| Claim/Topic | Key details (include quantitative values) | Organism/system | Source (authors, journal, year) | URL | Evidence strength/notes |
|---|---|---|---|---|---|
| Reaction catalyzed and EC number | 3-Dehydroquinate dehydratase (DHQD/DHQase) catalyzes conversion of 3-dehydroquinate (DHQ) to 3-dehydroshikimate (DHS/3-DHS) in the shikimate pathway; EC 4.2.1.10. This supports annotating **aroQ-III / Q88IJ6** as the dehydratase step in aromatic amino acid biosynthesis when family assignment is correct. (pqac-00000001, pqac-00000006) | General DHQD; inference applied to *Pseudomonas putida* KT2440 aroQ-III | Niraula et al., *BioTech*, 2025; Lee et al., *Journal of Microbiology and Biotechnology*, 2023 | https://doi.org/10.3390/biotech14010006 ; https://doi.org/10.4014/jmb.2305.05018 | Strong for enzyme class/reaction; indirect for Q88IJ6 because retrieved literature did not explicitly map UniProt Q88IJ6/PP_3003, so identity relies partly on supplied UniProt annotation. |
| Type I vs type II mechanistic distinction | Type I DHQDs perform **cis/syn-dehydration** via covalent **imine/Schiff-base** chemistry; type II DHQDs perform **trans/anti-dehydration** via an **enolate/E1CB-like** mechanism. Recent summaries note type II uses catalytic acid/base chemistry distinct from type I and has only weak covalent intermediates. (pqac-00000007, pqac-00000009, pqac-00000010, pqac-00000012) | General DHQD enzyme families | Niraula et al., *BioTech*, 2025; Lee et al., *J. Microbiol. Biotechnol.*, 2023; Isa & Kappo, *In Silico Pharmacology*, 2025 | https://doi.org/10.3390/biotech14010006 ; https://doi.org/10.4014/jmb.2305.05018 ; https://doi.org/10.1007/s40203-024-00298-x | Strong for mechanistic distinction at family level; useful for functional inference that aroQ-family enzymes are type II DHQDs. |
| Structural/oligomeric features of type II DHQD | Type II DHQD adopts a **flavodoxin-like α/β fold** and forms a **homododecamer** (four trimers, tetrahedral organization). In *Corynebacterium glutamicum*, crystal structures were solved as **8IDR** (citrate complex, **1.80 Å**) and **8IDU** (DHQ complex, ~**2.00–2.03 Å**). Solution mass ~**182.3 kDa** supported dodecamer formation; intertrimer interface area **723.9 Ų** (ΔiG **−4.8 kcal/mol**) and intratrimer area **686.5 Ų** (ΔiG **−4.6 kcal/mol**). (pqac-00000006, pqac-00000008, pqac-00000013) | Type II DHQD from *Corynebacterium glutamicum* (structural model for aroQ family) | Lee et al., *Journal of Microbiology and Biotechnology*, 2023 | https://doi.org/10.4014/jmb.2305.05018 | Strong direct structural evidence for type II DHQD family; informative but not organism-specific to *P. putida* Q88IJ6. |
| Kinetic parameters and mutation effects from Lee 2023 | Wild-type CgDHQD kinetics: **Vmax 3.00 μM/s, Km 348.20 μM, kcat 150.19 s^-1**. Variant **S103T**: **Vmax 3.99 μM/s, Km 745.3 μM, kcat 199.67 s^-1** (>10% higher activity but reduced substrate affinity). Mutations of catalytic residues (**N12, R19, Y24, N75, E99, H101, R108**) and substrate-binding residues (**H81, R112**) caused near-complete loss/no detectable activity. **P105A** lowered activity by **60%**; **P105I** and **P105V** lowered activity by **76%** and **58%**; **I102A** and **S103A** retained **35%** and **19%** activity. (pqac-00000011) | *Corynebacterium glutamicum* type II DHQD | Lee et al., *Journal of Microbiology and Biotechnology*, 2023 | https://doi.org/10.4014/jmb.2305.05018 | Strong biochemical evidence for catalytic mechanism/residue importance in type II DHQDs; extrapolation to Q88IJ6 should be made cautiously unless active-site conservation is verified. |
| *Pseudomonas putida* KT2440 metabolic engineering involving aroQ | In a combinatorial pABA engineering study, *P. putida* shikimate-pathway strains produced **2.0 ± 3.4 to 186.2 ± 0.32 mg/L** pABA in the initial screen and up to **232.1 ± 17.6 mg/L** after optimization. **Figure 2** reported **aroQ regression coefficient = −0.20**, indicating high aroQ overexpression had a statistically significant negative effect; authors concluded **mild** rather than high aroQ overexpression is preferable. aroQ is annotated there as **3-dehydroquinate dehydratase**. (pqac-00000002, pqac-00000003, pqac-00000004, pqac-00000014) | *Pseudomonas putida* KT2440 | Campos-Magaña et al., *bioRxiv*, 2024 | https://doi.org/10.1101/2024.06.17.599342 | Moderate evidence: organism-specific and directly relevant to aroQ pathway role, but preprint and not a direct biochemical characterization of Q88IJ6 protein. |
| Ralstonia aroQ1/aroQ2 mutant phenotypes | In *Ralstonia solanacearum*, deletion of both **aroQ1/aroQ2** abolished growth in minimal medium and caused strong in planta attenuation, while single deletions had no obvious defect, showing functional redundancy of AroQ enzymes. Wild type reached about **10^9–10^10 CFU g^-1 at ~4 dpi** then dropped to **~10^5–10^6 CFU g^-1 at 6 dpi**; the double mutant peaked only at **~10^6 CFU g^-1 at 4 dpi**. Shikimic acid supplementation partially/completely rescued growth defects, linking phenotype to shikimate-pathway disruption. (pqac-00000005) | *Ralstonia solanacearum* | Zhang et al., *Frontiers in Microbiology*, 2023 | https://doi.org/10.3389/fmicb.2023.1186688 | Moderate evidence: not *P. putida*, but a peer-reviewed, experimentally validated demonstration that bacterial AroQ enzymes are physiologically important for shikimate-pathway function. |
| Recent development: in silico inhibitor metrics for DHQD | A recent anti-tuberculosis in silico study targeting DHQD reported top docking energies of **−8.99 to −8.39 kcal/mol** versus reference ligand **−4.93 kcal/mol**; MD simulation RMSDs **1.57–2.34 Å** over **50 ns**; MM-GBSA binding energies down to **−32.70 kcal/mol** versus reference **−10.62 kcal/mol**. A cited Mtb DHQD structure had **1.9 Å** resolution. (pqac-00000010) | *Mycobacterium tuberculosis* DHQD (drug-target context) | Isa & Kappo, *In Silico Pharmacology*, 2025 | https://doi.org/10.1007/s40203-024-00298-x | Weak-to-moderate for functional annotation: useful as 2024/2025 development context showing DHQD remains a drug target, but results are computational and not directly about *P. putida* Q88IJ6. |


*Table: This table compiles the most relevant evidence for annotating aroQ-III (UniProt Q88IJ6) as a type II 3-dehydroquinate dehydratase in Pseudomonas putida KT2440. It combines direct organism-level pathway evidence with broader structural, mechanistic, and recent research context for the DHQD family.*