| Claim/Topic | Organism/Protein studied | Key quantitative/qualitative findings | Relevance to *P. putida* Q88EW3 (direct vs inferred) | Source |
|---|---|---|---|---|
| Gene identity and pathway placement | *Pseudomonas putida* KT2440 CheZ (PP_4339; UniProt Q88EW3) | KT2440 genome annotation places **cheZ/PP_4339** in a flagella-mediated swimming chemotaxis operon (PP4332–PP4340; linked cluster PP4331–PP4397); text states “the activity of the transducer CheY is regulated by the phosphatase CheZ.” (pqac-00000008) | **Direct** evidence for correct gene/protein identity and chemotaxis role in KT2440 | dos Santos et al., 2004, doi: https://doi.org/10.1007/978-1-4419-9086-0_3 |
| Biochemical function | Canonical CheZ family; *E. coli* / *H. pylori* CheZ homologs | CheZ is the canonical **CheY-P phosphatase** in bacterial chemotaxis; it dephosphorylates phosphorylated CheY to terminate the signal. Conserved catalytic mechanism involves active-site Asp/Gln promoting hydrolysis of the aspartyl phosphate. (pqac-00000004, pqac-00000007, pqac-00000009, pqac-00000010) | **Inferred** to Q88EW3 from family/domain conservation plus KT2440 genome annotation as CheZ | Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086; Frederick et al., 2026, doi: https://doi.org/10.1038/s42003-025-09475-w |
| Substrate specificity | *Campylobacter jejuni* Cj0700 (CheZ ortholog) | Purified CheZ ortholog dephosphorylates **CheY** and interacts strongly with CheY; weaker interactions with CheA-RR and CheV were reported, while no activity on unrelated RR RacR was detected, indicating preference for chemotaxis response regulators rather than generic RRs. (pqac-00000003) | **Inferred**: supports that CheZ-family enzymes such as Q88EW3 are primarily CheY-P phosphatases, though species-specific side-substrates may vary | Jama & Ketley, 2023, doi: https://doi.org/10.1101/2023.01.06.523011 |
| Catalytic residues / motif | *Azorhizobium caulinodans* CheZ; *H. pylori* CheZHP; CheZ family | CheZ-family phosphatases carry a conserved **DXXXQ** catalytic motif. In *A. caulinodans*, Asp165/Gln169 are conserved; in *H. pylori*, D189 and Q193 are required for activity; family summaries place the active site and CheY-P binding region in the C-terminal half. (pqac-00000006, pqac-00000009, pqac-00000011) | **Inferred**: Q88EW3 is annotated as CheZ-family/Chemotax_Pase_CheZ, so catalytic function is strongly supported by domain-level conservation | Liu et al., 2018, doi: https://doi.org/10.1128/AEM.01827-17; Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086 |
| CheY-P binding region | *H. pylori* CheZHP; CheZ family | A **C-terminal ~12-aa CheY-P binding region** is required for full phosphatase activity; the C-terminal half contains the catalytic residues and binding determinants. (pqac-00000004, pqac-00000011) | **Inferred** to Q88EW3 from family-level conservation; direct binding-site mapping in KT2440 not found | Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086 |
| Pathway role | Canonical chemotaxis systems / KT2440 annotation | CheZ lowers intracellular CheY-P, thereby resetting pathway output and biasing motor behavior away from persistent reversal/tumble states; KT2440 annotation specifically links CheZ to regulation of CheY in the swimming chemotaxis operon. (pqac-00000008, pqac-00000009, pqac-00000010) | **Direct + inferred**: direct for pathway membership in KT2440; inferred for detailed dynamic role from conserved mechanism | dos Santos et al., 2004, doi: https://doi.org/10.1007/978-1-4419-9086-0_3; Frederick et al., 2026, doi: https://doi.org/10.1038/s42003-025-09475-w |
| Localization | *E. coli* CheZ; *H. pylori* CheZHP | CheZ phosphatase activity is often spatially restricted. In *E. coli*, CheZ localizes to the chemotaxis cluster via CheA/CheAs; in *H. pylori*, CheZHP localizes to the pole via ChePep, with localization region mapped to aa ~40–241. Spatial restriction is proposed to prevent whole-cell CheY-P gradients. (pqac-00000004, pqac-00000005, pqac-00000009, pqac-00000012) | **Inferred only**: no direct localization study for KT2440 Q88EW3 found in gathered evidence | Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086 |
| Mutant phenotype | *A. caulinodans* CheZ | **cheZ disruption abolishes chemotactic ring formation** in soft agar while single-cell motility remains; complementation restores chemotaxis. This separates chemotaxis signaling from basal flagellar motility. (pqac-00000006) | **Inferred**: strongly supports expected phenotype for KT2440 CheZ loss, but not directly tested here | Liu et al., 2018, doi: https://doi.org/10.1128/AEM.01827-17 |
| Mutant phenotype | *H. pylori* CheZHP | Full **ΔcheZ** mutant shows poor soft-agar migration and hyper-reversal behavior; direction changes increase about **2-fold** from ~21.6/min (WT) to ~48/min (mutant), consistent with elevated CheY-P. Active-site mutants D189N/Q193R phenocopy the null. (pqac-00000002, pqac-00000011) | **Inferred**: illustrates expected behavioral consequence of losing CheZ-family phosphatase activity | Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086 |
| Quantitative catalytic effect | *Sinorhizobium meliloti* CheT (CheZ-like phosphatase) | CheT accelerates dephosphorylation of CheY1~P **2-fold**, reducing half-life from **26 s to 13 s**; does **not** enhance dephosphorylation of CheY2~P, showing substrate selectivity. Binding: KD ~**75 μM** for CheY1 and ~**2.9 μM** for phosphomimic CheY1-BeF3−. (pqac-00000001) | **Inferred**: quantitative family benchmark for expected phosphatase behavior of Q88EW3, but kinetics may differ by species | Agbekudzi, 2023, no DOI URL available in gathered evidence |
| Quantitative activation / complex effects | *E. coli* / *H. pylori* CheZ family context | Interaction with CheA-short can activate CheZ about **2.5-fold** in prior *E. coli* work cited within the H. pylori study; CheZ-family proteins are therefore modulated by pathway protein interactions as well as catalytic residues. (pqac-00000005, pqac-00000012) | **Inferred**: suggests Q88EW3 activity may also be influenced by chemotaxis-complex interactions, but no KT2440-specific data found | Lertsethtakarn et al., 2015, doi: https://doi.org/10.1111/mmi.13086 |
| Alternative phosphatases / annotation context | Broad bacterial chemotaxis systems | CheZ is canonical, but some taxa use CheC/FliY/CheX instead; comparative genomics indicates **Pseudomonas** genomes are predominantly **CheZ-only** in the cited dataset (1,375 CheZ-only; 1 both; 1 CheX-only), supporting the expectation that CheZ is the principal chemotaxis phosphatase in pseudomonads. (pqac-00000013) | **Inferred**: supports uniqueness/centrality of CheZ for *Pseudomonas* chemotaxis, though not specific to KT2440 experiment | Frederick et al., 2026, doi: https://doi.org/10.1038/s42003-025-09475-w |


*Table: This table compiles direct evidence for the identity and pathway placement of *Pseudomonas putida* KT2440 CheZ (PP_4339/Q88EW3) together with experimentally supported CheZ-family findings used to infer biochemical function, substrate specificity, localization logic, and likely phenotypes.*