Catalytic domain, repeat 2, of plant beta-type phospholipase D
Catalytic domain, repeat 2, of plant beta-type phospholipase D (PLDbeta, EC 3.1.4.4). Plant PLDbeta is a phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent PLD that possesses a regulatory calcium-dependent phospholipid-binding C2 domain in the N-terminus and requires nanomolar calcium and cytosolic factors for optimal activity. The C2 domain is unique to plant PLDs and is not present in animal or fungal PLDs. Sequence analysis shows that plant PLDbeta is evolutionarily divergent from alpha-type plant PLD, and plant PLDbeta is more closely related to mammalian and yeast PLDs than to plant PLDalpha. Like other PLD enzymes, the monomer of plant PLDbeta consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Plant PLDbeta may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group.
Comment:Based on similarity with Streptomyces sp. phospholipase D, which functions as a bi-lobed monomer with two catalytic domains. Each domain carries one copy of the conserved HKD motif and two domains form a single active site.
Comment:The HKD signature motif (expanded to H-x-K-x(4)-D-x(6)-G-S-x-N, where x represents any amino acid residue) characterizes the PLD superfamily.
Comment:Most residues in the HKD motif are part of the active site.
Jiyao W et al.(2023). "The conserved domain database in 2023.",