| Claim (what PqqB does) | Evidence type (experiment/structure/bioinformatics) | Key details (e.g., locus, fold change, motifs) | Source (author/year) | URL/DOI | Citation ID |
|---|---|---|---|---|---|
| PP_0379 in *Pseudomonas putida* KT2440 is **pqqB**, a coenzyme PQQ synthesis protein | Experiment/annotation | PP_0379 annotated as **pqqB**; adjacent to **pqqC (PP0378)** and **pqqA (PP0380)** in a clustered region | Fernández et al. 2012 | https://doi.org/10.1128/AAC.05398-11 | (pqac-00000002) |
| pqqB participates in a coordinately regulated **pqqCBA** biosynthetic region in KT2440 | Transcriptomics/experiment | In chloramphenicol-containing medium, **pqqB upregulated 2.2-fold**, with **pqqC 2.8-fold** and **pqqA 4.5-fold**, supporting pathway co-regulation | Fernández et al. 2012 | https://doi.org/10.1128/AAC.05398-11 | (pqac-00000017) |
| Disrupting **pqqB** affects a measurable cellular phenotype in KT2440, supporting functional importance of the gene | Mutant phenotype/experiment | **mut::pqqB** showed reduced chloramphenicol MIC relative to parental KT2440R and impaired growth under stress, consistent with a physiologically relevant PQQ-biosynthesis role | Fernández et al. 2012 | https://doi.org/10.1128/AAC.05398-11 | (pqac-00000000, pqac-00000018) |
| PqqB belongs to a **metallo-β-lactamase-fold** protein family rather than a classical β-lactamase enzyme | Structure/bioinformatics | Review notes PqqB is homologous to metallo-β-lactamase family proteins; crystal structure available (**PDB 3JXP**) | Klinman & Bonnot 2014 | https://doi.org/10.1021/cr400475g | (pqac-00000001, pqac-00000014) |
| PqqB likely acts as a **non-heme metallo-oxygenase** in PQQ biosynthesis | Structure-based functional inference | Putative active site retains a **2-His/1-carboxylate facial triad**, characteristic of non-heme oxygenases; comparison made to **PhnP** | Klinman & Bonnot 2014 | https://doi.org/10.1021/cr400475g | (pqac-00000001, pqac-00000014, pqac-00000015) |
| PqqB likely binds a **structural Zn²⁺** and may require a different catalytic metal at the active site | Structure/comparative analysis | Crystal structure shows **Zn²⁺ at a structural site**; active-site metal absent in solved structure; conserved cysteines support structural Zn-binding motif | Klinman & Bonnot 2014; He 2008 | https://doi.org/10.1021/cr400475g ; https://doi.org/10.4236/jbpc.2012.32023 | (pqac-00000014, pqac-00000015, pqac-00000016) |
| The leading mechanistic model is that PqqB **hydroxylates the conserved Tyr residue in PqqA** early in the pathway | Mechanistic inference/review | Proposed step occurs **before PqqE** radical-SAM chemistry; highlighted in pathway scheme and review discussion | Klinman & Bonnot 2014 | https://doi.org/10.1021/cr400475g | (pqac-00000004, pqac-00000011, pqac-00000013) |
| Recent literature continues to place PqqB in the core **PQQ biosynthetic enzyme set** and sometimes describes it as a hydroxylase | Recent review/application-oriented synthesis | 2024 study describes PQQ formation via **PqqE, PqqD, PqqB (dual hydroxylase), and PqqC**; emphasizes linkage to PQQ-dependent GDH and phosphate solubilization | Chen et al. 2024 | https://doi.org/10.1186/s13568-024-01745-w | (pqac-00000008) |
| Abundance of **pqqB** tracks with phosphate-solubilization output in a 2024 PSB study, supporting pathway relevance in applied settings | Quantitative correlation/application | In strain 51-Y1415 over **144 h**, correlation of **P release vs pqqB abundance = 0.902***; P release also correlated with **2-keto-D-gluconic acid** production | Chen et al. 2024 | https://doi.org/10.1186/s13568-024-01745-w | (pqac-00000022, pqac-00000025) |
| Direct biochemical substrate specificity of **P. putida** PqqB remains unresolved despite strong family-level inference | Evidence gap/assessment | Retrieved sources support pathway membership and structure-based oxygenase hypothesis, but do **not** provide direct kinetics or purified-enzyme substrate specificity for KT2440 PqqB | Synthesis from retrieved evidence | https://doi.org/10.1021/cr400475g ; https://doi.org/10.1128/AAC.05398-11 | (pqac-00000002, pqac-00000014, pqac-00000015) |


*Table: This table summarizes the main experimental, structural, and bioinformatic evidence supporting the annotation and likely pathway role of PqqB (PP_0379; UniProt Q88QV5) in *Pseudomonas putida* KT2440. It is useful for distinguishing direct strain-specific evidence from broader family-level functional inference.*