GLDP2 (At2g26080, UniProt O80988) - curation notes

Deep research could not be run in this environment (no provider API keys). These notes
are a manual literature summary built only from cached publications (publications/PMID_*.md)
and the UniProt record (GLDP2-uniprot.txt). No -deep-research-*.md file exists for this gene.

Identity

• Glycine dehydrogenase (decarboxylating) 2, mitochondrial; second P protein of the glycine
  decarboxylase complex (GDC). EC 1.4.4.2, PLP-dependent, GcvP family (PANTHER PTHR11773:SF1).
• Paralog of GLDP1 (At4g33010); 91% identical precursors PMID:17496108.

Molecular function

• P-protein reaction (glycine decarboxylation with transfer of the aminomethyl group to lipoyl-H
  protein) PMID:22303256.
• GLDP2 is catalytically active but weaker than GLDP1 PMID:33506579; GLDP2 (not GLDP1) is targeted for degradation by the F-box protein
  InLYP1 PMID:33506579 (abstract only).

Complex and location

• Part of the leaf GDC at ~1/4 the level of GLDP1 PMID:32311173.
• Mitochondrion (UniProt, experimental PubMed:14671022); matrix ATP-affinity proteome
  [PMID:17137349, abstract only]; detected in mitochondria in the ICP55 study, with lower abundance in
  icp55 PMID:25862457.
• Vacuole, cytosol, chloroplast and chloroplast envelope HDA rows are bulk-proteomics detections that
  conflict with the mitochondrial transit peptide and matrix localization; treated as contaminants.

Biological role

• Functionally redundant with GLDP1 PMID:17496108. GLDP2 transcripts
  dominate in roots PMID:17496108. gldp1 gldp2 double mutant is seedling lethal even
  at high CO2 PMID:17496108,
  showing GDC is required for one-carbon metabolism as well as photorespiration.
• Note: unlike GLDP1, GLDP2 has no IMP annotation in GOA, although the same paper characterised
  gldp2 alleles and the double mutant.

Annotation decisions (summary)

• Core: GO:0004375 (MF), GO:0019464 (BP), mitochondrion. NEW: GO:0005960 glycine cleavage complex
  (PMID:32311173) and GO:0009853 photorespiration (PMID:17496108; same comparator check as GLDP1).
• ATP binding (HDA, ATP-affinity capture): over-annotated; GcvP has no nucleotide-binding domain
  and capture of abundant matrix proteins can be indirect.
• mRNA binding (RNA interactome capture): over-annotated.