5X7N

Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicum

Summary for 5X7N

• Entry DOI: 10.2210/pdb5x7n/pdb
• Related: 5X7M
• Descriptor: Diaminopimelate decarboxylase, GLYCEROL, PYRIDOXAL-5'-PHOSPHATE, ... (5 entities in total)
• Functional Keywords: decarboxylase, lyase
• Biological source: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
• Total number of polymer chains: 2
• Total formula weight: 98581.61

Authors

Son, H.-F.,Kim, K.-J. (deposition date: 2017-02-27, release date: 2018-01-10, Last modification date: 2023-11-22)

Primary citation

Son, H.F.,Kim, K.J.
Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum.
Biochem. Biophys. Res. Commun., 495:1815-1821, 2018

PubMed Abstract: l-lysine is an essential amino acid that is widely used as a food supplement for humans and animals. meso-Diaminopimelic acid decarboxylase (DAPDC) catalyzes the final step in the de novol-lysine biosynthetic pathway by converting meso-diaminopimelic acid (meso-DAP) into l-lysine by decarboxylation reaction. To elucidate its molecular mechanisms, we determined the crystal structure of DAPDC from Corynebacterium glutamicum (CgDAPDC). The PLP cofactor is bound at the center of the barrel domain and forms a Schiff base with the catalytic Lys75 residue. We also determined the CgDAPDC structure in complex with both pyridoxal 5'-phosphate (PLP) and the l-lysine product and revealed that the protein has an optimal substrate binding pocket to accommodate meso-DAP as a substrate. Structural comparison of CgDAPDC with other amino acid decarboxylases with different substrate specificities revealed that the position of the α15 helix in CgDAPDC and the residues located on the helix are crucial for determining the substrate specificities of the amino acid decarboxylases.

PubMed: 29233695
DOI: 10.1016/j.bbrc.2017.11.097

Experimental method

X-RAY DIFFRACTION (1.72 Å)