pvdT

UniProt ID: Q88F88
Organism: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
Review Status: DRAFT
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Gene Description

pvdT encodes the ATP-binding/permease component of the PvdRT-OpmQ tripartite pyoverdine export system. PvdT is an inner-membrane ABC transporter component that binds pyoverdine and hydrolyzes ATP to drive secretion and recycling of the siderophore pyoverdine, supporting iron acquisition under iron-limited conditions.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005524 ATP binding
IEA
GO_REF:0000002 		KEEP AS NON CORE
Summary: ATP binding is required for the ABC transporter ATPase, but ATP hydrolysis is the more informative function.
Reason: Retain as non-core nucleotide binding.
Supporting Evidence:
file:PSEPK/pvdT/pvdT-uniprot.txt
KM=0.164 mM for ATP
GO:0005886 plasma membrane
IEA
GO_REF:0000120 		ACCEPT
Summary: PvdT is an inner/cell membrane multi-pass transporter component; GOA uses plasma membrane for bacterial cell membrane.
Reason: Retain the location annotation.
Supporting Evidence:
file:PSEPK/pvdT/pvdT-uniprot.txt
SUBCELLULAR LOCATION: Cell inner membrane
file:PSEPK/pvdT/pvdT-deep-research-falcon.md
Inner membrane (as the ABC ATPase/TMD component of the tripartite system spanning inner membrane
GO:0016020 membrane
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Generic membrane is less informative than the retained plasma/cell membrane annotation.
Reason: Retain GO:0005886 instead.
Supporting Evidence:
file:PSEPK/pvdT/pvdT-uniprot.txt
SUBCELLULAR LOCATION: Cell inner membrane
GO:0016887 ATP hydrolysis activity
IEA
GO_REF:0000002 		ACCEPT
Summary: ATP hydrolysis is the directly assayed energy-coupling activity of PvdT. Purified PvdT was shown biochemically to possess ATPase activity (PMID:36807028), and falcon deep research confirms PvdT is the ATP-hydrolyzing inner-membrane component of the PvdRT-OpmQ exporter.
Reason: Retain as a core molecular-function annotation directly supported by biochemical assay of purified PvdT.
Supporting Evidence:
file:PSEPK/pvdT/pvdT-uniprot.txt
This subunit binds PVD and drives
file:PSEPK/pvdT/pvdT-uniprot.txt
its secretion by hydrolyzing ATP
PMID:36807028
We show that PvdT possesses an ATPase activity that is stimulated by the addition of PvdR
file:PSEPK/pvdT/pvdT-deep-research-falcon.md
PvdT is an ATP-hydrolyzing component consistent with an ABC exporter
GO:0022857 transmembrane transporter activity
IEA
GO_REF:0000120 		ACCEPT
Summary: PvdT is the ATP-binding/permease component of a pyoverdine export system, so transporter activity is supported.
Reason: Retain until a pyoverdine-specific transporter GO term is available in the review.
Supporting Evidence:
file:PSEPK/pvdT/pvdT-uniprot.txt
Part of the tripartite efflux system PvdRT-OpmQ required for
file:PSEPK/pvdT/pvdT-uniprot.txt
the secretion into the extracellular milieu of the siderophore
file:PSEPK/pvdT/pvdT-deep-research-falcon.md
pyoverdine as the relevant substrate/ligand for the PvdT-containing complex
GO:0042626 ATPase-coupled transmembrane transporter activity
IC
PMID:36807028
The ABC transporter family efflux pump PvdRT-OpmQ of Pseudom... 		NEW
Summary: PvdT is the ATPase/permease component of the PvdRT-OpmQ export system and contributes to ATPase-coupled pyoverdine transport.
Reason: This term is more specific than generic transmembrane transporter activity while avoiding the overclaim that PvdT alone performs the full tripartite export reaction.
Supporting Evidence:
file:PSEPK/pvdT/pvdT-uniprot.txt
This subunit binds PVD and drives
PMID:36807028
PvdT possesses an ATPase activity that is stimulated by the addition of PvdR
file:PSEPK/pvdT/pvdT-deep-research-falcon.md
PvdT is the inner-membrane ABC (MacB-like) ATPase/permease component
file:PSEPK/pvdT/pvdT-deep-research-falcon.md
energizes export by ATP hydrolysis and forms a functional complex with the periplasmic adaptor
GO:0055085 transmembrane transport
IEA
GO_REF:0000108 		ACCEPT
Summary: PvdT participates directly in transmembrane export of pyoverdine. Genetic disruption of pvdRT-opmQ reduces pyoverdine in the medium (PMID:30346656), and falcon deep research frames the system as mediating secretion of newly synthesized and recycled pyoverdine.
Reason: Retain the process annotation.
Supporting Evidence:
file:PSEPK/pvdT/pvdT-uniprot.txt
responsible for export of newly synthesized PVD after the final steps
PMID:30346656
Deletion of pvdRT-opmQ leads to reduced amounts of pyoverdine in the medium and decreased growth under iron limitation
file:PSEPK/pvdT/pvdT-deep-research-falcon.md
secretion of newly synthesized and recycled pyoverdine
GO:1902495 transmembrane transporter complex
IEA
GO_REF:0000117 		ACCEPT
Summary: PvdT is part of the tripartite PvdRT-OpmQ transporter complex, working with the periplasmic adaptor PvdR and outer-membrane channel OpmQ.
Reason: Retain the complex annotation.
Supporting Evidence:
file:PSEPK/pvdT/pvdT-uniprot.txt
composed of an inner membrane component with both ATPase and permease
file:PSEPK/pvdT/pvdT-deep-research-falcon.md
energizes export by ATP hydrolysis and forms a functional complex with the periplasmic adaptor
GO:0005886 plasma membrane
EXP
PMID:36807028
The ABC transporter family efflux pump PvdRT-OpmQ of Pseudom... 		ACCEPT
Summary: PvdT is an inner/cell membrane multi-pass transporter component; GOA uses plasma membrane for bacterial cell membrane. Inner-membrane localization was directly determined for purified PvdT (PMID:36807028).
Reason: Retain the location annotation; experimentally supported subcellular localization.
Supporting Evidence:
file:PSEPK/pvdT/pvdT-uniprot.txt
SUBCELLULAR LOCATION: Cell inner membrane

Core Functions

PvdT is the inner-membrane ATP-binding/permease component of the PvdRT-OpmQ pyoverdine export system, hydrolyzing ATP to drive pyoverdine secretion and recycling.

