hutH (PA5098, Q9HU85) notes

Identity

UniProt Q9HU85 (HUTH_PSEAE), 509 aa, Swiss-Prot reviewed, PE 3. The functional
annotation is from HAMAP MF_00229
[file:PSEAE/hutH/hutH-uniprot.txt "Reaction=L-histidine = trans-urocanate + NH4(+)"].
PAL/histidase (aromatic amino acid ammonia-lyase) family, PANTHER PTHR10362, TIGR01225
hutH, PROSITE PS00488 (PAL_HISTIDASE active-site signature).
The MIO cofactor-forming Ala-Ser-Gly is at 142-144 (UniProt CROSSLNK 142..144; MOD_RES
Ser143 2,3-didehydroalanine).
In the PAO1 hut cluster, between the histidine transporter HutTh (PA5097) and the
urocanate transporter HutTu (PA5099) PMID:41641996.

Paralog PA5093 (Q9HU90)

The PAO1 hut locus also encodes a second HutH-like protein, PA5093 (Q9HU90, unreviewed,
"Probable histidine/phenylalanine ammonia-lyase"). It is the counterpart of the
P. fluorescens SBW25 HutH1, which lacks the active-site residues and is not a
functional histidase
PMID:17717196;
PMID:17717196.
My check (file:PSEAE/hutH/hutH-bioinformatics/RESULTS.md) found that PA5098 has
Ala-Ser-Gly at 142-144 and is 82% identical to the structurally characterised P. putida
HutH (P21310). PA5093 has no ASG tripeptide and is about 40% identical to either
histidase. So PA5098 is the PAO1 histidase (the HutH2 type), and PA5093 is the
MIO-less HutH1 type.
PANTHER places PA5093 and PA5098 as a PAO1-specific duplication (PTN002233699) under
PTN000796665. PA5093 therefore inherits IBAs for histidine ammonia-lyase activity and
L-histidine catabolic process (UniProt Q9HU90 DR GO lines show both as IBA:GO_Central),
almost certainly wrongly. This is a candidate for a NOT annotation at the PA5093 leaf
(PTN002233700).

Biology (literature)

Histidase eliminates ammonia from L-histidine to give trans-urocanate, step I of the hut
pathway. The MIO electrophile is formed autocatalytically from Ala-Ser-Gly
PMID:10220322.
P. aeruginosa histidase is induced by urocanate and subject to catabolite and nitrogen
control PMID:4290562;
PMID:4990767.
The first three steps of the pathway are catalysed by HutH, HutU and HutI
PMID:16475788.

PMID:4290562 (Lessie & Neidhardt 1967), the PseudoCAP seed reference

Abstract only. The scanned PMC276695 full text could not be retrieved: the MCP returned
empty and the PDF is behind a browser challenge.
The paper measures histidase directly. It partially purifies the P. aeruginosa enzyme,
estimates its molecular weight and Km, and describes sigmoid kinetics
PMID:4290562;
PMID:4290562.
210 kDa matches a homotetramer of the 53.8 kDa PA5098 subunit (about 215 kDa); HAL is
tetrameric (PMID:10220322).
The paper predates genes, so the link from this activity to PA5098 is an inference.
The inference is secure: PA5098 is the only MIO-containing PAL/histidase-family protein
in PAO1, and PA5093 lacks the motif. The activity claim is therefore sound. The
evidence is a direct assay of the wild-type enzyme, so IDA would fit better than
IMP. The mutants in the paper are urocanase-deficient and regulatory mutants,
not hutH mutants.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN000796617	GO:0016841 ammonia-lyase activity	9	269 (42 taxa)	GO:0004397 histidine ammonia-lyase activity, IMP, PMID:4290562 (PseudoCAP)	SOUND	Histidase activity of the P. aeruginosa enzyme was directly assayed (partially purified; Km, MW). The generic ammonia-lyase term at the MIO-lyase superfamily root is appropriate. The other 8 seeds (plant PAL, mammalian HAL) support it independently. The evidence code should be IDA, not IMP; that does not affect the IBD.
PTN000796665	GO:0004397 histidine ammonia-lyase activity	1 (sole seed)	21 (16 taxa)	GO:0004397 histidine ammonia-lyase activity, IMP, PMID:4290562 (PseudoCAP)	SOUND	The seed is sound for PA5098 (direct assay; PA5098 is the only MIO-motif HAL in PAO1). The node term suits a bacterial histidase clade. One problem: the node includes PA5093, a PAO1 in-paralog that lacks the Ala-Ser-Gly MIO motif (the HutH1 type, shown non-functional in P. fluorescens SBW25), so PA5093's IBA is an over-propagation. PAINT should add a NOT at PTN002233700.
PTN000796665	GO:0006548 L-histidine catabolic process	1 (sole seed)	21 (16 taxa)	GO:0006548 L-histidine catabolic process, IMP, PMID:4290562 (PseudoCAP)	SOUND	Histidase catalyses step I of histidine degradation, and the paper treats it as the first enzyme of the inducible pathway. Genetic confirmation of HutH-type genes is in SBW25 (PMID:17717196). The same PA5093 caveat applies.

