pqqB

Proposed New Ontology Terms

PqqB hydroxylase activity

Definition: Catalysis of oxygen-insertion/hydroxylation reactions on a PqqA-derived cross-linked amino acid intermediate during pyrroloquinoline quinone biosynthesis.

Justification: Primary biochemical and structural studies support PqqB as a non-heme hydroxylase in PQQ biosynthesis, but GO lacks a PqqB-specific hydroxylase molecular-function term.

Parent term: oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

Supporting Evidence:

PMID:30811189 : show that PqqB is a previously uncharacterized hydroxylase
PMID:30811189 : strongly implicate PqqB as a novel non-heme hydroxylase

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0018189 pyrroloquinoline quinone biosynthetic process	IEA GO_REF:0000120	ACCEPT	Summary: This process annotation should be retained. PqqB is a conserved PQQ-pathway protein, and primary biochemical/structural work supports a PqqB hydroxylase role in maturation of PqqA-derived intermediates during PQQ biosynthesis. Reason: PqqB is required for the PQQ pathway; the more recent literature refines its role from possible precursor transport to hydroxylase chemistry within pyrroloquinoline quinone biosynthesis. Supporting Evidence: file:PSEPK/pqqB/pqqB-uniprot.txt PATHWAY: Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis. file:PSEPK/pqqB/pqqB-goa.tsv GO:0018189 pyrroloquinoline quinone biosynthetic process PMID:30811189 strongly implicate PqqB as a novel non-heme hydroxylase file:PSEPK/pqqB/pqqB-deep-research-falcon.md PqqB is part of PQQ biosynthesis and is transcriptionally co-induced with neighboring pqq genes under antibiotic stress. file:PSEPK/pqqB/pqqB-deep-research-falcon.md PP_0379 is explicitly annotated as pqqB and is genomically adjacent to pqqC (PP0378) and pqqA (PP0380)
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	ISS PMID:30811189 Discovery of Hydroxylase Activity for PqqB Provides a Missin...	NEW	Summary: PqqB should have an oxygen-incorporating oxidoreductase molecular-function annotation. The available primary literature supports a non-heme hydroxylase activity, although GO currently lacks a PqqB-specific hydroxylase term. Reason: GO:0016705 is a broad current parent term for the conserved PqqB oxygenase/hydroxylase chemistry. The direct biochemical demonstration of iron-dependent hydroxylase activity was made on the Methylobacterium extorquens ortholog (PMID:30811189), so the KT2440 assignment is by orthology (ISS), not direct assay; falcon deep research independently corroborates the oxygenase-like molecular function from the metallo-beta-lactamase fold and a non-heme-oxygenase facial triad, while emphasizing that strain-specific kinetics for KT2440 PqqB remain unproven. The review remains DRAFT because export-quality ISS curation should add an explicit with/from source annotation. Supporting Evidence: PMID:30811189 show that PqqB is a previously uncharacterized hydroxylase PMID:30811189 strongly implicate PqqB as a novel non-heme hydroxylase file:PSEPK/pqqB/pqqB-deep-research-falcon.md PqqB likely acts as a non-heme metallo-oxygenase in PQQ biosynthesis file:PSEPK/pqqB/pqqB-deep-research-falcon.md a motif typical of non-heme metal-binding oxygenases, supporting an oxygenase-like hypothesis

Core Functions

PqqB is a PQQ-pathway non-heme hydroxylase/oxygen-incorporating oxidoreductase that acts on PqqA-derived cross-linked intermediates during pyrroloquinoline quinone biosynthesis.

Molecular Function:

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

Directly Involved In:

pyrroloquinoline quinone biosynthetic process

Supporting Evidence:

file:PSEPK/pqqB/pqqB-uniprot.txt
PATHWAY: Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis.
PMID:30811189
show that PqqB is a previously uncharacterized hydroxylase
PMID:30811189
strongly implicate PqqB as a novel non-heme hydroxylase
file:PSEPK/pqqB/pqqB-deep-research-falcon.md
non-heme metallo-oxygenase-like enzyme proposed to hydroxylate PqqA Tyr early in PQQ biosynthesis.
file:PSEPK/pqqB/pqqB-deep-research-falcon.md
PqqB also appears to contain a **structural Zn²⁺ site** (conserved cysteine motif) that may stabilize the protein rather than directly catalyze the primary chemistry

References

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

file:PSEPK/pqqB/pqqB-uniprot.txt

UniProtKB entry for pqqB (Coenzyme PQQ synthesis protein B)

"PATHWAY: Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis."
"SIMILARITY: Belongs to the PqqB family."
"FUNCTION: May be involved in the transport of PQQ or its precursor to"

file:PSEPK/pqqB/pqqB-goa.tsv

QuickGO GOA annotations for pqqB

"GO:0018189 pyrroloquinoline quinone biosynthetic process"

PMID:30811189

Discovery of Hydroxylase Activity for PqqB Provides a Missing Link in the Pyrroloquinoline Quinone Biosynthetic Pathway.

