GEP4 (YHR100C, UniProt P38812) notes

Function

• Mitochondrial PGP phosphatase (EC 3.1.3.27), HAD superfamily, PGPP1/Gep4 family [UniProt:P38812].
• "we identify a novel phosphatase in the mitochondrial matrix space, Gep4, and demonstrate that it dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during CL biosynthesis" PMID:20485265.
• Functional conservation with bacterial PgpA: "Expression of a mitochondrially targeted variant of Escherichia coli phosphatase PgpA restores CL levels in Gep4-deficient cells" PMID:20485265.
• Location: inner membrane, peripheral, matrix side [UniProt:P38812, citing PMID:16823961, PMID:20485265].

Pathway context (module cdp_dag_phospholipid_synthesis)

• Step 7 of the module: PGP -> PG, between Pgs1 (PGP synthase) and Crd1 (CL synthase).
• YeastCyc reaction list does not attach GEP4 to a reaction, but GOA still carries RCA rows from SGD_PWY:PHOS-PWY: cytosol (wrong; default compartment) and phospholipid biosynthetic process (too general).
• Not present in the gocams/index.tsv YeastPathways models.

Review decisions

• Accept PGPase MF (IBA/IEA/IDA/IMP/IGI), CL and PG biosynthesis, mitochondrion / inner membrane / matrix / extrinsic component of MIM.
• REMOVE RCA cytosol (PHOS-PWY default compartment).
• MODIFY RCA phospholipid biosynthetic process -> GO:0006655; MODIFY deep-node IBA cytoplasm -> mitochondrial matrix.