TreeGrafter-generated GO annotations

Biochemical evidence that phaZ gene encodes a specific intracellular medium chain length polyhydroxyalkanoate depolymerase in Pseudomonas putida KT2442: characterization of a paradigmatic enzyme.

Purified PhaZ is an intracellular, granule-localized depolymerase specific for medium-chain-length PHA.

"We have demonstrated that PhaZ is an intracellular depolymerase that is located in PHA granules and that hydrolyzes specifically mcl-PHAs containing aliphatic and aromatic monomers."

file:PSEPK/phaZ/phaZ-uniprot.txt

UniProt entry Q88D24 for the KT2440 PHA depolymerase locus PP_5004

UniProt identifies Q88D24 as a poly(3-hydroxyalkanoate) depolymerase

"SubName: Full=Poly(3-hydroxyalkanoate) depolymerase"
UniProt maps the entry to KT2440 locus PP_5004

"GN OrderedLocusNames=PP_5004"
UniProt still exposes phaB as the primary gene name despite the depolymerase assignment

"GN Name=phaB"

file:PSEPK/phaZ/phaZ-notes.md

phaZ literature and ontology review notes

PhaZ is the intracellular granule-associated depolymerase that mobilizes stored medium-chain-length PHA in KT2440

"PhaZ is the intracellular granule-associated depolymerase that mobilizes stored medium-chain-length PHA in KT2440."
The most specific existing molecular-function term is GO:0050527

"The best current molecular-function term is GO:0050527 poly(3-hydroxyoctanoate) depolymerase activity rather than triacylglycerol lipase activity."
phaZ deletion increases and stabilizes PHA accumulation in vivo

"Deletion of phaZ increases and stabilizes PHA accumulation, showing that PP_5004 participates in poly(3-hydroxyalkanoate) metabolic process in vivo."
PhaZ is associated with PHA granules

"PhaZ is associated with polyhydroxyalkanoate granules rather than glycerolipid catabolism."

file:PSEPK/phaZ/phaZ-deep-research-falcon.md

Falcon (Edison) deep research report on PSEPK phaZ (PP_5004, Q88D24)

PP_5004 is the intracellular medium-chain-length PHA depolymerase PhaZ and a model enzyme for mcl-PHA mobilization in KT2440

"described as a model enzyme for intracellular mcl-PHA mobilization in *P. putida* KT2440"
The enzyme acts almost exclusively on mcl-PHAs, establishing substrate specificity beyond a generic lipase

"acting **almost exclusively on mcl-PHAs**"
The major hydrolysis product is 3-hydroxyoctanoate with minor 3-hydroxyhexanoate, matching GO:0050527

"major released products included **3-hydroxyoctanoate** with minor **3-hydroxyhexanoate**"
PhaZKT adopts an alpha/beta-hydrolase fold with a lid domain and catalytic triad Ser102-Asp221-His248

"A catalytic triad of **Ser102, Asp221, and His248** has been identified for the KT2440 intracellular depolymerase"
PhaZ is an intracellular, granule-associated enzyme acting on the PHA inclusion surface rather than a secreted depolymerase

"Evidence places PhaZ as an **intracellular, granule-associated** enzyme acting on the surface of PHA inclusions rather than a secreted extracellular depolymerase"
A PhaZ-deficient mutant fails to release 3-hydroxy fatty acids, providing direct genetic evidence for depolymerase function

"crude extracts from a **PhaZ-deficient mutant did not release 3-hydroxy fatty acids**, directly supporting depolymerase function"
PP_5004 functions in PHA mobilization, coupling polymer breakdown to carbon and energy homeostasis

"PP_5004 functions in **PHA mobilization**, coupling polymer breakdown to carbon and energy homeostasis"
phaZ deletion is a widely used strategy to strengthen intracellular PHA accumulation, consistent with its in vivo catabolic role

"phaZ deletion is often used to strengthen polymer accumulation"

file:PSEPK/phaZ/phaZ-deep-research-openscientist.md

OpenScientist deep research on PSEPK PhaZ

Confirms PP_5004 as the intracellular granule-associated mcl-PHA depolymerase rather than a generic glycerolipid lipase.

"PP_5004/Q88D24 should be annotated as **phaZ, the intracellular mcl-PHA depolymerase**."
Direct biochemical evidence supports mcl-PHA specificity and granule localization.

"specifically hydrolyzes mcl-PHAs containing aliphatic and aromatic monomers"

PMID:12534463

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440