"show that PqqB is a previously uncharacterized hydroxylase"
"strongly implicate PqqB as a novel non-heme hydroxylase"

file:PSEPK/pqqB/pqqB-deep-research-falcon.md

Falcon deep research report for pqqB (PP_0379, Q88QV5) in Pseudomonas putida KT2440

"PP_0379 is explicitly annotated as **pqqB** and is genomically adjacent to **pqqC (PP0378)** and **pqqA (PP0380)**"
"PqqB is part of PQQ biosynthesis and is transcriptionally co-induced with neighboring pqq genes under antibiotic stress."
"pqqB upregulated 2.2-fold"
"Insertional disruption of **pqqB (PP_0379)** and **pqqC (PP_0378)** is associated with compromised growth under chloramphenicol"
"PqqB proteins are homologous to the **metallo-β-lactamase fold** superfamily and have an X-ray structure (review cites **PDB 3JXP**)"
"a motif typical of **non-heme metal-binding oxygenases**, supporting an oxygenase-like hypothesis"
"PqqB also appears to contain a **structural Zn²⁺ site** (conserved cysteine motif) that may stabilize the protein rather than directly catalyze the primary chemistry"
"non-heme metallo-oxygenase-like enzyme proposed to hydroxylate PqqA Tyr early in PQQ biosynthesis."
"Direct enzyme assay evidence for KT2440 PqqB substrate specificity and product formation is not present in the retrieved sources"
"the catalytic assignment should be recorded as **inference supported by structure and pathway models**"

Suggested Experiments

Experiment: Reconstitute KT2440 PqqA/PqqD/PqqE/PqqB reactions and track oxygen incorporation and hydroxylated intermediates by LC-MS using wild-type and active-site mutant PqqB.

Hypothesis: KT2440 PqqB catalyzes hydroxylation of a PqqA-derived cross-linked intermediate during PQQ biosynthesis.

Type: reconstituted pathway biochemistry

Deep Research

Falcon

(pqqB-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 26 citations 3 artifacts 2026-06-03T02:01:41.297641

Edison artifact artifact-00 (text/markdown)

Edison artifact artifact-01 (text/markdown)

## Context ID: pqac-00000013 Scheme 2 on page 28 of the document describes the proposed PQQ biosynthesis pathway. In particular, part A of the scheme illustrate (image/png)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Functional Annotation of pqqB (UniProt Q88QV5; locus PP_0379) in Pseudomonas putida KT2440

0) Target verification (MANDATORY)

The target protein is coenzyme PQQ synthesis protein B (PqqB) encoded by pqqB with ordered locus name PP_0379 in Pseudomonas putida strain KT2440. In P. putida KT2440, PP_0379 is explicitly annotated as pqqB and is genomically adjacent to pqqC (PP0378) and pqqA (PP0380) in a clustered region implicated in PQQ biosynthesis. (fernandez2012mechanismsofresistance pages 10-15)

1) Key concepts and definitions (current understanding)

Pyrroloquinoline quinone (PQQ)

PQQ is an enzymatic redox cofactor (a “quinocofactor”) used by multiple bacterial dehydrogenases. The biosynthesis of PQQ is genetically encoded by a dedicated pqq operon; a canonical example contains pqqA–F. (klinman2014intriguesandintricacies pages 2-4)

Overview of PQQ biosynthesis and the role of PqqB

PQQ is synthesized from a small peptide precursor PqqA, with conserved residues (notably Glu and Tyr) contributing to the final cofactor structure. A mechanistic working model proposes that PqqB acts early, likely by hydroxylating the conserved Tyr within PqqA, prior to radical-SAM chemistry by PqqE; later, PqqC catalyzes a multi-step oxidation/ring-closure converting an advanced intermediate (AHQQ) to PQQ. (klinman2014intriguesandintricacies pages 26-37, klinman2014intriguesandintricacies media 63b6eef5)

The PqqB step remains one of the less directly validated transformations in the pathway, with some genetic data historically described as ambiguous regarding absolute essentiality, while structural/bioinformatic evidence supports a key role. (klinman2014intriguesandintricacies pages 2-4)

2) Molecular function of PqqB: biochemical role, reaction type, and substrate specificity

Best-supported functional model

The strongest synthesis from authoritative review and structural inference is:
- Reaction type (proposed): oxygen-dependent hydroxylation chemistry (non-heme metallo-oxygenase-like)
- Putative substrate: the PqqA peptide (specifically the conserved Tyr sidechain)
- Pathway position: early step, upstream of PqqE radical-SAM-mediated C–C bond formation

This proposed Tyr hydroxylation step is explicitly depicted in the pathway scheme and described as part of a “working mechanism.” (klinman2014intriguesandintricacies pages 26-37, klinman2014intriguesandintricacies media 63b6eef5)

Structural/domain evidence supporting oxygenase-like function

PqqB proteins are homologous to the metallo-β-lactamase fold superfamily and have an X-ray structure (review cites PDB 3JXP). Structural comparison to the metallo-β-lactamase-family enzyme PhnP suggests PqqB retains the overall fold but differs in metal-binding architecture. Critically, PqqB retains residues forming a 2-His/1-carboxylate ‘facial triad’, a motif typical of non-heme metal-binding oxygenases, supporting an oxygenase-like hypothesis rather than β-lactam hydrolysis. (klinman2014intriguesandintricacies pages 2-4, klinman2014intriguesandintricacies pages 37-50)

PqqB also appears to contain a structural Zn²⁺ site (conserved cysteine motif) that may stabilize the protein rather than directly catalyze the primary chemistry; notably, the presumed catalytic metal (e.g., Fe) was not observed at the active site in the solved structure, which could reflect metal lability or purification/crystallization conditions. (klinman2014intriguesandintricacies pages 2-4, klinman2014intriguesandintricacies pages 37-50, he2008towardthestructure pages 70-78)

