Structural highlights
5e3p is a 1 chain structure with sequence from Corgl. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
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| Ligands: | PG4, SO4 |
| Related: | 5e3q, 5e3r |
| Gene: | dapD, Cgl1106, cg1256 (CORGL) |
| Activity: | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, with EC number 2.3.1.117 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[DAPD_CORGL] Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA.
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Sagong HY, Kim KJ. Crystal Structure and Biochemical Characterization of Tetrahydrodipicolinate N-Succinyltransferase from Corynebacterium glutamicum. J Agric Food Chem. 2015 Dec 16;63(49):10641-6. doi: 10.1021/acs.jafc.5b04785., Epub 2015 Dec 4. PMID:26602189 doi:https://dx.doi.org/10.1021/acs.jafc.5b04785