Molecular Function:
ATP hydrolysis activity
Directly Involved In:
transmembrane transport
Cellular Locations:
plasma membrane
In Complex:
transmembrane transporter complex
Supporting Evidence:
  • file:PSEPK/pvdT/pvdT-uniprot.txt
    Part of the tripartite efflux system PvdRT-OpmQ required for
  • file:PSEPK/pvdT/pvdT-uniprot.txt
    This subunit binds PVD and drives
  • file:PSEPK/pvdT/pvdT-uniprot.txt
    its secretion by hydrolyzing ATP
  • PMID:36807028
    PvdT possesses an ATPase activity that is stimulated by the addition of PvdR
  • file:PSEPK/pvdT/pvdT-deep-research-falcon.md
    PvdT is the inner-membrane ABC (MacB-like) ATPase/permease component
  • file:PSEPK/pvdT/pvdT-deep-research-falcon.md
    ATP-dependent component of a tripartite exporter required for efficient secretion/export and recycling of pyoverdine

References

GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms.
  • InterPro2GO supplies domain/family-based automated annotations that require review against the gene-specific UniProt and literature context.
file:PSEPK/pvdT/pvdT-uniprot.txt
UniProtKB reviewed entry for pvdT
  • UniProt identifies PvdT as the ATP-binding/permease subunit of the PvdRT-OpmQ pyoverdine export system, with ATPase activity and inner-membrane localization.
    "This subunit binds PVD and drives"
  • PvdT is also implicated in recycling of pyoverdine after ferri-PVD internalization and iron release in the periplasm.
    "is also responsible for recycling of PVD after internalization of"
GO_REF:0000120
Combined automated GO annotation using multiple IEA methods.
  • Combined automated methods provide provisional GO annotations that require gene-level review.
GO_REF:0000108
Gene Ontology annotation based on Ensembl/UniProtKB orthology or projection pipelines.
  • Automated projection supplies broad transport/process annotations that need curator review for substrate and mechanism specificity.
GO_REF:0000117
Electronic Gene Ontology annotations created by ARBA machine learning models.
  • ARBA supplies automated annotations that are useful but must be checked against direct gene evidence.
PMID:36807028
The ABC transporter family efflux pump PvdRT-OpmQ of Pseudomonas putida KT2440: purification and initial characterization.
  • Biochemical characterization shows PvdT ATPase activity, stimulation by PvdR, and interaction with pyoverdine.
    "We show that PvdT possesses an ATPase activity that is stimulated by the addition of PvdR"
  • PvdT and PvdR were purified as the inner-membrane and periplasmic-adapter components of the system, with first direct evidence of pyoverdine interaction.
    "purified and characterized the inner membrane component PvdT and the periplasmic adapter protein PvdR"
PMID:30346656
PvdRT-OpmQ and MdtABC-OpmB efflux systems are involved in pyoverdine secretion in Pseudomonas putida KT2440.
  • Genetic evidence links PvdRT-OpmQ to pyoverdine secretion and iron-limited growth.
    "Deletion of pvdRT-opmQ leads to reduced amounts of pyoverdine in the medium and decreased growth under iron limitation"
  • Expression of the pvdRT-opmQ system is induced by iron limitation, consistent with a role in siderophore-mediated iron acquisition.
    "Expression from the respective promoters is stimulated by iron limitation"
file:PSEPK/pvdT/pvdT-deep-research-falcon.md
Falcon deep research report for pvdT (Q88F88, PP_4210) in Pseudomonas putida KT2440
  • PvdT is the inner-membrane ABC (MacB-like) ATPase/permease component of the tripartite PvdRT-OpmQ pyoverdine efflux pump.
    "PvdT is the inner-membrane ABC (MacB-like) ATPase/permease component"
  • PvdT energizes pyoverdine export by ATP hydrolysis and assembles with the periplasmic adaptor PvdR (and outer-membrane channel OpmQ) into a functional complex.
    "energizes export by ATP hydrolysis and forms a functional complex with the periplasmic adaptor"
  • Pyoverdine is the cognate substrate/ligand for the PvdT-containing complex, supported by biochemical modulation of ATPase kinetics.
    "pyoverdine as the relevant substrate/ligand for the PvdT-containing complex"
  • The PvdRT-OpmQ system mediates secretion of both newly synthesized and recycled pyoverdine.
    "secretion of newly synthesized and recycled pyoverdine"
  • PvdT localizes to the inner membrane as the ABC ATPase/TMD component of the tripartite system spanning inner membrane to periplasm to outer membrane.
    "Inner membrane (as the ABC ATPase/TMD component of the tripartite system spanning inner membrane"
  • PvdRT-OpmQ contributes substantially but redundantly to pyoverdine export; deletion reduces but does not abolish secretion due to overlapping efflux systems.
    "consistent with a major role in export/recycling"

Suggested Questions for Experts

Q: Does PvdT directly determine pyoverdine substrate specificity, or is substrate recognition mainly imposed by PvdR/OpmQ or other pyoverdine pathway components?

