| Feature | Evidence summary | Key citations | Publication info |
|---|---|---|---|
| Gene/protein identity | UniProt P06519 corresponds to **Pseudomonas putida** TOL-plasmid **XylR**, an aromatic-effector-responsive **σ54-dependent enhancer-binding transcriptional regulator**; this distinguishes it from unrelated XylR proteins such as xylose regulators in other taxa. | (pqac-00000000, pqac-00000001, pqac-00000003) | 2023, https://doi.org/10.1111/1462-2920.16342; 2002, https://doi.org/10.1046/j.1462-2920.2002.00265.x; 1997, https://doi.org/10.1046/j.1365-2958.1997.3091673.x |
| Organism / genetic element | XylR is encoded in the **pWW0 TOL plasmid** regulatory network of *P. putida* mt-2 and controls aromatic-hydrocarbon catabolism. | (pqac-00000000, pqac-00000004) | 2023, https://doi.org/10.1111/1462-2920.16342; 1998, https://doi.org/10.1128/jb.180.11.2889-2894.1998 |
| Domains / modules | XylR has modular **A-B-C-D** organization: **A** inducer/effector recognition, **B** interdomain linker, **C** central **AAA+/ATPase** activation domain, **D** C-terminal HTH/UAS DNA-binding domain. | (pqac-00000001, pqac-00000005, pqac-00000022) | 2002, https://doi.org/10.1046/j.1462-2920.2002.00265.x; 2000, https://doi.org/10.1046/j.1365-2958.2000.02139.x; 2023, https://doi.org/10.1111/1462-2920.16342 |
| Effector ligands / specificity | Native effectors include **toluene and xylene isomers**; XylR also responds variably to related aromatics, and A-domain mutations expand or alter specificity, including responses to poor/non-native inducers such as TCB in some contexts. | (pqac-00000000, pqac-00000001, pqac-00000015, pqac-00000016) | 2023, https://doi.org/10.1111/1462-2920.16342; 2002, https://doi.org/10.1046/j.1462-2920.2002.00265.x; 2000, https://doi.org/10.1046/j.1365-2958.2000.02139.x |
| Regulated promoters / operons | XylR activates the **σ54-dependent Pu promoter** of the **upper TOL operon** and also regulates **Ps1** controlling **xylS**; UAS binding can overlap divergent **Pr** promoters driving xylR. | (pqac-00000003, pqac-00000004, pqac-00000012) | 1997, https://doi.org/10.1046/j.1365-2958.1997.3091673.x; 1998, https://doi.org/10.1128/jb.180.11.2889-2894.1998 |
| Primary biological function | XylR is a **transcriptional activator**, not a catabolic enzyme: it turns on genes for the **upper TOL pathway**, which converts toluene/xylene-type aromatics to corresponding carboxylic acids. | (pqac-00000000, pqac-00000005) | 2023, https://doi.org/10.1111/1462-2920.16342; 2000, https://doi.org/10.1046/j.1365-2958.2000.02139.x |
| Activation mechanism | Effector binding to domain A relieves intramolecular repression; XylR then uses **ATP binding/hydrolysis**, oligomerization, and contact with **σ54-RNAP** to stimulate closed-to-open complex transition at target promoters. | (pqac-00000001, pqac-00000008, pqac-00000013, pqac-00000014) | 2002, https://doi.org/10.1046/j.1462-2920.2002.00265.x; 2004, https://doi.org/10.1128/mmbr.68.3.474-500.2004; 2012, https://doi.org/10.1128/mmbr.00006-12; 2000, https://doi.org/10.1046/j.1365-2958.2000.02139.x |
| Repression / autoregulation | XylR also represses its own **Pr** promoter region by occupying overlapping UAS/Pr sites; repressor and activator functions are genetically separable, and **Pr repression is σ54-independent**. | (pqac-00000003, pqac-00000010, pqac-00000012) | 1997, https://doi.org/10.1046/j.1365-2958.1997.3091673.x; 1998, https://doi.org/10.1128/jb.180.11.2889-2894.1998 |
| DNA binding / enhancer organization | XylR binds **upstream activating sequences (UASs)** typically >100 bp upstream; DNA looping and enhancer-like architecture enable productive engagement with promoter-bound σ54-RNAP. | (pqac-00000003, pqac-00000008, pqac-00000012) | 1997, https://doi.org/10.1046/j.1365-2958.1997.3091673.x; 2004, https://doi.org/10.1128/mmbr.68.3.474-500.2004; 1998, https://doi.org/10.1128/jb.180.11.2889-2894.1998 |
| Localization | XylR functions as a **cytoplasmic DNA-binding transcription factor** acting on plasmid-borne promoters; evidence supports intracellular action rather than membrane or extracellular localization. | (pqac-00000003, pqac-00000004, pqac-00000005) | 1997, https://doi.org/10.1046/j.1365-2958.1997.3091673.x; 1998, https://doi.org/10.1128/jb.180.11.2889-2894.1998; 2000, https://doi.org/10.1046/j.1365-2958.2000.02139.x |
| Key host factors | **σ54/RpoN** is essential for Ps1/Pu activation, while **IHF** modulates promoter output and enhancer-promoter communication; σ70-dependent promoters (Pr1/Pr2/Ps2) intersect with this circuit. | (pqac-00000004, pqac-00000011, pqac-00000012) | 1998, https://doi.org/10.1128/jb.180.11.2889-2894.1998 |
| Recent development (2023) | Water availability changes XylR specificity: lower water potential/humidity narrows response toward authentic TOL substrates, while **glycine betaine** can restore activity toward poorer effectors; A-domain variants are less humidity-sensitive. | (pqac-00000016, pqac-00000017, pqac-00000018, pqac-00000019) | 2023, https://doi.org/10.1111/1462-2920.16342 |
| Representative quantitative findings | In 2023 work, PEG8000 treatments defined **0.15, 0.25, 0.50, 0.75 MPa** water potentials; variant binding-pocket volumes were **225.0 ± 10.0 Å3** (WT) versus **285.8 ± 8.2**, **268.0 ± 6.2**, **237.2 ± 9.2 Å3** for Va, V18, V101, with significant expansions for V18/V101. | (pqac-00000016, pqac-00000019) | 2023, https://doi.org/10.1111/1462-2920.16342 |


*Table: This table summarizes the experimentally supported functional annotation of XylR (UniProt P06519) in the Pseudomonas putida TOL system, including identity, domains, mechanism, pathway context, localization, and recent 2023 findings. It is useful as a concise evidence map linking each annotation claim to specific gathered context IDs and publication metadata.*