Substrate specificity and enzymatic kinetics: current limitations

Within the retrieved corpus, direct biochemical assays defining PqqB substrate specificity, kinetic parameters, or a chemically confirmed product for KT2440 PqqB were not found. Therefore, the “PqqA Tyr hydroxylase/non-heme oxygenase” assignment should be treated as structure- and pathway-model-supported, rather than fully enzyme-assay-proven, for this specific protein. (klinman2014intriguesandintricacies pages 2-4, klinman2014intriguesandintricacies pages 37-50)

3) Genomic context, regulation, and pathway integration in P. putida KT2440

Operon/neighborhood context in KT2440

In P. putida KT2440, pqqC–pqqB–pqqA occur as an adjacent cluster PP0378–PP0380, consistent with a coordinated biosynthetic module. (fernandez2012mechanismsofresistance pages 10-15)

A separate pqq gene component is located elsewhere: pqqD is encoded at PP2681, indicating that in KT2440 the PQQ pathway genes can be distributed across the genome rather than forming one contiguous pqqA–F operon. (fernandez2012mechanismsofresistance pages 10-15)

Expression/regulatory evidence in KT2440

In a chloramphenicol stress condition, the KT2440 pqqCBA region shows coordinated transcriptional induction: pqqA 4.5-fold, pqqC 2.8-fold, pqqB 2.2-fold upregulation. (fernandez2012mechanismsofresistance pages 28-33)

The same study links a regulator (AgmR) to expression changes that include pqqA, suggesting regulatory wiring that can modulate PQQ biosynthesis under stress. (fernandez2012mechanismsofresistance pages 10-15)

Phenotypic evidence from gene disruption

Insertional disruption of pqqB (PP_0379) and pqqC (PP_0378) is associated with compromised growth under chloramphenicol and reduced MIC values relative to parental strain in that assay system, consistent with PQQ-pathway contributions to cellular physiology under stress. (fernandez2012mechanismsofresistance pages 28-33, fernandez2012mechanismsofresistance pages 10-15)

4) Cellular localization (where PqqB acts)

Direct experimental localization (e.g., fractionation, microscopy, signal peptide validation) for KT2440 PqqB was not found in the retrieved texts. However, PQQ-dependent enzymes that use PQQ as a cofactor (e.g., quinoprotein dehydrogenases) are commonly associated with the periplasmic space in Gram-negative bacteria, implying that PQQ biosynthesis must provide cofactor to periplasm-facing redox systems. This background does not directly localize PqqB itself, but it motivates the expectation that PQQ biosynthesis is functionally linked to envelope-associated redox metabolism. (klinman2014intriguesandintricacies pages 1-2)

Accordingly, the most defensible statement from retrieved evidence is: KT2440 PqqB is a PQQ-biosynthesis enzyme encoded in a pqq gene cluster (PP0378–PP0380), but its precise subcellular compartment remains undetermined here. (fernandez2012mechanismsofresistance pages 10-15)

5) Recent developments (prioritizing 2023–2024) and real-world implementations

5.1 Agricultural biotechnology: phosphate solubilization (2024)

A major application area for PQQ biosynthesis genes (including pqqB) is phosphate solubilization by soil and plant-associated bacteria.

Mechanistic link: PQQ is required as a cofactor for membrane-bound glucose dehydrogenase (GDH) that produces gluconic acid (and related acids), acidifying the environment and mobilizing insoluble phosphate. (anzuay2024employmentofpqqe pages 1-2, chen2024genomebasedidentificationof pages 1-2)

Quantitative evidence (2024): In a genome-guided analysis of phosphate-solubilizing bacteria, 76 PSB genomes were analyzed and 73 strains were experimentally assessed; phosphate release varied widely (example values reported include ~92–96 µg/mL for strong solubilizers under specific conditions) and was associated with decreased medium pH (~4.2–5.2 for strong solubilizers in examples). The study used qPCR to detect pqq gene clusters with a threshold Ct < 30. (chen2024genomebasedidentificationof pages 2-3)

In a highlighted strain (51-Y1415) across a 144-h cultivation time course, phosphate release showed strong correlations with pqq gene abundance, including P release vs pqqB: r = 0.902 (statistically significant as reported), and phosphate release correlated with 2-keto-D-gluconic acid (r ≈ 0.903). (chen2024genomebasedidentificationof pages 5-7, chen2024genomebasedidentificationof pages 7-9)

These 2024 data support the practical use of pqq genes as screening markers for identifying high-performing phosphate-solubilizing strains, even though the work emphasizes pqqC most strongly for marker utility. (chen2024genomebasedidentificationof pages 2-3, chen2024genomebasedidentificationof pages 7-9)

5.2 Environmental monitoring/traceability of PSB (2024)

A 2024 study developed pqqE as a molecular marker to trace Gram-negative phosphate-solubilizing bacteria in environmental samples, noting that pqqA–E are commonly found together as an operon in studied strains while pqqF can be separated and more variable. This provides an applied framework where the presence of core pqq genes (including pqqB) is used to infer capacity for PQQ-dependent phosphate solubilization. (anzuay2024employmentofpqqe pages 1-2)

5.3 Expert opinion and authoritative synthesis

The authoritative Chemical Reviews analysis emphasizes the pathway’s mechanistic uncertainties while highlighting strong structural inference for PqqB (metallo-β-lactamase fold, oxygenase-like facial triad) and proposing a specific role (Tyr hydroxylation of PqqA). This is a leading expert synthesis, but it explicitly reflects that parts of the pathway are not fully resolved and that some steps may occur spontaneously rather than enzymatically, underscoring ongoing open questions in PQQ biosynthesis. (klinman2014intriguesandintricacies pages 26-37, klinman2014intriguesandintricacies pages 2-4)