Suggested experts: Pseudomonas siderophore transport experts

Suggested Experiments

Experiment: Reconstitute PvdRT-OpmQ variants with ATPase-dead PvdT and PvdR-interaction mutants, then measure pyoverdine binding, ATP hydrolysis, and export in iron-limited cells or proteoliposomes.

Type: transporter reconstitution and secretion assay

Deep Research

Falcon

(pvdT-deep-research-falcon.md)
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 18 citations 2 artifacts 2026-06-03T03:34:57.569056
Edison artifact artifact-00 (text/markdown)
## Context ID: pqac-00000006 I have extracted two relevant figures from the document. The first is an operon model showing the genetic allocation of the PvdRT-O (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 pvdT (UniProt Q88F88; locus PP_4210) in Pseudomonas putida KT2440

0) Target verification (gene/protein identity)

The evidence gathered here pertains specifically to Pseudomonas putida KT2440 and to the PvdRT–OpmQ tripartite efflux pump implicated in pyoverdine (PVD) secretion/recycling, in which PvdT is the inner-membrane ABC (MacB-like) ATPase/permease component. This matches the UniProt-provided identity context for Q88F88 (pvdT/PP_4210) as a MacB-like ABC transporter subunit involved in pyoverdine export. (stein2023navigatingpyoverdineand pages 29-31, stein2023therndefflux pages 1-2)

1) Key concepts and current understanding

1.1 Pyoverdine and the “export/recycling” concept

Pyoverdine is a high-affinity siderophore used by fluorescent pseudomonads to acquire iron under iron-limiting conditions. After iron capture and uptake, the siderophore can be re-exported for reuse (“recycling”), enabling repeated iron-scavenging cycles. A recent authoritative review summarizes this recycling logic for Pseudomonas pyoverdines, in which the siderophore is not chemically modified during iron release and is directed back to an efflux pump for export. (schalk2025bacterialsiderophoresdiversity pages 46-46)

1.2 Tripartite efflux pumps and the role of PvdT

Tripartite efflux pumps in Gram-negative bacteria span the inner membrane, periplasm, and outer membrane, consisting of an inner-membrane transporter, a periplasmic adaptor protein, and an outer-membrane channel. In P. putida KT2440, the ABC-type tripartite pump PvdRT–OpmQ is described as a transporter responsible for secretion of newly synthesized and recycled pyoverdine. (stein2023therndefflux pages 1-2)

Within this system, PvdT is identified as the inner-membrane ABC ATPase component (MacB-like architecture) that energizes export by ATP hydrolysis and forms a functional complex with the periplasmic adaptor PvdR (and the outer-membrane channel OpmQ for full tripartite transport). (stein2023navigatingpyoverdineand pages 29-31, stein2023navigatingpyoverdineand pages 43-46)

2) Mechanism, substrate specificity, pathway role, and localization (evidence-driven)

2.1 Substrate/function: pyoverdine export and recycling

Multiple sources in the retrieved corpus explicitly frame PvdRT–OpmQ as mediating pyoverdine secretion, including both “newly synthesized” and “recycled” pyoverdine in P. putida KT2440. (stein2023therndefflux pages 1-2)

Biochemical experiments described in a 2023 dissertation provide direct interaction/ligand evidence consistent with pyoverdine as the relevant substrate/ligand for the PvdT-containing complex. Specifically, pyoverdine affected ATPase kinetics and strengthened interaction parameters between the inner-membrane component (PvdT) and adaptor protein (PvdR), consistent with substrate-stabilized assembly and/or coupling. (stein2023navigatingpyoverdineand pages 46-49)

2.2 Cellular localization and complex architecture

PvdT is an inner-membrane component of the PvdRT–OpmQ exporter; together with PvdR (periplasmic adaptor) and OpmQ (outer-membrane channel), the complex supports export to the extracellular milieu. This is visually summarized in schematic models of efflux-pump organization and pyoverdine secretion networks in KT2440. (stein2023navigatingpyoverdineand pages 29-31, stein2023navigatingpyoverdineand media 41401d62, stein2023navigatingpyoverdineand media 1c3e68be)

2.3 Quantitative biochemical evidence (ATPase kinetics; effect of pyoverdine)

A key recent biochemical result is quantitative ATPase characterization showing that complex formation and pyoverdine presence measurably alter catalytic parameters:

  • PvdT alone (detergent): Vmax 9.91; KM(ATP) 0.16 mM; kcat 0.08 s−1; kcat/KM 583.6 M−1 s−1. (stein2023navigatingpyoverdineand pages 46-49)
  • PvdRT (PvdT complexed with PvdR): Vmax 69.97; KM(ATP) 2.58 mM; kcat 0.58 s−1; kcat/KM 214.2 M−1 s−1. (stein2023navigatingpyoverdineand pages 46-49)
  • With pyoverdine: PvdT+PVD Vmax 6.43; KM(ATP) 0.06 mM; kcat 0.05 s−1; kcat/KM 955.9 M−1 s−1; and PvdRT+PVD Vmax 40.41; KM(ATP) 1.30 mM; kcat 0.34 s−1; kcat/KM 241.7 M−1 s−1. (stein2023navigatingpyoverdineand pages 46-49)

Interpreting these results at the functional-annotation level: (i) PvdT is an ATP-hydrolyzing component consistent with an ABC exporter; (ii) adaptor complexation changes ATPase behavior; and (iii) pyoverdine can modulate these parameters, consistent with it being a cognate ligand/substrate that couples to complex assembly and/or transport activity. (stein2023navigatingpyoverdineand pages 46-49)

