Photorespiratory C2 cycle (2-phosphoglycolate to 3-phosphoglycerate) in land plants

The photorespiratory C2 cycle salvages 2-phosphoglycolate, the two-carbon product of the oxygenase reaction of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), and returns three of every four carbons to the Calvin-Benson cycle as 3-phosphoglycerate. The pathway runs through three organelles. In the chloroplast, 2-phosphoglycolate phosphatase dephosphorylates 2-phosphoglycolate to glycolate, which the inner-envelope glycolate/glycerate translocator exports. In the peroxisome, glycolate oxidase oxidizes glycolate to glyoxylate with O2, generating H2O2 that catalase removes, and glyoxylate is transaminated to glycine, mainly by glutamate:glyoxylate aminotransferase. In the mitochondrion, the glycine decarboxylase (glycine cleavage) complex converts one glycine to CO2, NH3 and 5,10-methylenetetrahydrofolate, and serine hydroxymethyltransferase uses the one-carbon unit and a second glycine to make serine. Back in the peroxisome, serine:glyoxylate aminotransferase converts serine to hydroxypyruvate while aminating a second glyoxylate, and hydroxypyruvate reductase reduces hydroxypyruvate to glycerate; a cytosolic hydroxypyruvate reductase provides a bypass. In the chloroplast, D-glycerate 3-kinase phosphorylates glycerate to 3-phosphoglycerate. The NH3 released in the mitochondrion is refixed in the chloroplast by plastidic glutamine synthetase and ferredoxin-dependent glutamate synthase, which return the glutamate used by the glyoxylate transamination. Loss of most core steps makes plants unable to grow in normal air but viable at elevated CO2. The Rubisco oxygenase reaction itself, the Calvin-Benson cycle, the transporters for the other intermediates (largely unidentified), supply of NADH to the peroxisome, alternative glycolate routes in algae and cyanobacteria, and C4 or CAM carbon-concentrating mechanisms are outside this module's boundary.

Arabidopsis thaliana proteins are used as representative members; the module itself is phrased for land plants. Every Arabidopsis representative, and the glycine decarboxylase subunits named in step 5 (GLDP1, GLDP2, GDCH, GDCST, mtLPD1, mtLPD2), has a gene review under genes/ARATH/, and each annoton molecular function matches a core function of the corresponding review. Photorespiration (GO:0009853) is the process term for every step except catalase, matching the GOA experimental rows and the gene reviews' core functions; GO:0009854 oxidative photosynthetic carbon pathway, which is part_of it, is accepted in the reviews where GOA carries it but is not used here, so that the carbon-cycle steps and ammonia refixation share one term. Catalase removes the H2O2 that glycolate oxidase produces but does no carbon chemistry of the cycle, and no catalase in GO carries photorespiration, so its annoton uses GO:0042744 hydrogen peroxide catabolic process. GO:0008891 glycolate oxidase activity is obsolete, so the glycolate oxidase step uses its parent GO:0003973 (S)-2-hydroxy-acid oxidase activity, which is the term UniProt assigns to GLO1 and GLO2. The glycine decarboxylase step reuses the glycine_cleavage_system module by reference; its Arabidopsis subunits are named in that node's description. No PANTHER family ids are asserted: they have not been checked against interpro/panther/panther.obo for these families. Paralogs not listed (GLU2, the other PGLP, GOX and CAT genes) are not modelled. No production GO-CAM in gocams/index.tsv contains these Arabidopsis gene products.