1kgt: Difference between revisions
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'''Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA''' | {{Structure | ||
|PDB= 1kgt |SIZE=350|CAPTION= <scene name='initialview01'>1kgt</scene>, resolution 2.3Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=PML:PIMELIC+ACID'>PML</scene> and <scene name='pdbligand=SCA:SUCCINYL-COENZYME A'>SCA</scene> | |||
|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] | |||
|GENE= dapD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1765 Mycobacterium bovis]) | |||
}} | |||
'''Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1KGT is a [ | 1KGT 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=1KGT OCA]. | ||
==Reference== | ==Reference== | ||
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:// | 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] | ||
[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]] | [[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]] | ||
[[Category: Mycobacterium bovis]] | [[Category: Mycobacterium bovis]] | ||
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[[Category: left-handed parallel beta helix]] | [[Category: left-handed parallel beta helix]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:17:16 2008'' | ||
Revision as of 13:17, 20 March 2008
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| , resolution 2.3Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Gene: | dapD (Mycobacterium bovis) | ||||||
| Activity: | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, with EC number 2.3.1.117 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA
OverviewOverview
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.
About this StructureAbout this Structure
1KGT is a Single protein structure of sequence from Mycobacterium bovis. Full crystallographic information is available from OCA.
ReferenceReference
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
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