2.4 Genetic/physiological evidence: partial dependence and redundancy

Deletion/inactivation evidence indicates PvdRT–OpmQ is important but not unique for pyoverdine export:

  • Deletion of PvdRT–OpmQ reduces pyoverdine secretion by ~50–60% and leads to periplasmic accumulation of pyoverdine, consistent with a major role in export/recycling but incomplete loss due to compensatory pathways. (stein2023navigatingpyoverdineand pages 29-31)
  • A peer-reviewed 2023 study emphasizes that in KT2440, pyoverdine secretion reflects a network of overlapping tripartite systems, where deletion of other systems (e.g., the ParXY RND-type system) can reveal conditional phenotypes under iron limitation, and PvdRT–OpmQ and MdtABC–OpmB are highlighted as primary secretion routes. (stein2023therndefflux pages 1-2)

3) Recent developments (prioritizing 2023–2024)

3.1 2023: Biochemical “first evidence” for interaction and kinetic modulation

A 2023 KT2440-focused body of work reports biochemical interaction evidence between the PvdRT–OpmQ system and pyoverdine and provides quantitative ATPase kinetics (above), supporting a substrate-coupled transporter model for PvdT within this exporter. (stein2023navigatingpyoverdineand pages 46-49, stein2023navigatingpyoverdineand pages 43-46)

3.2 2023: Systems view—multiple efflux pumps contribute to siderophore secretion

A 2023 peer-reviewed study (Microbiology Spectrum) frames pyoverdine export as a property of overlapping efflux systems, and emphasizes that phenotypes can be masked unless multiple exporters are perturbed—important context for annotation and for experimental design (e.g., interpreting partial secretion phenotypes). (stein2023therndefflux pages 1-2)

3.3 2024: Continued emphasis on secretion as a key knowledge gap and an application lever

A 2024 review highlights that secretion mechanisms remain incompletely understood across organisms and argues for deeper genetic and mechanistic study of siderophore synthesis/secretion genes as a route to applications across agriculture, medicine, and environmental contexts. (xie2024exploringthebiological pages 13-15)

4) Current applications and real-world implementations (connected to pyoverdine/export systems)

Direct “productized” deployments specifically requiring P. putida PvdT are not established in the retrieved corpus; however, pyoverdine/siderophore production and (by implication) effective export are repeatedly positioned as enabling technologies in multiple domains:

  • Environmental sensing/bioremediation concepts: pyoverdine has been used as a biosensor component (example given: fluorescence quenching-based detection of the carcinogen furazolidone). (stein2023navigatingpyoverdineand pages 22-25)
  • Environmental remediation and metal handling: siderophores’ ability to chelate metals is repeatedly described as enabling removal/management of toxic metals and radionuclides and recovery of valuable elements (e.g., rare earths), with multiple organism examples. (schalk2025bacterialsiderophoresdiversity pages 12-14, schalk2025bacterialsiderophoresdiversity pages 38-42)
  • Agriculture/biocontrol: siderophore-producing microbes are described as potential biofertilizers/biopesticides by improving plant metal nutrition and disrupting pathogen iron acquisition. (schalk2025bacterialsiderophoresdiversity pages 38-42, schalk2025bacterialsiderophoresdiversity pages 12-14)
  • Biomedical/therapeutic concepts: siderophore pathways can be leveraged for targeted delivery (Trojan-horse-like strategies) and for diagnostics/imaging agent development, in addition to siderophores’ roles in pathogenesis/virulence contexts. (xie2024exploringthebiological pages 15-17, schalk2025bacterialsiderophoresdiversity pages 38-42)

Because export is required to place siderophores in the extracellular environment, PvdT-mediated function is best understood as an upstream enabler of these siderophore-dependent phenomena (iron capture, competition, and siderophore-based technologies), even when PvdT is not named in application papers. (stein2023therndefflux pages 1-2, stein2023navigatingpyoverdineand pages 22-25)

5) Expert opinions/authoritative synthesis

  • A high-authority, recent review presents pyoverdine recycling as a structured pathway in which pyoverdine is directed back to an efflux pump for re-export, highlighting export/recycling as an integral part of siderophore-mediated iron acquisition cycles. (schalk2025bacterialsiderophoresdiversity pages 46-46)
  • KT2440-focused primary literature emphasizes redundancy/overlap among tripartite exporters affecting pyoverdine secretion, implying that “one-gene” knockout phenotypes may be incomplete and that functional annotation should consider network context. (stein2023therndefflux pages 1-2, stein2023navigatingpyoverdineand pages 29-31)

6) Practical functional annotation summary (for databases / genome annotation)

Gene: pvdT (PP_4210; UniProt Q88F88)

Recommended functional name: Pyoverdine export ATP-binding/permease protein PvdT (inner-membrane ABC/MacB-like subunit of PvdRT–OpmQ)

Primary function: ATP-dependent component of a tripartite exporter required for efficient secretion/export and recycling of pyoverdine in P. putida KT2440. (stein2023therndefflux pages 1-2, stein2023navigatingpyoverdineand pages 29-31)

Substrate (best supported): Pyoverdine (siderophore), supported by biochemical modulation of ATPase kinetics by pyoverdine and complex stabilization effects. (stein2023navigatingpyoverdineand pages 46-49)

Cellular localization: Inner membrane (as the ABC ATPase/TMD component of the tripartite system spanning inner membrane → periplasm (PvdR) → outer membrane (OpmQ)). (stein2023navigatingpyoverdineand pages 29-31, stein2023navigatingpyoverdineand media 41401d62)

