GLYK (D-glycerate 3-kinase; At1g80380) is the single-copy ATP-dependent glycerate kinase of Arabidopsis, which phosphorylates D-glycerate to 3-phospho-D-glycerate (EC 2.7.1.31). This is the concluding reaction of the photorespiratory C2 cycle: glycerate formed in peroxisomes from serine is imported into the chloroplast, and the 3-phosphoglycerate made by GLYK re-enters the Calvin-Benson cycle. GLYK has a P-loop NTPase fold related to phosphoribulokinase and uridine kinase but has neither of those activities, and it founded a glycerate kinase family, present in plants, fungi and some cyanobacteria, that is unrelated to the bacterial and animal glycerate kinases. The main isoform carries a chloroplast transit peptide and acts in the stroma. Knockout mutants lack leaf glycerate kinase activity, accumulate glycerate and cannot survive in normal air but grow in CO2-enriched air. Phytochrome-controlled use of an alternative promoter produces a shorter, cytoplasmic GLYK isoform in shade, which provides a cytosolic photorespiratory bypass that reduces photoinhibition under fluctuating light.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the phosphoribulokinase/uridine kinase domain (IPR006083) to ATP binding. Reason: True: GLYK uses ATP as the phosphoryl donor and has a P-loop (Walker A) motif at residues 215-222, and the enzyme binds to and is eluted from dye affinity columns with ATP during purification. ATP binding is part of the glycerate kinase mechanism rather than a separate function, so it is kept as non-core. Supporting Evidence: PMID:15980259 The protein contains an ATP/GTP binding site motif A (P-loop) domain typical for a family of nucleoside triphosphate hydrolases ( SSF52540 ; amino acids 215 to 222) PMID:22303256 The chloroplastic D-glycerate 3-kinase (GLYK, EC 2.7.1.31) catalyzes the phosphorylation of glycerate to 3-phosphoglycerate with ATP as a co-substrate. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | REMOVE | Summary: AtSubP sequence-based prediction of nuclear location. Reason: Unsupported computational prediction. GLYK's experimentally characterized isoforms are in the chloroplast (transit-peptide-containing isoform 1) and the cytoplasm (isoform 3, which lacks the transit peptide). None of the cited studies reports nuclear localization or a nuclear role, and the protein is a metabolic enzyme of the chloroplast C2-cycle step. The AtSubP prediction contradicts the experimental localization. Supporting Evidence: PMID:29129375 For instance, shade-grown plants accumulate a cytoplasmic isoform of glycerate kinase (GLYK), an essential photorespiration enzyme that was previously thought to localize exclusively to the chloroplast. |
| GO:0005737 cytoplasm | EXP PMID:29129375 Light Controls Protein Localization through Phytochrome-Medi... | KEEP AS NON CORE | Summary: Under shade, phytochrome-regulated alternative promoter selection produces an N-terminally truncated GLYK isoform without the transit peptide (UniProt isoform 3) that accumulates in the cytoplasm. Reason: Experimentally supported (abstract-only in cache; UniProt records the cytoplasmic location of isoform 3 with experimental evidence from this paper). The cytoplasmic isoform is a conditional bypass of the main stromal reaction, so the location is kept as non-core. The abstract says "cytoplasmic", so no more specific term (for example cytosol) is proposed without the full text. Supporting Evidence: PMID:29129375 Cytoplasmic GLYK constitutes a photorespiratory bypass that alleviates fluctuating light-induced photoinhibition. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference of cytoplasmic activity at a deep PRK/uridine-kinase family node (PTN000032154), whose experimental members include uridine kinases, phosphoribulokinase and At1g80380 (GLYK) itself. Reason: The claim holds for GLYK: GO places the chloroplast within the cytoplasm, and the shade isoform is cytoplasmic. GLYK's own experimental cytoplasm annotation is among the node's donor evidence, which is expected for an IBA. The specific, core location of the main isoform is chloroplast stroma, and the cytoplasmic pool is conditional, so this is kept as non-core rather than accepted. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000032154 · PTN000032154 SUPPORTS TRANSFER Deep node spanning uridine kinases and PRK-like kinases; the target's own experimental cytoplasm annotation (shade isoform) is among the descendants, and the main stromal isoform is also within GO cytoplasm. Supporting Evidence: PMID:29129375 Cytoplasmic GLYK constitutes a photorespiratory bypass that alleviates fluctuating light-induced photoinhibition. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular-location mapping from the curated cytoplasmic location of isoform 3. Reason: Correct mapping of an experimentally supported, conditional isoform location; see the EXP row. Supporting Evidence: PMID:29129375 Through this mechanism, protein isoforms with different N termini are produced that display light-dependent differences in localization. |
| GO:0005739 mitochondrion | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: Assignment from large-scale size-exclusion profiling of detergent-solubilized membrane-associated leaf proteins. Reason: No targeted study places GLYK in mitochondria. Its N-terminal sequence is a plastid-targeting peptide, the enzyme purifies from leaves as a soluble protein, and the dedicated localization study found chloroplast and cytoplasmic isoforms. The profiling study combined plastid and mitochondria in its localization classes and relied on SUBAcon predictions for organelle calls, so a single high-throughput detection is more likely a fractionation artefact than a mitochondrial pool. The study is not refuted, but the annotation overstates what is known. Supporting Evidence: PMID:28887381 Protein coverage of proteins with a known and single localization based on the SUBAcon database: endomembrane system (Golgi, endoplasmic reticulum, plasma membrane, nucleus, peroxisome), plastid/mitochondria, or cytosolic/secreted. PMID:15980259 the protein sequence includes a plastid-targeting sequence with three potential cleavage sites (after amino acids 63, 107, and 118) |
| GO:0008887 glycerate kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference at the plant/fungal GLYK node (PTN002469695), seeded by the experimental annotation of At1g80380. Reason: Correct and core. Using GLYK as the seed for its own clade is expected. The inference also fits the experimentally confirmed glycerate kinase activity of the yeast homolog, so the activity is inherited across the GLYK family and not limited to plants. Supporting Evidence: PMID:15980259 As shown in Table 2 , the yeast enzyme is a GLYK and does not accept other substrates, such as ribulose 5-phosphate or uridine. |
| GO:0008887 glycerate kinase activity | IDA PMID:15980259 D-GLYCERATE 3-KINASE, the last unknown enzyme in the photore... | ACCEPT | Summary: GLYK was purified from Arabidopsis leaves by activity, identified by MS as the At1g80380 product, and recombinant protein made in E. coli has glycerate kinase activity without PRK or uridine kinase activity. Reason: Direct biochemical evidence, together with loss of all leaf activity in two independent knockouts. Core molecular function. Supporting Evidence: PMID:15980259 After induction, the recombinant bacteria showed substantially greater GLYK activity in comparison with control cells bearing the empty vector ( Figure 4 ). PMID:15980259 These data demonstrate that At GLYK represents the only significant source of GLYK activity in Arabidopsis. |
| GO:0008887 glycerate kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation from the UniProt catalytic activity (Rhea:23516, EC 2.7.1.31), itself backed by experimental evidence. Reason: Correct mapping, consistent with the IDA and IBA rows. Core molecular function. Supporting Evidence: PMID:15980259 The exclusive catalytic properties of the gene product were confirmed after heterologous expression in Escherichia coli . |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | ACCEPT | Summary: Detected in a large-scale MS analysis of purified Arabidopsis chloroplasts. Reason: Consistent with the transit peptide and the chloroplastic location of the final C2-cycle step; stroma is the precise compartment. Supporting Evidence: PMID:18431481 we present a large scale analysis by nanoLC-Q-TOF and nanoLC-LTQ-Orbitrap mass spectrometry (MS) of ten independent chloroplast preparations from Arabidopsis thaliana which unambiguously identified 1325 proteins |