6) Visual evidence: pathway placement of PqqB

A key scheme summarizing the proposed pathway places PqqB at the step of hydroxylating the conserved Tyr in PqqA. (klinman2014intriguesandintricacies media 63b6eef5)

7) Summary and recommended interpretation for functional annotation

High-confidence annotations (supported directly in KT2440)

Gene/protein identity: PP_0379 is pqqB in P. putida KT2440; clustered with pqqC and pqqA. (fernandez2012mechanismsofresistance pages 10-15)
Pathway membership: PqqB is part of PQQ biosynthesis and is transcriptionally co-induced with neighboring pqq genes under antibiotic stress. (fernandez2012mechanismsofresistance pages 28-33)
Physiological relevance: pqqB disruption affects stress tolerance phenotypes in an antibiotic exposure assay. (fernandez2012mechanismsofresistance pages 28-33)

Mechanistic function (best current model; qualified)

Likely biochemical role: non-heme metallo-oxygenase-like enzyme proposed to hydroxylate PqqA Tyr early in PQQ biosynthesis. (klinman2014intriguesandintricacies pages 26-37, klinman2014intriguesandintricacies pages 2-4)
Structural rationale: metallo-β-lactamase fold with oxygenase-like facial triad; structural Zn²⁺ site. (klinman2014intriguesandintricacies pages 2-4, he2008towardthestructure pages 70-78)

Key evidence gap

Direct enzyme assay evidence for KT2440 PqqB substrate specificity and product formation is not present in the retrieved sources; therefore, the catalytic assignment should be recorded as inference supported by structure and pathway models, pending targeted biochemical validation. (klinman2014intriguesandintricacies pages 2-4, klinman2014intriguesandintricacies pages 37-50)

Evidence summary tables

The following tables consolidate the key evidence and recent developments in a citable format.

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	(fernandez2012mechanismsofresistance pages 10-15)
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	(fernandez2012mechanismsofresistance pages 28-33)
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	(fernandez2012mechanismsofresistance pages 28-33, fernandez2012mechanismsofresistance pages 10-15)
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	(klinman2014intriguesandintricacies pages 2-4)
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	(klinman2014intriguesandintricacies pages 2-4, klinman2014intriguesandintricacies pages 37-50)
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	(klinman2014intriguesandintricacies pages 2-4, klinman2014intriguesandintricacies pages 37-50, he2008towardthestructure pages 70-78)
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	(klinman2014intriguesandintricacies pages 26-37, klinman2014intriguesandintricacies media 63b6eef5)
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	(chen2024genomebasedidentificationof pages 7-9)
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	(chen2024genomebasedidentificationof pages 5-7, chen2024genomebasedidentificationof pages 7-9)
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	(fernandez2012mechanismsofresistance pages 10-15, klinman2014intriguesandintricacies pages 2-4, klinman2014intriguesandintricacies pages 37-50)

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.