Pathway role: Siderophore secretion/export and recycling within pyoverdine-mediated iron acquisition; contributes substantially but redundantly (overlapping with other efflux systems). (stein2023therndefflux pages 1-2, stein2023navigatingpyoverdineand pages 29-31)

Evidence map (key sources)

Source (first author, year) Publication type Organism/strain What it says about PvdT/PvdRT-OpmQ (function/substrate/localization) Key quantitative data URL/DOI
Stein, 2023 Dissertation Pseudomonas putida KT2440 Identifies PvdT as the inner-membrane ABC ATPase component of the tripartite exporter PvdRT-OpmQ. The system is described as a MacB-like/ABC tripartite exporter involved in export and recycling of the siderophore pyoverdine; PvdT works with periplasmic adapter PvdR and outer-membrane channel OpmQ to move substrate to the exterior. Biochemical interaction data support pyoverdine as a ligand/substrate and support PvdT-PvdR complex formation. Deletion phenotypes are consistent with a major but non-exclusive role in pyoverdine secretion. (stein2023navigatingpyoverdineand pages 46-49, stein2023navigatingpyoverdineand pages 29-31, stein2023navigatingpyoverdineand pages 43-46, stein2023navigatingpyoverdineand pages 49-52) Deletion of PvdRT-OpmQ reduces pyoverdine secretion by ~50–60%; purification yielded 0.2–0.4 mg PvdR/PvdT from 45 mg total membrane protein. ATPase kinetics reported for PvdT and PvdRT with/without pyoverdine: PvdT Vmax 9.91, KM 0.16 mM, kcat 0.08 s-1, kcat/KM 583.6 M-1 s-1; PvdRT Vmax 69.97, KM 2.58 mM, kcat 0.58 s-1, kcat/KM 214.2 M-1 s-1; PvdT+pyoverdine Vmax 6.43, KM 0.06 mM, kcat 0.05 s-1, kcat/KM 955.9 M-1 s-1; PvdRT+pyoverdine Vmax 40.41, KM 1.30 mM, kcat 0.34 s-1, kcat/KM 241.7 M-1 s-1. (stein2023navigatingpyoverdineand pages 46-49, stein2023navigatingpyoverdineand pages 29-31, stein2023navigatingpyoverdineand pages 43-46) https://doi.org/10.5282/edoc.32605
Stein, 2023 Peer-reviewed research article (Microbiology Spectrum) Pseudomonas putida KT2440 States that the ABC-type tripartite efflux system PvdRT-OpmQ mediates secretion of newly synthesized and recycled pyoverdine. Loss of these systems impairs pyoverdine secretion and growth under iron limitation, but effects are partial because of redundancy with other tripartite exporters such as MdtABC-OpmB and ParXY. The excerpt does not resolve subunit-level localization beyond the general tripartite architecture spanning inner membrane, periplasm, and outer membrane. (stein2023therndefflux pages 15-16, stein2023therndefflux pages 1-2) No PvdT-specific kinetic or binding values in the available snippet; qualitative evidence indicates impaired secretion and iron-limited growth upon inactivation of relevant systems, with partial redundancy. (stein2023therndefflux pages 15-16, stein2023therndefflux pages 1-2) https://doi.org/10.1128/spectrum.02300-23

Table: This table summarizes the source-backed evidence available in context for PvdT/PvdRT-OpmQ in Pseudomonas putida KT2440. It highlights what each source supports about transporter function, substrate, localization, and any quantitative data useful for functional annotation.

Limitations of this evidence set

A 2023 FEBS Letters primary article on purification/initial characterization of PvdRT–OpmQ in KT2440 is referenced within the retrieved corpus but was not directly obtainable in this run; thus, the report relies on the 2023 dissertation’s quantitative biochemical data and a 2023 peer-reviewed study’s contextual and genetic claims for KT2440, plus recent high-authority reviews for broader pathway synthesis. (stein2023therndefflux pages 15-16, stein2023navigatingpyoverdineand pages 46-49, schalk2025bacterialsiderophoresdiversity pages 46-46)

References

  1. (stein2023navigatingpyoverdineand pages 29-31): Nicola Victoria Maria Stein. Navigating pyoverdine and beyond: the role of tripartite efflux pumps in pseudomonas putida kt2440. Dissertation, Jan 2023. URL: https://doi.org/10.5282/edoc.32605, doi:10.5282/edoc.32605. This article has 1 citations.

  2. (stein2023therndefflux pages 1-2): Nicola Victoria Stein, Michelle Eder, Fabienne Burr, Sarah Stoss, Lorenz Holzner, Hans-Henning Kunz, and Heinrich Jung. The rnd efflux system parxy affects siderophore secretion in pseudomonas putida kt2440. Dec 2023. URL: https://doi.org/10.1128/spectrum.02300-23, doi:10.1128/spectrum.02300-23. This article has 8 citations and is from a domain leading peer-reviewed journal.

  3. (schalk2025bacterialsiderophoresdiversity pages 46-46): Isabelle J. Schalk. Bacterial siderophores: diversity, uptake pathways and applications. Nature reviews. Microbiology, 23:24-40, Sep 2025. URL: https://doi.org/10.1038/s41579-024-01090-6, doi:10.1038/s41579-024-01090-6. This article has 211 citations.

  4. (stein2023navigatingpyoverdineand pages 43-46): Nicola Victoria Maria Stein. Navigating pyoverdine and beyond: the role of tripartite efflux pumps in pseudomonas putida kt2440. Dissertation, Jan 2023. URL: https://doi.org/10.5282/edoc.32605, doi:10.5282/edoc.32605. This article has 1 citations.

