ppk

Gene Description

Polyphosphate kinase 1 (PPK1; EC 2.7.4.1), the principal enzyme responsible for inorganic polyphosphate (polyP) synthesis in Pseudomonas putida KT2440 (locus PP_5217). It catalyzes the reversible, processive transfer of the terminal gamma-phosphate of ATP onto a growing linear polyP chain ([phosphate](n) + ATP = [phosphate](n+1) + ADP), using Mg2+ as cofactor and proceeding through an autophosphorylated histidine intermediate (His472 in this protein). The enzyme is a cytoplasmic ~82 kDa member of the PPK1 family, belonging to the phospholipase D superfamily of phosphotransferases. PolyP made by PPK1 serves as a phosphate and high-energy phosphate (ATP) reservoir and as a metal-ion chelator. In P. putida, ppk deletion lowers intracellular polyP by roughly 70-90%, identifying PPK1 as the dominant polyP polymerase, and impairs stationary-phase survival, swimming motility, biofilm formation, and tolerance to multiple stresses (UV, beta-lactams, heavy metals, solvents, heat), partly through effects on the stress sigma factor RpoS. The gene is adjacent to the exopolyphosphatase gene ppx (PP_5216), with which it forms the polyP homeostasis module.

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0006799 polyphosphate biosynthetic process	IEA GO_REF:0000120	ACCEPT	Summary: Core biological process. PPK1 is the enzyme that synthesizes long-chain polyP from ATP, and deletion of ppk in P. putida KT2440 reduces intracellular polyP by ~70-90%, directly confirming its role in polyP biosynthesis. Reason: The IEA annotation is fully consistent with the experimentally validated function of this protein. Nikel et al. (2013, PMID:23687963) showed Delta-ppk abolishes the majority of cellular polyP, establishing PP_5217 as the main polyP polymerase. This is a core function of the gene.
GO:0008976 polyphosphate kinase activity	IEA GO_REF:0000120	ACCEPT	Summary: Core molecular function. This is the defining catalytic activity of PPK1 (EC 2.7.4.1, RHEA:19573): ATP + [phosphate](n) = ADP + [phosphate](n+1). Supported by the conserved PPK1 active-site histidine (His472) and ATP/Mg2+ binding residues, family membership, and the experimental polyP phenotype. Reason: The molecular function annotation is well supported by family/domain assignment (HAMAP MF_00347, PPK1 family) and corroborated experimentally in P. putida (PMID:23687963). This is the core function of the gene.
GO:0009358 polyphosphate kinase complex	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: Cellular component annotation derived from InterPro2GO. PPK1 enzymes are cytoplasmic and the active form is oligomeric, so a "polyphosphate kinase complex" annotation is plausible. However, this is purely an InterPro electronic mapping with no direct evidence for a defined complex in P. putida, and the more informative localization is cytoplasm. Reason: The annotation is not wrong (PPK1 functions as a homo-oligomer), but it is a generic InterPro2GO inference without organism-specific complex evidence and is not the core descriptor of the gene's activity. Retained as non-core rather than removed, per guidance against over-ruling electronic CC mappings that are biologically reasonable.

Core Functions

ATP-dependent synthesis of long-chain inorganic polyphosphate, the dominant polyP-polymerizing activity in P. putida KT2440.

Molecular Function:

polyphosphate kinase activity

Directly Involved In:

polyphosphate biosynthetic process

Supporting Evidence:

PMID:23687963
Deletion of ppk (PP_5217) decreased intracellular polyphosphate by ~70-90%, identifying it as the principal polyphosphate kinase responsible for polyP accumulation in P. putida KT2440.

Gene Description

Existing Annotations Review

Core Functions

ATP-dependent synthesis of long-chain inorganic polyphosphate, the dominant polyP-polymerizing activity in P. putida KT2440.

References

Deep Research

Falcon

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