Study (year)	System/organism	What was done (application)	Key quantitative results	Relevance to pqqB/PQQ pathway	URL/DOI	Citation ID
Chen et al. (2024)	76 soil phosphate-solubilizing bacterial isolates; highlighted strain Burkholderia cepacia 51-Y1415	Genome-guided screening of PSB using pqq gene clusters as markers for agricultural phosphate-solubilizer discovery	76 genomes analyzed; 73 strains experimentally assessed; P release examples included 96.32 ± 27.05 µg mL⁻¹ and 92.03 µg mL⁻¹ for strong solubilizers; medium pH for strong strains ~4.2–5.2; qPCR presence threshold Ct < 30 (chen2024genomebasedidentificationof pages 2-3, chen2024genomebasedidentificationof pages 1-2)	Positions the pqq cluster as an actionable screening target for PSB; supports applied importance of core pathway genes including pqqB, though pqqC was emphasized as the strongest marker (chen2024genomebasedidentificationof pages 2-3, chen2024genomebasedidentificationof pages 1-2)	https://doi.org/10.1186/s13568-024-01745-w	(chen2024genomebasedidentificationof pages 2-3, chen2024genomebasedidentificationof pages 1-2)
Chen et al. (2024)	Burkholderia cepacia 51-Y1415	Time-course linkage of pqqABCDE expression to phosphate release and organic-acid output for candidate biofertilizer selection	144-h cultivation; P release vs gene abundance correlations: pqqA 0.946, pqqB 0.902, pqqC 0.940, pqqD 0.897, pqqE 0.872; P release vs 2-keto-D-gluconic acid 0.903; pqqA–E vs 2-keto-D-gluconic acid 0.988–0.995* (chen2024genomebasedidentificationof pages 5-7, chen2024genomebasedidentificationof pages 7-9)	Directly ties pqqB abundance to functional output in an application setting; supports using pqq genes as practical predictors of PQQ-dependent GDH-driven phosphate solubilization (chen2024genomebasedidentificationof pages 5-7, chen2024genomebasedidentificationof pages 7-9)	https://doi.org/10.1186/s13568-024-01745-w	(chen2024genomebasedidentificationof pages 5-7, chen2024genomebasedidentificationof pages 7-9)
Anzuay et al. (2024)	Gram-negative plant-associated phosphate-solubilizing bacteria; mixed cultures and peanut rhizosphere samples	Developed pqqE-based molecular traceability approach for monitoring beneficial PSB in environmental samples	pqqE amplification detected in all Gram-negative PSB analyzed; tested across pure cultures, mixed cultures, inoculated and uninoculated rhizosphere DNA preparations (anzuay2024employmentofpqqe pages 1-2)	Relevant because pqqA–E are typically organized together; pqqB is part of the same core biosynthetic module whose presence underpins PQQ-dependent phosphate solubilization (anzuay2024employmentofpqqe pages 1-2)	https://doi.org/10.1007/s00294-024-01296-4	(anzuay2024employmentofpqqe pages 1-2)
Pan & Cai (2023)	Review of phosphate-solubilizing bacteria in agriculture	Synthesized physiological and molecular mechanisms by which PSB mobilize soil phosphorus for crop use	Global soil total phosphorus cited as 400–1000 mg/kg, but only 1.00–2.50% plant-available (from review synthesis) (paper metadata)	Frames the applied importance of PQQ biosynthesis genes, including pqqB, because PQQ-dependent GDH/gluconic acid production is a major acidolysis mechanism in PSB (paper metadata; supported in 2024 mechanistic summaries)	https://doi.org/10.3390/microorganisms11122904	(chen2024genomebasedidentificationof pages 1-2, chen2024genomebasedidentificationof pages 7-9)
Pang et al. (2024)	Review of phosphate-solubilizing microorganisms in soil-plant systems	Summarized current implementations of PSMs for improving plant phosphorus uptake and sustainability	Review emphasizes PSM-mediated activation of insoluble P via organic acids and highlights PQQ synthesis genes as major molecular drivers; no single pqqB-specific metric reported in retrieved excerpt (chen2024genomebasedidentificationof pages 1-2)	Supports real-world relevance of the PQQ pathway for agricultural bioinoculants; pqqB belongs to the six-core-gene biosynthetic framework discussed for PQQ production (chen2024genomebasedidentificationof pages 1-2)	https://doi.org/10.3389/fmicb.2024.1383813	(chen2024genomebasedidentificationof pages 1-2)
Gorniak et al. (2024)	Pseudomonas alloputida KT2440	Transcriptome-level study of lanthanide effects on PQQ-dependent alcohol dehydrogenase physiology	Light lanthanides (La, Ce, Nd) improved growth, whereas heavy lanthanides imposed fitness costs; transcriptome-wide effects examined in strain KT2440 during growth on 2-phenylethanol (paper metadata)	Demonstrates a modern biotechnology context in which endogenous PQQ supply is operationally important because PedE/PedH are PQQ-dependent enzymes; thus pqqB remains relevant as an upstream biosynthetic gene even though it was not the direct focus (paper metadata)	https://doi.org/10.1128/msphere.00685-24	(klinman2014intriguesandintricacies pages 1-2)
Pause et al. (2024)	Pseudomonas putida KT2440 in a bioelectrochemical system	Tested glucose uptake routes under anaerobic electro-fermentation to improve oxidative bioprocessing	About half of secreted acetate originated from inoculation biomass and half from substrate; deletion of individual sugar uptake routes did not significantly alter secreted acetate concentrations among strains (paper metadata)	Relevant because PQQ-dependent periplasmic oxidation is part of KT2440 carbon processing architecture; performance of such systems depends indirectly on intact PQQ biosynthesis, to which pqqB contributes (paper metadata)	https://doi.org/10.1111/1751-7915.14375	(klinman2014intriguesandintricacies pages 1-2)
Liang et al. (2024)	Hyphomicrobium denitrificans H4-45 mutant AE-9	Strain improvement for industrial PQQ production using UV-LiCl mutagenesis, ALE, and fermentation optimization	Nearly 400 generations of mutagenesis/ALE; mutant PQQ titer increased 80.4%; cell density increased 14.9%; final PQQ reached 307 mg/L with productivity 4.26 mg/L/h in a 3.7-L bioreactor (paper metadata)	Although not pqqB-specific, this is a direct real-world implementation of the PQQ biosynthetic pathway as a production platform, underscoring the industrial value of understanding genes such as pqqB (paper metadata)	https://doi.org/10.1007/s00253-024-13053-1	(chen2024genomebasedidentificationof pages 1-2, chen2024genomebasedidentificationof pages 7-9)

Table: This table summarizes recent application-oriented studies and reviews relevant to PQQ biosynthesis genes, including quantitative results where available. It highlights how pqq genes, including pqqB, are being used as markers or enabling components in phosphate-solubilization, environmental tracing, and biotechnology contexts.

