5E3P

Crystal structure of DapD from Corynebacterium glutamicum

Summary for 5E3P

• Entry DOI: 10.2210/pdb5e3p/pdb
• Related: 5E3Q 5E3R
• Descriptor: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, TETRAETHYLENE GLYCOL, SULFATE ION, ... (4 entities in total)
• Functional Keywords: transferase, corynebacterium glutamicum, l-lysine
• Biological source: Corynebacterium glutamicum
• Total number of polymer chains: 1
• Total formula weight: 32200.14

Authors

Sagong, H.-Y.,Kim, K.-J. (deposition date: 2015-10-03, release date: 2015-11-04, Last modification date: 2023-11-08)

Primary citation

Sagong, H.Y.,Kim, K.J.
Crystal Structure and Biochemical Characterization of Tetrahydrodipicolinate N-Succinyltransferase from Corynebacterium glutamicum.
J.Agric.Food Chem., 63:10641-10646, 2015

PubMed Abstract: 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 β-helix (LβH) domain, and a β 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.

PubMed: 26602189
DOI: 10.1021/acs.jafc.5b04785

Experimental method

X-RAY DIFFRACTION (2.01 Å)