1kgt: Difference between revisions
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==Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA== | ==Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA== | ||
<StructureSection load='1kgt' size='340' side='right' caption='[[1kgt]], [[Resolution|resolution]] 2.30Å' scene=''> | <StructureSection load='1kgt' size='340' side='right'caption='[[1kgt]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1kgt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_tuberculosis_typus_bovinus"_lehmann_and_neumann_1907 "mycobacterium tuberculosis typus bovinus" lehmann and neumann 1907]. 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 [http:// | <table><tr><td colspan='2'>[[1kgt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_tuberculosis_typus_bovinus"_lehmann_and_neumann_1907 "mycobacterium tuberculosis typus bovinus" lehmann and neumann 1907]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1KGT FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PML:PIMELIC+ACID'>PML</scene>, <scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene></td></tr> | </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> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tdt|1tdt]], [[2tdt|2tdt]], [[3tdt|3tdt]], [[1kgq|1kgq]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1tdt|1tdt]], [[2tdt|2tdt]], [[3tdt|3tdt]], [[1kgq|1kgq]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1765 "Mycobacterium tuberculosis typus bovinus" Lehmann and Neumann 1907])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1765 "Mycobacterium tuberculosis typus bovinus" Lehmann and Neumann 1907])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1kgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kgt OCA], [http://pdbe.org/1kgt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kgt RCSB], [http://www.ebi.ac.uk/pdbsum/1kgt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kgt ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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[[Category: Mycobacterium tuberculosis typus bovinus lehmann and neumann 1907]] | [[Category: Mycobacterium tuberculosis typus bovinus lehmann and neumann 1907]] | ||
[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]] | [[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]] | ||
[[Category: Large Structures]] | |||
[[Category: Beaman, T W]] | [[Category: Beaman, T W]] | ||
[[Category: Blanchard, J S]] | [[Category: Blanchard, J S]] | ||
Revision as of 10:44, 25 November 2020
Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoACrystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA
Structural highlights
Function[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). Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedTetrahydrodipicolinate 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. 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:11910040[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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