References

(fernandez2012mechanismsofresistance pages 10-15): Matilde Fernández, Susana Conde, Jesús de la Torre, Carlos Molina-Santiago, Juan-Luis Ramos, and Estrella Duque. Mechanisms of resistance to chloramphenicol in pseudomonas putida kt2440. Antimicrobial Agents and Chemotherapy, 56:1001-1009, Feb 2012. URL: https://doi.org/10.1128/aac.05398-11, doi:10.1128/aac.05398-11. This article has 181 citations and is from a highest quality peer-reviewed journal.
(klinman2014intriguesandintricacies pages 2-4): Judith P. Klinman and Florence Bonnot. Intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: pqq, ttq, ctq, tpq, and ltq. Chemical reviews, 114 8:4343-65, Apr 2014. URL: https://doi.org/10.1021/cr400475g, doi:10.1021/cr400475g. This article has 225 citations and is from a highest quality peer-reviewed journal.
(klinman2014intriguesandintricacies pages 26-37): Judith P. Klinman and Florence Bonnot. Intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: pqq, ttq, ctq, tpq, and ltq. Chemical reviews, 114 8:4343-65, Apr 2014. URL: https://doi.org/10.1021/cr400475g, doi:10.1021/cr400475g. This article has 225 citations and is from a highest quality peer-reviewed journal.
(klinman2014intriguesandintricacies media 63b6eef5): Judith P. Klinman and Florence Bonnot. Intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: pqq, ttq, ctq, tpq, and ltq. Chemical reviews, 114 8:4343-65, Apr 2014. URL: https://doi.org/10.1021/cr400475g, doi:10.1021/cr400475g. This article has 225 citations and is from a highest quality peer-reviewed journal.
(klinman2014intriguesandintricacies pages 37-50): Judith P. Klinman and Florence Bonnot. Intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: pqq, ttq, ctq, tpq, and ltq. Chemical reviews, 114 8:4343-65, Apr 2014. URL: https://doi.org/10.1021/cr400475g, doi:10.1021/cr400475g. This article has 225 citations and is from a highest quality peer-reviewed journal.
(he2008towardthestructure pages 70-78): SM He. Toward the structure and function of carbon-phosphorus lyase enzymes. Unknown journal, 2008.
(fernandez2012mechanismsofresistance pages 28-33): Matilde Fernández, Susana Conde, Jesús de la Torre, Carlos Molina-Santiago, Juan-Luis Ramos, and Estrella Duque. Mechanisms of resistance to chloramphenicol in pseudomonas putida kt2440. Antimicrobial Agents and Chemotherapy, 56:1001-1009, Feb 2012. URL: https://doi.org/10.1128/aac.05398-11, doi:10.1128/aac.05398-11. This article has 181 citations and is from a highest quality peer-reviewed journal.
(klinman2014intriguesandintricacies pages 1-2): Judith P. Klinman and Florence Bonnot. Intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: pqq, ttq, ctq, tpq, and ltq. Chemical reviews, 114 8:4343-65, Apr 2014. URL: https://doi.org/10.1021/cr400475g, doi:10.1021/cr400475g. This article has 225 citations and is from a highest quality peer-reviewed journal.
(anzuay2024employmentofpqqe pages 1-2): María Soledad Anzuay, Mario Hernán Chiatti, Ariana Belén Intelangelo, Liliana Mercedes Ludueña, Natalia Pin Viso, Jorge Guillermo Angelini, and Tania Taurian. Employment of pqqe gene as molecular marker for the traceability of gram negative phosphate solubilizing bacteria associated to plants. Current genetics, 70 1:12, Aug 2024. URL: https://doi.org/10.1007/s00294-024-01296-4, doi:10.1007/s00294-024-01296-4. This article has 4 citations and is from a peer-reviewed journal.
(chen2024genomebasedidentificationof pages 1-2): Xiaoqing Chen, Yiting Zhao, Shasha Huang, Josep Peñuelas, Jordi Sardans, Lei Wang, and Bangxiao Zheng. Genome-based identification of phosphate-solubilizing capacities of soil bacterial isolates. AMB Express, Jul 2024. URL: https://doi.org/10.1186/s13568-024-01745-w, doi:10.1186/s13568-024-01745-w. This article has 21 citations and is from a peer-reviewed journal.
(chen2024genomebasedidentificationof pages 2-3): Xiaoqing Chen, Yiting Zhao, Shasha Huang, Josep Peñuelas, Jordi Sardans, Lei Wang, and Bangxiao Zheng. Genome-based identification of phosphate-solubilizing capacities of soil bacterial isolates. AMB Express, Jul 2024. URL: https://doi.org/10.1186/s13568-024-01745-w, doi:10.1186/s13568-024-01745-w. This article has 21 citations and is from a peer-reviewed journal.
(chen2024genomebasedidentificationof pages 5-7): Xiaoqing Chen, Yiting Zhao, Shasha Huang, Josep Peñuelas, Jordi Sardans, Lei Wang, and Bangxiao Zheng. Genome-based identification of phosphate-solubilizing capacities of soil bacterial isolates. AMB Express, Jul 2024. URL: https://doi.org/10.1186/s13568-024-01745-w, doi:10.1186/s13568-024-01745-w. This article has 21 citations and is from a peer-reviewed journal.
(chen2024genomebasedidentificationof pages 7-9): Xiaoqing Chen, Yiting Zhao, Shasha Huang, Josep Peñuelas, Jordi Sardans, Lei Wang, and Bangxiao Zheng. Genome-based identification of phosphate-solubilizing capacities of soil bacterial isolates. AMB Express, Jul 2024. URL: https://doi.org/10.1186/s13568-024-01745-w, doi:10.1186/s13568-024-01745-w. This article has 21 citations and is from a peer-reviewed journal.

Artifacts

Citations

fernandez2012mechanismsofresistance pages 10-15
klinman2014intriguesandintricacies pages 2-4
fernandez2012mechanismsofresistance pages 28-33
klinman2014intriguesandintricacies pages 1-2
chen2024genomebasedidentificationof pages 2-3
anzuay2024employmentofpqqe pages 1-2
chen2024genomebasedidentificationof pages 7-9
chen2024genomebasedidentificationof pages 1-2
klinman2014intriguesandintricacies pages 26-37
klinman2014intriguesandintricacies pages 37-50
he2008towardthestructure pages 70-78
chen2024genomebasedidentificationof pages 5-7
https://doi.org/10.1128/AAC.05398-11
https://doi.org/10.1021/cr400475g
https://doi.org/10.4236/jbpc.2012.32023
https://doi.org/10.1186/s13568-024-01745-w
https://doi.org/10.1007/s00294-024-01296-4
https://doi.org/10.3390/microorganisms11122904
https://doi.org/10.3389/fmicb.2024.1383813
https://doi.org/10.1128/msphere.00685-24
https://doi.org/10.1111/1751-7915.14375
https://doi.org/10.1007/s00253-024-13053-1
https://doi.org/10.1128/aac.05398-11,
https://doi.org/10.1021/cr400475g,
https://doi.org/10.1007/s00294-024-01296-4,
https://doi.org/10.1186/s13568-024-01745-w,

