5X7M

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

5X7M の概要

• エントリーDOI: 10.2210/pdb5x7m/pdb
• 関連するPDBエントリー: 5X7N
• 分子名称: Diaminopimelate decarboxylase, PYRIDOXAL-5'-PHOSPHATE (3 entities in total)
• 機能のキーワード: decarboxylase, lyase
• 由来する生物種: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 97550.46

構造登録者

Son, H.-F.,Kim, K.-J. (登録日: 2017-02-27, 公開日: 2018-01-10, 最終更新日: 2023-11-22)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.4 Å)