1kgt: Difference between revisions

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-[[Image:1kgt.gif|left|200px]]<br /><applet load="1kgt" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1kgt, resolution 2.3&Aring;" />
-'''Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA'''<br />
-==Overview==
+==Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA==
-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.
+<StructureSection load='1kgt' size='340' side='right'caption='[[1kgt]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1kgt]] 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=1KGT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KGT FirstGlance]. <br>
-KGT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_bovis Mycobacterium bovis] with <scene name='pdbligand=PML:'>PML</scene> and <scene name='pdbligand=SCA:'>SCA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KGT OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PML:PIMELIC+ACID'>PML</scene>, <scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kgt OCA], [https://pdbe.org/1kgt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kgt RCSB], [https://www.ebi.ac.uk/pdbsum/1kgt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kgt ProSAT]</span></td></tr>
-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://ispc.weizmann.ac.il//pmbin/getpm?pmid=11910040 11910040]
+</table>
-[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]
+== Function ==
-[[Category: Mycobacterium bovis]]
+[https://www.uniprot.org/uniprot/DAPD_UNKP DAPD_UNKP]
-[[Category: Single protein]]
+== Evolutionary Conservation ==
-[[Category: Beaman, T W.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Blanchard, J S.]]
+Check<jmol>
-[[Category: Drueckhammer, D G.]]
+  <jmolCheckbox>
-[[Category: Roderick, S L.]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kg/1kgt_consurf.spt"</scriptWhenChecked>
-[[Category: Vogel, K W.]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: PML]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: SCA]]
+  </jmolCheckbox>
-[[Category: left-handed parallel beta helix]]
+</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=1kgt ConSurf].
+<div style="clear:both"></div>
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:34:01 2008''
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Mycobacterium tuberculosis variant bovis]]
+[[Category: Beaman TW]]
+[[Category: Blanchard JS]]
+[[Category: Drueckhammer DG]]
+[[Category: Roderick SL]]
+[[Category: Vogel KW]]