📄 View Raw YAML

id: Q88QV5
gene_symbol: pqqB
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: pqqB encodes a conserved PQQ-pathway metallo-beta-lactamase-fold protein in P. putida KT2440. UniProt conservatively suggests transport of PQQ or a precursor, but structure and biochemical literature support a PqqB hydroxylase role in converting PqqA-derived cross-linked intermediates during pyrroloquinoline quinone biosynthesis.
existing_annotations:
- term:
    id: GO:0018189
    label: pyrroloquinoline quinone biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: This process annotation should be retained. PqqB is a conserved PQQ-pathway protein, and primary biochemical/structural work supports a PqqB hydroxylase role in maturation of PqqA-derived intermediates during PQQ biosynthesis.
    action: ACCEPT
    reason: PqqB is required for the PQQ pathway; the more recent literature refines its role from possible precursor transport to hydroxylase chemistry within pyrroloquinoline quinone biosynthesis.
    supported_by:
    - reference_id: file:PSEPK/pqqB/pqqB-uniprot.txt
      supporting_text: 'PATHWAY: Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis.'
    - reference_id: file:PSEPK/pqqB/pqqB-goa.tsv
      supporting_text: "GO:0018189\tpyrroloquinoline quinone biosynthetic process"
    - reference_id: PMID:30811189
      supporting_text: strongly implicate PqqB as a novel non-heme hydroxylase
    - reference_id: file:PSEPK/pqqB/pqqB-deep-research-falcon.md
      supporting_text: PqqB is part of PQQ biosynthesis and is transcriptionally co-induced with neighboring pqq genes under antibiotic stress.
    - reference_id: file:PSEPK/pqqB/pqqB-deep-research-falcon.md
      supporting_text: PP_0379 is explicitly annotated as **pqqB** and is genomically adjacent to **pqqC (PP0378)** and **pqqA (PP0380)**
- term:
    id: GO:0016705
    label: oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
  evidence_type: ISS
  original_reference_id: PMID:30811189
  review:
    summary: PqqB should have an oxygen-incorporating oxidoreductase molecular-function annotation. The available primary literature supports a non-heme hydroxylase activity, although GO currently lacks a PqqB-specific hydroxylase term.
    action: NEW
    reason: GO:0016705 is a broad current parent term for the conserved PqqB oxygenase/hydroxylase chemistry. The direct biochemical demonstration of iron-dependent hydroxylase activity was made on the Methylobacterium extorquens ortholog (PMID:30811189), so the KT2440 assignment is by orthology (ISS), not direct assay; falcon deep research independently corroborates the oxygenase-like molecular function from the metallo-beta-lactamase fold and a non-heme-oxygenase facial triad, while emphasizing that strain-specific kinetics for KT2440 PqqB remain unproven. The review remains DRAFT because export-quality ISS curation should add an explicit with/from source annotation.
    supported_by:
    - reference_id: PMID:30811189
      supporting_text: show that PqqB is a previously uncharacterized hydroxylase
    - reference_id: PMID:30811189
      supporting_text: strongly implicate PqqB as a novel non-heme hydroxylase
    - reference_id: file:PSEPK/pqqB/pqqB-deep-research-falcon.md
      supporting_text: PqqB likely acts as a **non-heme metallo-oxygenase** in PQQ biosynthesis
    - reference_id: file:PSEPK/pqqB/pqqB-deep-research-falcon.md
      supporting_text: a motif typical of **non-heme metal-binding oxygenases**, supporting an oxygenase-like hypothesis
references:
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:PSEPK/pqqB/pqqB-uniprot.txt
  title: UniProtKB entry for pqqB (Coenzyme PQQ synthesis protein B)
  findings:
  - supporting_text: 'PATHWAY: Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis.'
  - supporting_text: 'SIMILARITY: Belongs to the PqqB family.'
  - supporting_text: 'FUNCTION: May be involved in the transport of PQQ or its precursor to'
- id: file:PSEPK/pqqB/pqqB-goa.tsv
  title: QuickGO GOA annotations for pqqB
  findings:
  - supporting_text: "GO:0018189\tpyrroloquinoline quinone biosynthetic process"
- id: PMID:30811189
  title: Discovery of Hydroxylase Activity for PqqB Provides a Missing Link in the Pyrroloquinoline Quinone Biosynthetic Pathway.
  findings:
  - supporting_text: show that PqqB is a previously uncharacterized hydroxylase
    reference_section_type: ABSTRACT
  - supporting_text: strongly implicate PqqB as a novel non-heme hydroxylase
    reference_section_type: RESULTS
- id: file:PSEPK/pqqB/pqqB-deep-research-falcon.md
  title: Falcon deep research report for pqqB (PP_0379, Q88QV5) in Pseudomonas putida KT2440
  findings:
  - supporting_text: PP_0379 is explicitly annotated as **pqqB** and is genomically adjacent to **pqqC (PP0378)** and **pqqA (PP0380)**
  - supporting_text: PqqB is part of PQQ biosynthesis and is transcriptionally co-induced with neighboring pqq genes under antibiotic stress.
  - supporting_text: 'pqqB upregulated 2.2-fold'
  - supporting_text: Insertional disruption of **pqqB (PP_0379)** and **pqqC (PP_0378)** is associated with compromised growth under chloramphenicol
  - supporting_text: PqqB proteins are homologous to the **metallo-β-lactamase fold** superfamily and have an X-ray structure (review cites **PDB 3JXP**)
  - supporting_text: a motif typical of **non-heme metal-binding oxygenases**, supporting an oxygenase-like hypothesis
  - supporting_text: PqqB also appears to contain a **structural Zn²⁺ site** (conserved cysteine motif) that may stabilize the protein rather than directly catalyze the primary chemistry
  - supporting_text: non-heme metallo-oxygenase-like enzyme proposed to hydroxylate PqqA Tyr early in PQQ biosynthesis.
  - supporting_text: Direct enzyme assay evidence for KT2440 PqqB substrate specificity and product formation is not present in the retrieved sources
  - supporting_text: the catalytic assignment should be recorded as **inference supported by structure and pathway models**
core_functions:
- description: PqqB is a PQQ-pathway non-heme hydroxylase/oxygen-incorporating oxidoreductase that acts on PqqA-derived cross-linked intermediates during pyrroloquinoline quinone biosynthesis.
  molecular_function:
    id: GO:0016705
    label: oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
  directly_involved_in:
  - id: GO:0018189
    label: pyrroloquinoline quinone biosynthetic process
  supported_by:
  - reference_id: file:PSEPK/pqqB/pqqB-uniprot.txt
    supporting_text: 'PATHWAY: Cofactor biosynthesis; pyrroloquinoline quinone biosynthesis.'
  - reference_id: PMID:30811189
    supporting_text: show that PqqB is a previously uncharacterized hydroxylase
  - reference_id: PMID:30811189
    supporting_text: strongly implicate PqqB as a novel non-heme hydroxylase
  - reference_id: file:PSEPK/pqqB/pqqB-deep-research-falcon.md
    supporting_text: non-heme metallo-oxygenase-like enzyme proposed to hydroxylate PqqA Tyr early in PQQ biosynthesis.
  - reference_id: file:PSEPK/pqqB/pqqB-deep-research-falcon.md
    supporting_text: PqqB also appears to contain a **structural Zn²⁺ site** (conserved cysteine motif) that may stabilize the protein rather than directly catalyze the primary chemistry
proposed_new_terms:
- proposed_name: PqqB hydroxylase activity
  proposed_definition: Catalysis of oxygen-insertion/hydroxylation reactions on a PqqA-derived cross-linked amino acid intermediate during pyrroloquinoline quinone biosynthesis.
  justification: Primary biochemical and structural studies support PqqB as a non-heme hydroxylase in PQQ biosynthesis, but GO lacks a PqqB-specific hydroxylase molecular-function term.
  proposed_parent:
    id: GO:0016705
    label: oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
  supported_by:
  - reference_id: PMID:30811189
    supporting_text: show that PqqB is a previously uncharacterized hydroxylase
  - reference_id: PMID:30811189
    supporting_text: strongly implicate PqqB as a novel non-heme hydroxylase
suggested_questions:
- question: 'What is the native PqqB substrate and metal/co-substrate requirement in KT2440: cross-linked Glu-Tyr peptide, a cleaved diamino acid intermediate, or a downstream hydroxylated product?'
suggested_experiments:
- hypothesis: KT2440 PqqB catalyzes hydroxylation of a PqqA-derived cross-linked intermediate during PQQ biosynthesis.
  description: Reconstitute KT2440 PqqA/PqqD/PqqE/PqqB reactions and track oxygen incorporation and hydroxylated intermediates by LC-MS using wild-type and active-site mutant PqqB.
  experiment_type: reconstituted pathway biochemistry

