hutF (PA5106, Q9HU77) notes

Identity

UniProt Q9HU77 (HUTF_PSEAE), 453 aa, Swiss-Prot reviewed. N-formimino-L-glutamate
deiminase (formimidoylglutamate deiminase, FIGLU iminohydrolase, EC 3.5.3.13).
Amidohydrolase superfamily, HutF family (InterPro IPR010252, NCBIfam TIGR02022,
Pfam PF22429 HutF_N; PANTHER PTHR11271:SF48). Five PDB structures (3MDU, 3MDW,
4RDV, 4RDW, 4RZB). Zinc ligands His56, His58, His232, Asp320; His269 general base.
In the PAO1 hut cluster; first enzyme of the five-step (deiminase) FIGLU branch,
followed by HutG (PA5091, N-formylglutamate amidohydrolase). The four-step branch
uses HutE (PA3175, FIGLU iminohydrolase/formiminoglutamase), outside the operon.

Biology (literature)

Functional assignment by enzymology:
PMID:16475788.
Two competing FIGLU routes coexist in P. aeruginosa
PMID:16475788.
Mechanism: Zn-dependent; mutation of Glu235, His269 or Asp320 drops activity
2-6 orders of magnitude
PMID:17128965.
Structure with inhibitors; single zinc in the active site
PMID:25559274.
Lessie and Neidhardt 1967 (the PseudoCAP IMP reference; abstract only here,
PMC276695 is a scanned article and could not be read, rechecked 2026-10-29)
reports measurements of histidase,
urocanase and "the capacity to degrade formiminoglutamate" (step IV) in
P. aeruginosa extracts, with urocanase-deficient, auxotrophic and repression
mutants PMID:4290562.
Two enzymes degrade FIGLU in PAO1 (HutF and HutE), so the step IV activity of a
1967 extract cannot be attributed to PA5106, and no hutF mutant appears in the
abstract. Because that second point rests on the abstract's silence, the
WRONG_REFERENCE defect is recorded as SUSPECTED rather than PROBABLE.

Consistency with completed reviews

genes/PSEAE/hutH: same 1967 paper judged SOUND for histidase (step I assayed
directly and only one functional HAL in PAO1); IMP should be IDA.
genes/PSEAE/hutI: same paper judged UNVERIFIABLE (step III not mentioned in the
abstract); its reference defects are likewise SUSPECTED.
hutF: step IV is mentioned, but only as a pooled extract activity that two
different PAO1 enzymes provide, and without a hutF mutant. The IMP cannot tie the
process to PA5106, so the verdict is UNVERIFIABLE, as for hutI. The claim itself is
correct and supported independently by PMID:16475788.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN000138516	GO:0006548 L-histidine catabolic process	1 (sole seed)	8 (8 taxa)	GO:0006548 L-histidine catabolic process, IMP, PMID:4290562 (PseudoCAP)	UNVERIFIABLE	The 1967 abstract measures a pooled FIGLU-degrading capacity (step IV) that HutF and HutE both provide, and describes no hutF mutant; as a pre-cloning study it cannot assign anything to PA5106. The claim is correct (HutF catalyses the first step of the deiminase FIGLU branch, PMID:16475788), so the IBD conclusion is sound for HutF-family leaves; the anchor should be PMID:16475788. Node breadth: three nematode leaves (C. elegans cpin-1 Q20166, C. briggsae, Pristionchus) lack the HutF family signatures (IPR010252, TIGR02022, HutF_N) that the bacterial leaves carry; their IBAs may be over-propagation.
PTN000138516	GO:0050416 formimidoylglutamate deiminase activity	1 (sole seed)	8 (8 taxa)	GO:0050416 formimidoylglutamate deiminase activity, IDA, PMID:16475788 (PseudoCAP); also UniProt EXP PMID:17128965	SOUND	Purified PA5106 deiminates FIGLU to N-formylglutamate and ammonia, with kinetics, metal dependence and mutagenesis (PMID:17128965) and structures (PMID:25559274). The term suits the bacterial HutF leaves (all TIGR02022). Same nematode caveat.

Decisions summary

ACCEPT: formimidoylglutamate deiminase activity (IBA, IEA, EXP, IDA), L-histidine
catabolic process (IBA, IMP), cytosol (IBA).
MODIFY to GO:0050416: hydrolase activity, hydrolase activity acting on C-N bonds
(descendants); deaminase activity (lateral: GO:0050416 is not placed under
GO:0019239 in GO).
Source defects: PSEUDOCAP WRONG_REFERENCE CHECK (PROBABLE) on the IMP row, re-key
to PMID:16475788; GO_CENTRAL CHECK (SUSPECTED) on PTN000138516 for re-anchoring the
BP IBD and for the nematode leaves (raised to CONFIRMED after the tree check below).

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. Step IV is measured only as crude-extract formiminoglutamate degradation (shared by HutF and HutE in PAO1) and there is no hutF mutant. The WRONG_REFERENCE defect on the IMP row is now CONFIRMED and the reference is marked MISCITED.

PANTHER tree check (2026-11-05)

Topology fetched with projects/PSEUDOCAP/panther_tree.py node PTN000138516 --depth 5 --leaves (PTHR11271). PTN000138516 is the family's LUCA SPECIATION root; every leaf is
subfamily PTHR11271:SF48.

Child node	Event / taxon	Leaves	Subfamilies	Verdict
PTN000884852	SPECIATION, Rhabditida-Chromadorea	3 (Q20166 cpin-1, A8Y0T4 cpin-1, A0A2A6BT36)	SF48:3	Over-propagated: no HutF signatures, no known histidine-degradation route
PTN000138520	SPECIATION, Eubacteria	5 (Q9HU77 hutF, Q9KZ77, Q89GV1, Q8PAA5 sdeB, Q9ZC76)	SF48:5	Correct anchor for both IBDs
PTN000138522	SPECIATION, Proteobacteria	4	SF48:4	Narrower option
PTN001681702	SPECIATION, Gammaproteobacteria	3 (Q8PAA5, Q9HU77, Q9ZC76)	SF48:3	Narrowest clade option; smallest clade holding Q9HU77 is its own leaf PTN002462020

The earlier concern is confirmed by the topology: the nematode leaves are not scattered
through the tree but form one clean child clade, so moving the GO:0006548 and GO:0050416
IBDs from PTN000138516 to PTN000138520 removes all three unsupported leaf IBAs without
touching any bacterial leaf. Note that within the bacterial clade only Q9HU77 is a
characterised formimidoylglutamate deiminase; the other four leaves are named
chlorohydrolase/hydrolase, which the tree cannot resolve further - that would need
enzymology on one of Q9KZ77, Q89GV1, Q8PAA5 or Q9ZC76. The P. aeruginosa leaf IBAs
reviewed here are unaffected (ACCEPT stands).