GLYK (At1g80380; UniProtKB:Q944I4) 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 in publications/
and the UniProt record (GLYK-uniprot.txt). No -deep-research-*.md file exists for
this gene.

Identity

• UniProt Q944I4, "D-glycerate 3-kinase, chloroplastic"; 456 aa precursor; predicted
  transit peptide; P-loop NTPase fold with a PRK/URK-like domain (InterPro IPR006083,
  Pfam PF00485); UniProt places it in the "GLYK kinase family"; PANTHER PTHR10285
  (uridine kinase family). Three isoforms in UniProt; isoform 3 lacks residues 1-92 (no
  transit peptide).
• Structurally unrelated to bacterial and animal glycerate kinases PMID:15980259.

Molecular function: D-glycerate 3-kinase (EC 2.7.1.31)

• Purified from leaves and identified by MS PMID:15980259.
• Recombinant protein active; substrate specificity tested PMID:15980259 and neither PRK nor uridine kinase activity PMID:15980259.
• The only GLYK activity source in leaves PMID:15980259.
• UniProt catalytic activity: (R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H+
  (Rhea:23516; ECO:0000269 PubMed:15980259). ATP-binding P-loop at 215-222 (ECO:0000255).
• A 2024 study on thermostability engineering of GLYK (PMID:39550762, not cached) reports
  Km values for ATP and glycerate for AtGLYK; not used here.

Biological process: photorespiration (final step of the C2 cycle)

• PMID:15980259
• Glycerate accumulates ~200-fold in the mutants PMID:15980259.
• Review PMID:22303256 and PMID:22303256. Unlike most photorespiratory genes, GLYK is not
  light induced PMID:22303256.
• GO:0009854 "oxidative photosynthetic carbon pathway" (C2 pathway: 2-phosphoglycolate to
  3-phosphoglycerate) is part_of GO:0009853 photorespiration (verified via OLS
  hierarchicalParents); both are correct for GLYK.

Location: chloroplast stroma (isoform 1); cytoplasm (isoform 3, shade)

• Plastid-targeting sequence PMID:15980259. Stroma: HDA (PMID:18633119, PMID:20061580); the enzyme purifies as a soluble
  protein from leaf extracts (no detergent in the purification protocol).
• Alternative promoter selection controlled by phytochrome gives a cytoplasmic isoform in
  shade PMID:29129375 that functions as a bypass
  PMID:29129375. Abstract-only in cache; UniProt records
  isoform 1 chloroplast (light) and isoform 3 cytoplasm (dark), ECO:0000269 PubMed:29129375.
• HDA mitochondrion (PMID:28887381) and envelope (PMID:12938931) and ISM nucleus are not
  supported by targeted studies; judged as likely contaminants or predictions.

Family

• GLYK homologs in fungi and some cyanobacteria; yeast homolog is also a glycerate kinase
  PMID:15980259.