3tdt: Difference between revisions

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-{{STRUCTURE_3tdt|  PDB=3tdt  |  SCENE=  }}
-===COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AMINO-6-OXOPIMELATE AND COENZYME A===
-{{ABSTRACT_PUBMED_9671504}}
-==Function==
+==COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AMINO-6-OXOPIMELATE AND COENZYME A==
-[[http://www.uniprot.org/uniprot/DAPD_MYCBO DAPD_MYCBO]] Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA (By similarity).
+<StructureSection load='3tdt' size='340' side='right'caption='[[3tdt]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3tdt]] 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=3TDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TDT FirstGlance]. <br>
+</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>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=26P:2-AMINO-6-OXOPIMELIC+ACID'>26P</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tdt OCA], [https://pdbe.org/3tdt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tdt RCSB], [https://www.ebi.ac.uk/pdbsum/3tdt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tdt ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DAPD_UNKP DAPD_UNKP]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/td/3tdt_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=3tdt ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Tetrahydrodipicolinate (THDP) N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to L-2-(succinylamino)-6-oxopimelate and CoA. This reaction represents the committed step of the succinylase branch of the diaminopimelate/L-lysine biosynthetic pathway by which many bacteria synthesize meso-diaminopimelate, a component of peptidoglycan, and L-lysine from L-aspartate. The crystal structures of THDP succinyltransferase in complex with the substrate/cofactor pairs L-2-aminopimelate/coenzyme A and L-2-amino-6-oxopimelate/coenzyme A have been determined and refined to 2.0 A resolution. The active site of the enzyme is a long narrow groove located at the interface between two left-handed parallel beta-helix (LbetaH) structural domains of the trimeric enzyme. On binding the amino acid acceptor and cofactor, this groove is covered by residues from the C-terminus of one subunit and a flexible loop excluded from the LbetaH domain of an adjacent subunit to form a tunnel. This conformational change is directly related to interactions between the enzyme and the bound amino acid substrate and cofactor and serves to shield the ligands from bulk solvent and to orient the nucleophilic amino group of the amino acid acceptor toward the mercaptoethylamine group of the cofactor.
-==About this Structure==
+The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase.,Beaman TW, Blanchard JS, Roderick SL Biochemistry. 1998 Jul 21;37(29):10363-9. PMID:9671504<ref>PMID:9671504</ref>
-[[3tdt]] is a 1 chain structure with 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=3TDT OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:009671504</ref><ref group="xtra">PMID:011880627</ref><ref group="xtra">PMID:011917145</ref><references group="xtra"/><references/>
+</div>
-[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]
+<div class="pdbe-citations 3tdt" style="background-color:#fffaf0;"></div>
-[[Category: Mycobacterium bovis]]
+== References ==
-[[Category: Beaman, T W.]]
+<references/>
-[[Category: Blanchard, J S.]]
+__TOC__
-[[Category: Roderick, S L.]]
+</StructureSection>
-[[Category: Acyltransferase]]
+[[Category: Large Structures]]
-[[Category: Lysine biosynthesis]]
+[[Category: Mycobacterium tuberculosis variant bovis]]
+[[Category: Beaman TW]]
+[[Category: Blanchard JS]]
+[[Category: Roderick SL]]