spuD (PA0300, Q9I6J1) review notes

Periplasmic solute-binding protein of the PotD/PotF family (PIRNR019574;
Pfam SBP_bac_8; InterPro IPR001188), 367 aa with a 24-residue signal peptide.
Part of the spuDEFGH ABC transporter locus (spermidine and putrescine
utilization) together with its paralog SpuE (57% identical).

Literature (no deep-research provider available; own reading)

Lu et al. 2002 (full text cached, PMC135167): spuD and spuE mutants are both
defective in spermidine uptake PMID:12081945; the authors concluded that spermidine rather than
putrescine is the preferred ligand PMID:12081945. This is the
PseudoCAP IMP source for polyamine transport.
Wu et al. 2012 (abstract only; UniProt curated text from this paper): ITC and
crystal structures show SpuD is putrescine-preferential PMID:22300763. UniProt: "Binds putrescine with high affinity
(KD=3 nM), spermidine with relatively low affinity (KD=6.8 uM)." This is the
PseudoCAP IDA source for putrescine binding.
The two papers differ on SpuD's preferred ligand (uptake competition versus
direct binding). Direct binding favours putrescine; the uptake data show SpuD
also contributes to spermidine uptake. Both putrescine transport and
spermidine transport are therefore supported, and the general polyamine
transport rows are modified to both.

PseudoCAP IBA-seed assessment

Other seeds' experimental support queried live in QuickGO on 2026-11-05.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN001249912	GO:0015846 polyamine transport	4	78 (57 taxa)	GO:0015846, IMP, PMID:12081945 (PseudoCAP)	SOUND	Full text shows spuD mutant greatly reduced in spermidine uptake. Term is general but correct; node term suits a PotD/PotF clade.	SpuE Q9I6J0 (same paper), E. coli PotD P0AFK9 and PotF P31133 (experimental binding/transport)	Yes
PTN008624361	GO:0019810 putrescine binding	3	35 (10 taxa)	GO:0019810, IDA, PMID:22300763 (PseudoCAP)	SOUND	Abstract states SpuD is putrescine-preferential; UniProt curated KD 3 nM from the paper.	E. coli PotF P31133 (IDA PMID:8416922, IPI), PotD P0AFK9 (IDA PMID:1939142, PMID:8366082)	Yes

No PSEUDOCAP defect on spuD. The PTN008624361 putrescine-binding IBD is sound
for SpuD, PotF and PotD, but the node term does not suit the whole clade: it
propagates to SpuE, which does not bind putrescine. That node-level
GO_CENTRAL MISSING_NEGATION defect is recorded once, on the spuE GO:0019810 IBA
row (genes/PSEAE/spuE), where the direct evidence sits.

SpuD's own spermidine-binding IBA (from PTN008624361, seeded by SpuE and PotD)
is correct but low affinity (KD 6.8 uM), so it is kept as non-core. Open
question, not a defect: E. coli PotF (P31133) also receives the spermidine
binding IBA, although its curated function records only putrescine binding; I
have not read the PotF papers, so I raise this as a question only.