D3VIU4

UniProt ID: D3VIU4
Organism: Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / CCUG 14189 / LMG 1036 / NCIMB 9965 / AN6)
Review Status: DRAFT
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Gene Description

FliY (locus tag XNC1_0570) is a periplasmic solute-binding protein of the bacterial solute-binding protein family 3 (SBP_bac_3, PF00497) in the Gram-negative entomopathogenic bacterium Xenorhabdus nematophila. It functions as the substrate-capture component of the FliY-YecSC (TcyJLN) ATP-binding cassette (ABC) transporter system, which imports L-cystine with high affinity (Km ~30 nM in E. coli orthologs). FliY is synthesized with an N-terminal signal peptide (residues 1-28) that directs its secretion into the periplasmic space, where it binds extracellular L-cystine and delivers it to the inner-membrane-associated YecSC complex for ATP-driven translocation into the cytoplasm. The imported cystine is reduced to L-cysteine, which serves as a central hub for synthesis of methionine, glutathione, iron-sulfur clusters, and other sulfur-containing biomolecules. Despite the "fliY" gene name (which derives solely from chromosomal proximity to flagellar genes), this protein has no role in flagellar assembly or motility; its function is restricted to cystine transport for sulfur assimilation. The protein is 262 amino acids long and contains the conserved Solute-binding protein family 3/N-terminal domain (IPR001638).

Existing Annotations Review

GO Term Evidence Action Reason
GO:0030288 outer membrane-bounded periplasmic space
IEA
GO_REF:0000117 		ACCEPT
Summary: FliY is a periplasmic solute-binding protein in Gram-negative bacteria. It contains an N-terminal signal peptide (residues 1-28) directing export across the inner membrane into the periplasm. As a component of the FliY-YecSC ABC transporter, it operates as a soluble protein in the outer membrane-bounded periplasmic space, where it captures L-cystine and delivers it to the inner-membrane YecSC complex. This localization is well-supported by the protein's signal peptide, its membership in the bacterial solute-binding protein 3 family, and the conserved architecture of Gram-negative ABC import systems. The ARBA prediction is consistent with the known biology.
GO:0030313 cell envelope
IEA
GO_REF:0000044 		KEEP AS NON CORE
Summary: The cell envelope annotation is derived from UniProtKB-SubCell mapping and is not incorrect -- FliY does reside within the cell envelope. However, this is a very broad term (GO:0030313) that encompasses the outer membrane, periplasmic space, inner membrane, and cell wall. The more specific annotation to outer membrane-bounded periplasmic space (GO:0030288) already captures the precise localization of FliY. Retaining this annotation as non-core since it is accurate but less informative than the periplasmic space annotation.
GO:0016597 amino acid binding
ISS
file:XENNA/D3VIU4/D3VIU4-deep-research-falcon.md 		NEW
Summary: FliY is the periplasmic substrate-binding protein of the FliY-YecSC (TcyJLN) ABC transporter. Its primary molecular function is binding L-cystine with high affinity in the periplasm. The amino acid binding term captures this substrate-binding role. This is inferred from sequence similarity to the well-characterized E. coli FliY ortholog and from membership in the bacterial solute-binding protein family 3. The CDD annotation (cd13711, PBP2_Ngo0372_TcyA) further supports this functional assignment.
Supporting Evidence:
file:XENNA/D3VIU4/D3VIU4-deep-research-falcon.md
[Inferred from E. coli ortholog] FliY serves as the periplasmic substrate-binding component of an ATP-binding cassette (ABC) transporter complex designated FliY-YecSC. This system functions as a high-affinity importer of L-cystine.
GO:0015811 L-cystine transport
ISS
file:XENNA/D3VIU4/D3VIU4-deep-research-falcon.md 		NEW
Summary: FliY functions as the substrate-capture component of the cystine ABC transporter system. Its role in L-cystine transport is inferred from sequence similarity to the E. coli FliY ortholog, which has been experimentally demonstrated to be essential for cystine import via the FliY-YecSC system. The UniProt submission name ("Cysteine transport protein") and CDD domain hit (PBP2_Ngo0372_TcyA) are consistent with this functional assignment.
Supporting Evidence:
file:XENNA/D3VIU4/D3VIU4-deep-research-falcon.md
[Inferred from E. coli ortholog] Genetic deletion studies definitively established that FliY, together with a second cystine transporter YdjN (TcyP), constitutes one of only two cystine import systems in the bacterium. Double mutants lacking both fliY and ydjN are completely unable to import detectable levels of cystine.
GO:0043190 ATP-binding cassette (ABC) transporter complex
ISS
file:XENNA/D3VIU4/D3VIU4-deep-research-falcon.md 		NEW
Summary: FliY is the periplasmic binding protein subunit of the FliY-YecSC ABC transporter complex. This complex membership is inferred from homology to the E. coli system where FliY, YecS, and YecC form the three-component ABC transporter, and from the UniProt annotation as an ABC superfamily periplasmic binding protein.
Supporting Evidence:
file:XENNA/D3VIU4/D3VIU4-deep-research-falcon.md
[Inferred from E. coli ortholog] The FliY-YecSC system operates through the canonical ABC transporter mechanism involving three protein components: FliY is the periplasmic substrate-binding protein, YecS the ATPase component, and YecC the integral membrane permease.

Core Functions

FliY is the periplasmic substrate-binding protein component of the FliY-YecSC (TcyJLN) ABC transporter complex. It captures L-cystine in the periplasm with high affinity and delivers it to the membrane-associated transporter components for ATP-dependent import. This supports sulfur assimilation under conditions of sulfur limitation.

Molecular Function:
amino acid binding
Directly Involved In:
L-cystine transport
Cellular Locations:
outer membrane-bounded periplasmic space
In Complex:
ATP-binding cassette (ABC) transporter complex
Supporting Evidence:
  • file:XENNA/D3VIU4/D3VIU4-deep-research-falcon.md
    [Inferred from E. coli ortholog characterization] FliY serves as the periplasmic substrate-binding component of an ATP-binding cassette (ABC) transporter complex designated FliY-YecSC (also known as TcyJLN). This system functions as a high-affinity importer of L-cystine. The FliY-YecSC system achieves half-maximal transport at approximately 30 nanomolar cystine concentration.

References

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External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

ProtNLM2 External predictions

View prediction review YAML · D3VIU4-protnlm-predictions-review.yaml · Review status: COMPLETE

The signal peptide and soluble solute-binding domain are incompatible with intrinsic ligand-gated channel activity.

Source documents: genes/XENNA/D3VIU4/D3VIU4-uniprot.txt · genes/XENNA/D3VIU4/D3VIU4-goa.tsv · genes/XENNA/D3VIU4/D3VIU4-hypotheses/prediction-ligand-gated-ion-channel/openscientist.md

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0015276 ligand-gated monoatomic ion channel activity GO_MF
NPI — Nonparalog incorrect Review score: 0/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
DOMAIN ARCHITECTURE MISMATCH
Review rationale: The 262-residue target has an N-terminal signal peptide followed by a solute-binding protein family 3 domain covering residues 40–259. This is the architecture of an exported ligand-binding component, without a membrane-spanning channel pore after signal-peptide removal. Binding a transported ligand does not make the binding component a ligand-gated ion channel. The predicted intrinsic channel activity is absent from the cached annotations and is contradicted by the available architecture.
Supporting Evidence:

Deep Research

Falcon

(D3VIU4-deep-research-falcon.md)

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OpenScientist

(D3VIU4-hypotheses/prediction-ligand-gated-ion-channel/openscientist.md)

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📄 View Raw YAML

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