that interact with or give accessible active site volume to the cofactor succinyl group. These residues account at least in part for the substrate specificity that commits metabolic intermediates to either the succinylase or acetylase branches of the meso-diaminopimelate/lysine biosynthetic pathway.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kg/1kgq_consurf.spt"</scriptWhenChecked>
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1KGQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_bovis Mycobacterium bovis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KGQ OCA].
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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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==Reference==
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</jmolCheckbox>
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Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase., Beaman TW, Vogel KW, Drueckhammer DG, Blanchard JS, Roderick SL, Protein Sci. 2002 Apr;11(4):974-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11910040 11910040]
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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=1kgq ConSurf].
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[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]
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<div style="clear:both"></div>
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[[Category: Mycobacterium bovis]]
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__TOC__
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[[Category: Single protein]]
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</StructureSection>
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[[Category: Beaman, T W.]]
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[[Category: Large Structures]]
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[[Category: Blanchard, J S.]]
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[[Category: Mycobacterium tuberculosis variant bovis]]
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[[Category: Drueckhammer, D G.]]
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[[Category: Beaman TW]]
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[[Category: Roderick, S L.]]
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[[Category: Blanchard JS]]
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[[Category: Vogel, K W.]]
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[[Category: Drueckhammer DG]]
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[[Category: NPI]]
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[[Category: Roderick SL]]
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[[Category: SCO]]
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[[Category: Vogel KW]]
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[[Category: left-handed parallel beta helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:17:14 2008''
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Current revision

Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with L-2-aminopimelate and Succinamide-CoA

PDB ID 1kgq

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