9H8L

Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lysinibacillus fusiformis bound to TMP

Summary for 9H8L

• Entry DOI: 10.2210/pdb9h8l/pdb
• Descriptor: Polyphosphate kinase, THYMIDINE-5'-PHOSPHATE, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: transferase, polyphosphate, nucleotide, phosphorylation
• Biological source: Lysinibacillus fusiformis
• Total number of polymer chains: 1
• Total formula weight: 32477.72

Authors

Friedrich, F.,Kuge, M.,Keppler, M.,Gerhardt, S.,Einsle, O.,Andexer, J.N. (deposition date: 2024-10-29, release date: 2025-02-05, Last modification date: 2025-03-12)

Primary citation

Kuge, M.,Keppler, M.,Friedrich, F.,Saleem-Batcha, R.,Winter, J.,Prucker, I.,Germer, P.,Gerhardt, S.,Einsle, O.,Jung, M.,Jessen, H.J.,Andexer, J.N.
Structural Insights into Broad-Range Polyphosphate Kinase 2-II Enzymes Applicable for Pyrimidine Nucleoside Diphosphate Synthesis.
Chembiochem, 26:e202400970-e202400970, 2025

PubMed Abstract: Polyphosphate kinases (PPK) play crucial roles in various biological processes, including energy storage and stress responses, through their interaction with inorganic polyphosphate (polyP) and the intracellular nucleotide pool. Members of the PPK family 2 (PPK2s) catalyse polyP‑consuming phosphorylation of nucleotides. In this study, we characterised two PPK2 enzymes from Bacillus cereus (BcPPK2) and Lysinibacillus fusiformis (LfPPK2) to investigate their substrate specificity and potential for selective nucleotide synthesis. Both enzymes exhibited a broad substrate scope, selectively converting over 85% of pyrimidine nucleoside monophosphates (NMPs) to nucleoside diphosphates (NDPs), while nucleoside triphosphate (NTP) formation was observed only with purine NMPs. Preparative enzymatic synthesis of cytidine diphosphate (CDP) was applied to achieve an yield of 49%. Finally, structural analysis of five crystal structures of BcPPK2 and LfPPK2 provided insights into their active sites and substrate interactions. This study highlights PPK2-II enzymes as promising biocatalysts for the efficient and selective synthesis of pyrimidine NDPs.

PubMed: 39846220
DOI: 10.1002/cbic.202400970

Experimental method

X-RAY DIFFRACTION (2.1 Å)