  5. (stein2023navigatingpyoverdineand pages 46-49): Nicola Victoria Maria Stein. Navigating pyoverdine and beyond: the role of tripartite efflux pumps in pseudomonas putida kt2440. Dissertation, Jan 2023. URL: https://doi.org/10.5282/edoc.32605, doi:10.5282/edoc.32605. This article has 1 citations.

  6. (stein2023navigatingpyoverdineand media 41401d62): Nicola Victoria Maria Stein. Navigating pyoverdine and beyond: the role of tripartite efflux pumps in pseudomonas putida kt2440. Dissertation, Jan 2023. URL: https://doi.org/10.5282/edoc.32605, doi:10.5282/edoc.32605. This article has 1 citations.

  7. (stein2023navigatingpyoverdineand media 1c3e68be): Nicola Victoria Maria Stein. Navigating pyoverdine and beyond: the role of tripartite efflux pumps in pseudomonas putida kt2440. Dissertation, Jan 2023. URL: https://doi.org/10.5282/edoc.32605, doi:10.5282/edoc.32605. This article has 1 citations.

  8. (xie2024exploringthebiological pages 13-15): Benkang Xie, Xinpei Wei, Chu Wan, Wei Zhao, Renfeng Song, Shuquan Xin, and Kai Song. Exploring the biological pathways of siderophores and their multidisciplinary applications: a comprehensive review. Molecules, 29:2318, May 2024. URL: https://doi.org/10.3390/molecules29102318, doi:10.3390/molecules29102318. This article has 75 citations.

  9. (stein2023navigatingpyoverdineand pages 22-25): Nicola Victoria Maria Stein. Navigating pyoverdine and beyond: the role of tripartite efflux pumps in pseudomonas putida kt2440. Dissertation, Jan 2023. URL: https://doi.org/10.5282/edoc.32605, doi:10.5282/edoc.32605. This article has 1 citations.

  10. (schalk2025bacterialsiderophoresdiversity pages 12-14): Isabelle J. Schalk. Bacterial siderophores: diversity, uptake pathways and applications. Nature reviews. Microbiology, 23:24-40, Sep 2025. URL: https://doi.org/10.1038/s41579-024-01090-6, doi:10.1038/s41579-024-01090-6. This article has 211 citations.

  11. (schalk2025bacterialsiderophoresdiversity pages 38-42): Isabelle J. Schalk. Bacterial siderophores: diversity, uptake pathways and applications. Nature reviews. Microbiology, 23:24-40, Sep 2025. URL: https://doi.org/10.1038/s41579-024-01090-6, doi:10.1038/s41579-024-01090-6. This article has 211 citations.

  12. (xie2024exploringthebiological pages 15-17): Benkang Xie, Xinpei Wei, Chu Wan, Wei Zhao, Renfeng Song, Shuquan Xin, and Kai Song. Exploring the biological pathways of siderophores and their multidisciplinary applications: a comprehensive review. Molecules, 29:2318, May 2024. URL: https://doi.org/10.3390/molecules29102318, doi:10.3390/molecules29102318. This article has 75 citations.

  13. (stein2023navigatingpyoverdineand pages 49-52): Nicola Victoria Maria Stein. Navigating pyoverdine and beyond: the role of tripartite efflux pumps in pseudomonas putida kt2440. Dissertation, Jan 2023. URL: https://doi.org/10.5282/edoc.32605, doi:10.5282/edoc.32605. This article has 1 citations.

  14. (stein2023therndefflux pages 15-16): Nicola Victoria Stein, Michelle Eder, Fabienne Burr, Sarah Stoss, Lorenz Holzner, Hans-Henning Kunz, and Heinrich Jung. The rnd efflux system parxy affects siderophore secretion in pseudomonas putida kt2440. Dec 2023. URL: https://doi.org/10.1128/spectrum.02300-23, doi:10.1128/spectrum.02300-23. This article has 8 citations and is from a domain leading peer-reviewed journal.

Artifacts

Citations

  1. schalk2025bacterialsiderophoresdiversity pages 46-46
  2. stein2023therndefflux pages 1-2
  3. stein2023navigatingpyoverdineand pages 46-49
  4. stein2023navigatingpyoverdineand pages 29-31
  5. xie2024exploringthebiological pages 13-15
  6. stein2023navigatingpyoverdineand pages 22-25
  7. stein2023navigatingpyoverdineand pages 43-46
  8. schalk2025bacterialsiderophoresdiversity pages 12-14
  9. schalk2025bacterialsiderophoresdiversity pages 38-42
  10. xie2024exploringthebiological pages 15-17
  11. stein2023navigatingpyoverdineand pages 49-52
  12. stein2023therndefflux pages 15-16
  13. https://doi.org/10.5282/edoc.32605
  14. https://doi.org/10.1128/spectrum.02300-23
  15. https://doi.org/10.5282/edoc.32605,
  16. https://doi.org/10.1128/spectrum.02300-23,
  17. https://doi.org/10.1038/s41579-024-01090-6,
  18. https://doi.org/10.3390/molecules29102318,

