Catalytic C-terminal domain, second repeat, of prokaryotic polyphosphate kinase 1 and similar proteins
Catalytic C-terminal domain, second repeat (C2 domain), of bacterial polyphosphate kinases 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. Each PPK1 monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of PPK1 are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. There is a second bacterial-type enzyme, PPK2, which is involved in the synthesis of poly P from GTP or ATP. PPK2 shows no sequence similarity to PPK1 and belongs to different superfamily.
Structure:1XDP_A; Escherichia coli Polyphosphate kinase binds AMP-PNP; contacts at 4A.
Comment:Polyphosphate Kinase (PPK1) contains two closely related C-terminal catalytic domains (C1 and C2 domain) that, together with the N domain, form a structural tunnel, in which the PPK1 catalytic reactions are carried out.
Jiyao W et al.(2023). "The conserved domain database in 2023.",