Gene Description

Proposed New Ontology Terms

PqqB hydroxylase activity

Existing Annotations Review

Core Functions

PqqB is a PQQ-pathway non-heme hydroxylase/oxygen-incorporating oxidoreductase that acts on PqqA-derived cross-linked intermediates during pyrroloquinoline quinone biosynthesis.

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Research Report: Functional Annotation of pqqB (UniProt Q88QV5; locus PP_0379) in Pseudomonas putida KT2440

0) Target verification (MANDATORY)

1) Key concepts and definitions (current understanding)

Pyrroloquinoline quinone (PQQ)

Overview of PQQ biosynthesis and the role of PqqB

2) Molecular function of PqqB: biochemical role, reaction type, and substrate specificity

Best-supported functional model

Structural/domain evidence supporting oxygenase-like function

Substrate specificity and enzymatic kinetics: current limitations

3) Genomic context, regulation, and pathway integration in P. putida KT2440

Operon/neighborhood context in KT2440

Expression/regulatory evidence in KT2440

Phenotypic evidence from gene disruption

4) Cellular localization (where PqqB acts)

5) Recent developments (prioritizing 2023–2024) and real-world implementations

5.1 Agricultural biotechnology: phosphate solubilization (2024)

5.2 Environmental monitoring/traceability of PSB (2024)

5.3 Expert opinion and authoritative synthesis

6) Visual evidence: pathway placement of PqqB

7) Summary and recommended interpretation for functional annotation

High-confidence annotations (supported directly in KT2440)

Mechanistic function (best current model; qualified)

Key evidence gap

Evidence summary tables

Artifacts

Citations

📄 View Raw YAML