📄 View Raw YAML

 
id: Q88F88
gene_symbol: pvdT
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: pvdT encodes the ATP-binding/permease component of the PvdRT-OpmQ tripartite pyoverdine export system. PvdT is an inner-membrane ABC transporter component that binds pyoverdine and hydrolyzes ATP to drive secretion and recycling of the siderophore pyoverdine, supporting iron acquisition under iron-limited conditions.
existing_annotations:
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: ATP binding is required for the ABC transporter ATPase, but ATP hydrolysis is the more informative function.
    action: KEEP_AS_NON_CORE
    reason: Retain as non-core nucleotide binding.
    supported_by:
    - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
      supporting_text: KM=0.164 mM for ATP
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: PvdT is an inner/cell membrane multi-pass transporter component; GOA uses plasma membrane for bacterial cell membrane.
    action: ACCEPT
    reason: Retain the location annotation.
    supported_by:
    - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cell inner membrane'
    - reference_id: file:PSEPK/pvdT/pvdT-deep-research-falcon.md
      supporting_text: Inner membrane (as the ABC ATPase/TMD component of the tripartite system spanning inner membrane
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Generic membrane is less informative than the retained plasma/cell membrane annotation.
    action: MARK_AS_OVER_ANNOTATED
    reason: Retain GO:0005886 instead.
    supported_by:
    - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cell inner membrane'
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: ATP hydrolysis is the directly assayed energy-coupling activity of PvdT. Purified PvdT was shown biochemically to possess ATPase activity (PMID:36807028), and falcon deep research confirms PvdT is the ATP-hydrolyzing inner-membrane component of the PvdRT-OpmQ exporter.
    action: ACCEPT
    reason: Retain as a core molecular-function annotation directly supported by biochemical assay of purified PvdT.
    supported_by:
    - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
      supporting_text: This subunit binds PVD and drives
    - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
      supporting_text: its secretion by hydrolyzing ATP
    - reference_id: PMID:36807028
      supporting_text: We show that PvdT possesses an ATPase activity that is stimulated by the addition of PvdR
    - reference_id: file:PSEPK/pvdT/pvdT-deep-research-falcon.md
      supporting_text: PvdT is an ATP-hydrolyzing component consistent with an ABC exporter
- term:
    id: GO:0022857
    label: transmembrane transporter activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: PvdT is the ATP-binding/permease component of a pyoverdine export system, so transporter activity is supported.
    action: ACCEPT
    reason: Retain until a pyoverdine-specific transporter GO term is available in the review.
    supported_by:
    - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
      supporting_text: Part of the tripartite efflux system PvdRT-OpmQ required for
    - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
      supporting_text: the secretion into the extracellular milieu of the siderophore
    - reference_id: file:PSEPK/pvdT/pvdT-deep-research-falcon.md
      supporting_text: pyoverdine as the relevant substrate/ligand for the PvdT-containing complex
- term:
    id: GO:0042626
    label: ATPase-coupled transmembrane transporter activity
  qualifier: contributes_to
  evidence_type: IC
  original_reference_id: PMID:36807028
  review:
    summary: PvdT is the ATPase/permease component of the PvdRT-OpmQ export system and contributes to ATPase-coupled pyoverdine transport.
    action: NEW
    reason: This term is more specific than generic transmembrane transporter activity while avoiding the overclaim that PvdT alone performs the full tripartite export reaction.
    supported_by:
    - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
      supporting_text: This subunit binds PVD and drives
    - reference_id: PMID:36807028
      supporting_text: PvdT possesses an ATPase activity that is stimulated by the addition of PvdR
    - reference_id: file:PSEPK/pvdT/pvdT-deep-research-falcon.md
      supporting_text: PvdT is the inner-membrane ABC (MacB-like) ATPase/permease component
    - reference_id: file:PSEPK/pvdT/pvdT-deep-research-falcon.md
      supporting_text: energizes export by ATP hydrolysis and forms a functional complex with the periplasmic adaptor
- term:
    id: GO:0055085
    label: transmembrane transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000108
  review:
    summary: PvdT participates directly in transmembrane export of pyoverdine. Genetic disruption of pvdRT-opmQ reduces pyoverdine in the medium (PMID:30346656), and falcon deep research frames the system as mediating secretion of newly synthesized and recycled pyoverdine.
    action: ACCEPT
    reason: Retain the process annotation.
    supported_by:
    - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
      supporting_text: responsible for export of newly synthesized PVD after the final steps
    - reference_id: PMID:30346656
      supporting_text: Deletion of pvdRT-opmQ leads to reduced amounts of pyoverdine in the medium and decreased growth under iron limitation
    - reference_id: file:PSEPK/pvdT/pvdT-deep-research-falcon.md
      supporting_text: secretion of newly synthesized and recycled pyoverdine
- term:
    id: GO:1902495
    label: transmembrane transporter complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: PvdT is part of the tripartite PvdRT-OpmQ transporter complex, working with the periplasmic adaptor PvdR and outer-membrane channel OpmQ.
    action: ACCEPT
    reason: Retain the complex annotation.
    supported_by:
    - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
      supporting_text: composed of an inner membrane component with both ATPase and permease
    - reference_id: file:PSEPK/pvdT/pvdT-deep-research-falcon.md
      supporting_text: energizes export by ATP hydrolysis and forms a functional complex with the periplasmic adaptor
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: EXP
  original_reference_id: PMID:36807028
  review:
    summary: PvdT is an inner/cell membrane multi-pass transporter component; GOA uses plasma membrane for bacterial cell membrane. Inner-membrane localization was directly determined for purified PvdT (PMID:36807028).
    action: ACCEPT
    reason: Retain the location annotation; experimentally supported subcellular localization.