Decisions summary

ACCEPT: histidine ammonia-lyase activity (IBA, IEA, IMP), L-histidine catabolic process
(IBA, IEA, IMP), cytoplasm (IEA).
MODIFY to GO:0004397: catalytic activity (IEA), ammonia-lyase activity (IEA).
Source defects: PSEUDOCAP WRONG_EVIDENCE_CODE (IMP should be IDA; CHECK, PROBABLE) on the
MF IMP row. GO_CENTRAL MISSING_NEGATION for PA5093 at PTN002233700 (PROBABLE), recorded
on the IBA MF row because PA5093 has no review in this repository.

Full-text check of PMID:4290562 (2026-11-05)

The full text of Lessie and Neidhardt 1967 (J Bacteriol 93, 1800-1810) was supplied by the user and read. Its mutants are a urocanase-deficient strain, a histidine auxotroph and regulatory mutants with altered repression. Histidase is assayed directly, partly purified and characterised (about 210 kDa; Km for histidine 1.8 to 2 mM); no histidase-deficient structural mutant is described. The IMP-to-IDA WRONG_EVIDENCE_CODE defect is now CONFIRMED.

PANTHER tree check (2026-11-05)

The node's family could not be resolved automatically (none of its IBD seeds has a
PANTHER cross-reference in UniProt), so the family was taken from this gene's own UniProt
record (DR PANTHER; PTHR10362; HISTIDINE AMMONIA-LYASE) and passed as
--family PTHR10362. PTN002233700 is in that family, so the node is correctly placed.

Ancestor path of the PA5093 leaf (panther_tree.py, PTHR10362):

Node	Event / taxon	Leaves	Note
PTN000796617	SPECIATION, LUCA	424	family root
PTN000796665	SPECIATION, Eubacteria	21	the node carrying the GO:0004397 / GO:0006548 IBDs seeded by PA5098
PTN000796672	SPECIATION, Proteobacteria	11
PTN001621799	SPECIATION, Gammaproteobacteria	10
PTN002233699	DUPLICATION	2	PA5093 + hutH, both P. aeruginosa, both PTHR10362:SF7
PTN002233700	LEAF, P. aeruginosa	1 (Q9HU90 PA5093)	target for the NOT annotations
PTN002233701	LEAF, P. aeruginosa	1 (Q9HU85 hutH)	the seed gene

The topology confirms the defect and removes its one open alternative. PTN002233699 is a
terminal, P. aeruginosa-specific DUPLICATION whose only two members are hutH and PA5093,
so the IBAs on PA5093 are inherited directly from its own in-paralog, and there is no
HutH1-type clade in PTHR10362 that a node-level NOT could cover. The NOT annotations for
GO:0004397 and GO:0006548 belong at the leaf PTN002233700. Confidence raised PROBABLE ->
CONFIRMED. Nothing in this review's own annotation actions changes: PA5098 is the
functional histidase and its rows stand.