spuD

UniProt ID: Q9I6J1
Organism: Pseudomonas aeruginosa PAO1
Review Status: COMPLETE
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Gene Description

SpuD (PA0300) is a periplasmic polyamine-binding protein of the PotD/PotF family in Pseudomonas aeruginosa, the substrate-binding component, with its paralog SpuE, of the SpuDEFGH ABC transporter for polyamine uptake. SpuD binds putrescine with nanomolar affinity and spermidine much more weakly, closing around the ligand in an open-to-closed conformational change like E. coli PotF. Mutation of spuD greatly reduces spermidine uptake.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0015846 polyamine transport
IEA
GO_REF:0000002 		MODIFY
Summary: InterPro2GO from the spermidine/putrescine-binding signature.
Reason: Correct but general; consistent with the IMP row for the same term. Both specific descendants are supported for SpuD, putrescine transport (direct high-affinity binding) and spermidine transport (uptake defect of the spuD mutant).
GO:0015846 polyamine transport
IMP
PMID:12081945
Functional analysis and regulation of the divergent spuABCDE... 		MODIFY
Summary: PseudoCAP seed row. The full text shows spermidine uptake greatly reduced in the spuD mutant. Seed verdict SOUND; the term is correct for the gene and for the PTN001249912 clade.
Reason: The claim is sound but more specific terms are supported. The uptake data show spermidine transport; the direct binding data (PMID:22300763) make putrescine the high-affinity ligand, so both descendants are listed.
Supporting Evidence:
PMID:12081945
Second, spermidine uptake is inducible in spermidine-grown cells and is greatly reduced in either spuD or spuE mutant (Fig.
PMID:22300763
we found that SpuD is a putrescine-preferential binding protein, while SpuE binds to spermidine exclusively.
GO:0015847 putrescine transport
IBA
GO_REF:0000033 		ACCEPT
Summary: IBA from PTN008624361, seeded by E. coli PotF and PotD.
Reason: SpuD is a PotF-like putrescine-binding protein with nanomolar affinity, so a role in putrescine uptake is well founded.
Supporting Evidence:
file:PSEAE/spuD/spuD-uniprot.txt
Binds putrescine with high affinity (KD=3 nM), spermidine with relatively low affinity (KD=6.8 uM).
GO:0019808 polyamine binding
IEA
GO_REF:0000002 		TOO GENERAL
Summary: InterPro2GO polyamine binding.
Reason: Entailed by GO:0019810 putrescine binding (is_a GO:0019808), accepted below.
GO:0019809 spermidine binding
IBA
GO_REF:0000033 		KEEP AS NON CORE
Summary: IBA from PTN008624361, seeded by SpuE and E. coli PotD.
Reason: True for SpuD, but weak (KD 6.8 uM versus 3 nM for putrescine); the high-affinity ligand is putrescine.
Supporting Evidence:
file:PSEAE/spuD/spuD-uniprot.txt
Binds putrescine with high affinity (KD=3 nM), spermidine with relatively low affinity (KD=6.8 uM).
GO:0019810 putrescine binding
IBA
GO_REF:0000033 		ACCEPT
Summary: IBA from PTN008624361, seeded by E. coli PotF and PotD (IDA) and the IDA on Q9I6J1 itself (expected, not circular). Correct for SpuD. The node term over-propagates to SpuE; that GO_CENTRAL defect is recorded on the spuE review.
Reason: Core activity, shown by ITC and a putrescine-bound crystal structure.
Supporting Evidence:
PMID:22300763
we found that SpuD is a putrescine-preferential binding protein, while SpuE binds to spermidine exclusively.
GO:0019810 putrescine binding
IDA
PMID:22300763
Structural basis of substrate binding specificity revealed b... 		ACCEPT
Summary: PseudoCAP seed row. The abstract states SpuD is putrescine-preferential and reports a SpuD-putrescine structure; UniProt gives KD 3 nM from this paper.
Reason: Seed verdict SOUND.
Supporting Evidence:
PMID:22300763
we found that SpuD is a putrescine-preferential binding protein, while SpuE binds to spermidine exclusively.
GO:0030288 outer membrane-bounded periplasmic space
IBA
GO_REF:0000033 		ACCEPT
Summary: IBA from PTN008624361; SpuD has a 24-residue signal peptide.
Reason: Correct location for a Gram-negative periplasmic solute-binding protein.
GO:0042597 periplasmic space
IEA
GO_REF:0000120 		TOO GENERAL
Summary: Combined IEA periplasm.
Reason: Entailed by GO:0030288 outer membrane-bounded periplasmic space (is_a GO:0042597), accepted above.

Core Functions

Periplasmic high-affinity putrescine-binding protein (weak spermidine binding) that delivers polyamines to the SpuFGH ABC transporter.

Molecular Function:
putrescine binding
Directly Involved In:
putrescine transport
Cellular Locations:
outer membrane-bounded periplasmic space
Supporting Evidence:
  • PMID:22300763
    we found that SpuD is a putrescine-preferential binding protein, while SpuE binds to spermidine exclusively.
  • PMID:12081945
    Second, spermidine uptake is inducible in spermidine-grown cells and is greatly reduced in either spuD or spuE mutant (Fig.

References

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Suggested Questions for Experts

Q: Does E. coli PotF bind spermidine at all? It receives a spermidine binding IBA from PTN008624361, but its curated function records only putrescine binding.

Q: Why are both SpuD and SpuE needed for optimal spermidine uptake, when SpuD binds spermidine only weakly?

Suggested Experiments

Experiment: Measure radiolabelled putrescine and spermidine uptake in spuD, spuE and spuD spuE mutants side by side to reconcile the uptake and binding data.

📚 Additional Documentation

Notes

(spuD-notes.md)

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