5e3q: Difference between revisions

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-'''Unreleased structure'''
-The entry 5e3q is ON HOLD
+==Crystal structure of DapD in complex with succinyl-CoA from Corynebacterium glutamicum==
+<StructureSection load='5e3q' size='340' side='right'caption='[[5e3q]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5e3q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E3Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E3Q 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</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=5e3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e3q OCA], [https://pdbe.org/5e3q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e3q RCSB], [https://www.ebi.ac.uk/pdbsum/5e3q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e3q ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DAPD_CORGL DAPD_CORGL] Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Tetrahydrodipicolinate N-succinyltransferase (DapD) is an enzyme involved in the biosynthesis of l-lysine by converting tetrahydrodipicolinate into N-succinyl-l-2-amino-6-oxopimelate, using succinyl-CoA as a cofactor. We determined the crystal structure of DapD from Corynebacterium glutamicum (CgDapD). CgDapD functions as a trimer, and each monomer consists of three domains: an N-terminal helical domain (NTD), a left-handed beta-helix (LbetaH) domain, and a beta C-terminal domain (CTD). The mode of cofactor binding to CgDapD, elucidated by determining the structure in complex with succinyl-CoA, reveals that the position of the CTD changes slightly as the cofactor binds to the enzyme. The superposition of this structure with that of Mycobacterium tuberculosis shows differences in residues that make up cofactor-binding sites. Moreover, we determined the structure of CgDapD in complex with the substrate analogue 2-aminopimelate and revealed that the analogue was stabilized by conserved residues. The catalytic and substrate binding sites of CgDapD were confirmed by site-directed mutagenesis experiments.
-Authors: Sagong, H.-Y., Kim, K.-J.
+Crystal Structure and Biochemical Characterization of Tetrahydrodipicolinate N-Succinyltransferase from Corynebacterium glutamicum.,Sagong HY, Kim KJ J Agric Food Chem. 2015 Dec 16;63(49):10641-6. doi: 10.1021/acs.jafc.5b04785., Epub 2015 Dec 4. PMID:26602189<ref>PMID:26602189</ref>
-Description: Crystal strcuture of DapD from Corynebacterium glutamicum
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Kim, K.-J]]
+<div class="pdbe-citations 5e3q" style="background-color:#fffaf0;"></div>
-[[Category: Sagong, H.-Y]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Corynebacterium glutamicum ATCC 13032]]
+[[Category: Large Structures]]
+[[Category: Kim K-J]]
+[[Category: Sagong H-Y]]