    supported_by:
    - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cell inner membrane'
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms.
  findings:
  - statement: InterPro2GO supplies domain/family-based automated annotations that require review against the gene-specific UniProt and literature context.
- id: file:PSEPK/pvdT/pvdT-uniprot.txt
  title: UniProtKB reviewed entry for pvdT
  findings:
  - statement: UniProt identifies PvdT as the ATP-binding/permease subunit of the PvdRT-OpmQ pyoverdine export system, with ATPase activity and inner-membrane localization.
    supporting_text: This subunit binds PVD and drives
  - statement: PvdT is also implicated in recycling of pyoverdine after ferri-PVD internalization and iron release in the periplasm.
    supporting_text: is also responsible for recycling of PVD after internalization of
- id: GO_REF:0000120
  title: Combined automated GO annotation using multiple IEA methods.
  findings:
  - statement: Combined automated methods provide provisional GO annotations that require gene-level review.
- id: GO_REF:0000108
  title: Gene Ontology annotation based on Ensembl/UniProtKB orthology or projection pipelines.
  findings:
  - statement: Automated projection supplies broad transport/process annotations that need curator review for substrate and mechanism specificity.
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models.
  findings:
  - statement: ARBA supplies automated annotations that are useful but must be checked against direct gene evidence.
- id: PMID:36807028
  title: 'The ABC transporter family efflux pump PvdRT-OpmQ of Pseudomonas putida KT2440: purification and initial characterization.'
  findings:
  - statement: Biochemical characterization shows PvdT ATPase activity, stimulation by PvdR, and interaction with pyoverdine.
    supporting_text: We show that PvdT possesses an ATPase activity that is stimulated by the addition of PvdR
    reference_section_type: ABSTRACT
  - statement: PvdT and PvdR were purified as the inner-membrane and periplasmic-adapter components of the system, with first direct evidence of pyoverdine interaction.
    supporting_text: purified and characterized the inner membrane component PvdT and the periplasmic adapter protein PvdR
    reference_section_type: ABSTRACT
- id: PMID:30346656
  title: PvdRT-OpmQ and MdtABC-OpmB efflux systems are involved in pyoverdine secretion in Pseudomonas putida KT2440.
  findings:
  - statement: Genetic evidence links PvdRT-OpmQ to pyoverdine secretion and iron-limited growth.
    supporting_text: Deletion of pvdRT-opmQ leads to reduced amounts of pyoverdine in the medium and decreased growth under iron limitation
    reference_section_type: ABSTRACT
  - statement: Expression of the pvdRT-opmQ system is induced by iron limitation, consistent with a role in siderophore-mediated iron acquisition.
    supporting_text: Expression from the respective promoters is stimulated by iron limitation
    reference_section_type: ABSTRACT
- id: file:PSEPK/pvdT/pvdT-deep-research-falcon.md
  title: Falcon deep research report for pvdT (Q88F88, PP_4210) in Pseudomonas putida KT2440
  findings:
  - statement: PvdT is the inner-membrane ABC (MacB-like) ATPase/permease component of the tripartite PvdRT-OpmQ pyoverdine efflux pump.
    supporting_text: PvdT is the inner-membrane ABC (MacB-like) ATPase/permease component
  - statement: PvdT energizes pyoverdine export by ATP hydrolysis and assembles with the periplasmic adaptor PvdR (and outer-membrane channel OpmQ) into a functional complex.
    supporting_text: energizes export by ATP hydrolysis and forms a functional complex with the periplasmic adaptor
  - statement: Pyoverdine is the cognate substrate/ligand for the PvdT-containing complex, supported by biochemical modulation of ATPase kinetics.
    supporting_text: pyoverdine as the relevant substrate/ligand for the PvdT-containing complex
  - statement: The PvdRT-OpmQ system mediates secretion of both newly synthesized and recycled pyoverdine.
    supporting_text: secretion of newly synthesized and recycled pyoverdine
  - statement: PvdT localizes to the inner membrane as the ABC ATPase/TMD component of the tripartite system spanning inner membrane to periplasm to outer membrane.
    supporting_text: Inner membrane (as the ABC ATPase/TMD component of the tripartite system spanning inner membrane
  - statement: PvdRT-OpmQ contributes substantially but redundantly to pyoverdine export; deletion reduces but does not abolish secretion due to overlapping efflux systems.
    supporting_text: consistent with a major role in export/recycling
core_functions:
- description: PvdT is the inner-membrane ATP-binding/permease component of the PvdRT-OpmQ pyoverdine export system, hydrolyzing ATP to drive pyoverdine secretion and recycling.
  molecular_function:
    id: GO:0016887
    label: ATP hydrolysis activity
  contributes_to_molecular_function:
    id: GO:0042626
    label: ATPase-coupled transmembrane transporter activity
  directly_involved_in:
  - id: GO:0055085
    label: transmembrane transport
  locations:
  - id: GO:0005886
    label: plasma membrane
  in_complex:
    id: GO:1902495
    label: transmembrane transporter complex
  supported_by:
  - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
    supporting_text: Part of the tripartite efflux system PvdRT-OpmQ required for
  - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
    supporting_text: This subunit binds PVD and drives
  - reference_id: file:PSEPK/pvdT/pvdT-uniprot.txt
    supporting_text: its secretion by hydrolyzing ATP
  - reference_id: PMID:36807028
    supporting_text: PvdT possesses an ATPase activity that is stimulated by the addition of PvdR
  - reference_id: file:PSEPK/pvdT/pvdT-deep-research-falcon.md
    supporting_text: PvdT is the inner-membrane ABC (MacB-like) ATPase/permease component
  - reference_id: file:PSEPK/pvdT/pvdT-deep-research-falcon.md
    supporting_text: ATP-dependent component of a tripartite exporter required for efficient secretion/export and recycling of pyoverdine
proposed_new_terms: []
suggested_questions:
- question: Does PvdT directly determine pyoverdine substrate specificity, or is substrate recognition mainly imposed by PvdR/OpmQ or other pyoverdine pathway components?
  experts:
  - Pseudomonas siderophore transport experts
suggested_experiments:
- description: Reconstitute PvdRT-OpmQ variants with ATPase-dead PvdT and PvdR-interaction mutants, then measure pyoverdine binding, ATP hydrolysis, and export in iron-limited cells or proteoliposomes.
  experiment_type: transporter reconstitution and secretion assay