| GO:0009507 chloroplast | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | ACCEPT | Summary: Chloroplast assignment from a leaf protein-complex profiling study. Reason: The gene-level data are in supplementary tables not in the cache, but the chloroplast location of the main GLYK isoform is independently established. Supporting Evidence: PMID:22303256 The chloroplastic D-glycerate 3-kinase (GLYK, EC 2.7.1.31) catalyzes the phosphorylation of glycerate to 3-phosphoglycerate with ATP as a co-substrate. |
| GO:0009507 chloroplast | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of chloroplast activity at a plant GLYK node (PTN007430558), seeded by GLYK's own experimental localization. Reason: Correct; the plastid-targeted GLYK of land plants acts in the chloroplast. The node placement is restricted to the plant clade, which is appropriate because the fungal homologs are not plastid-targeted. Supporting Evidence: PMID:15980259 the protein sequence includes a plastid-targeting sequence with three potential cleavage sites (after amino acids 63, 107, and 118) |
| GO:0009507 chloroplast | IDA Q944I4-1 PMID:29129375 Light Controls Protein Localization through Phytochrome-Medi... | ACCEPT | Summary: Localization of the full-length, transit-peptide-containing isoform (isoform 1, expressed in the light) to the chloroplast. Reason: Direct localization evidence for the main isoform (UniProt records this with experimental evidence from this paper). Core location. Supporting Evidence: PMID:29129375 Through this mechanism, protein isoforms with different N termini are produced that display light-dependent differences in localization. |
| GO:0009507 chloroplast | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (Plastid, chloroplast; isoform 1). Reason: Correct. Supporting Evidence: PMID:15980259 the protein sequence includes a plastid-targeting sequence with three potential cleavage sites (after amino acids 63, 107, and 118) |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP sequence-based prediction of chloroplast location. Reason: Consistent with experimental localization of isoform 1. Supporting Evidence: PMID:15980259 the protein sequence includes a plastid-targeting sequence with three potential cleavage sites (after amino acids 63, 107, and 118) |
| GO:0009507 chloroplast | ISS PMID:15980259 D-GLYCERATE 3-KINASE, the last unknown enzyme in the photore... | ACCEPT | Summary: Chloroplast location inferred in the GLYK identification paper from TargetP and ChloroP prediction and comparison with the rice homolog's transit peptide. Reason: Correct and later confirmed experimentally for isoform 1. Supporting Evidence: PMID:15980259 Sequence comparison with the homologous rice protein ( BAD73764 ; Sasaki et al., 2002 ) points to a length most likely of 118 amino acids for the plastid-targeting peptide. |
| GO:0009570 chloroplast stroma | HDA PMID:18633119 Quantitative proteomics of a chloroplast SRP54 sorting mutan... | ACCEPT | Summary: Detected in quantitative chloroplast proteomics of a cpSRP54 mutant and wild type. Reason: Stroma is the expected compartment for a soluble, transit-peptide-containing Calvin-cycle-linked kinase that returns 3-phosphoglycerate to the stroma. Core location. Supporting Evidence: PMID:18633119 A differential response between young and mature leaves was also found in carbon metabolism, with an up-regulation of the Calvin cycle and the photorespiratory pathway in peroxisomes and mitochondria in young leaves but not in old leaves. |
| GO:0009570 chloroplast stroma | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | ACCEPT | Summary: Stromal assignment in the AT_CHLORO subplastidial proteome database. Reason: Subfractionation proteomics agrees with the expected stromal location. Core location. Supporting Evidence: PMID:20061580 We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). |
| GO:0009853 photorespiration | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of involvement in photorespiration at the GLYK node (PTN002469695), seeded by At1g80380. Reason: Correct for GLYK, which catalyses the final step of the C2 cycle. The node also includes fungal homologs, which do not photorespire, so the process may be over-propagated to those members, but that does not affect this target. Supporting Evidence: PMID:15980259 Arabidopsis T-DNA insertional knockout mutants show no GLYK activity and are not viable in normal air; however, they grow under elevated CO 2 , providing direct evidence of the obligatory nature of the ultimate step of the C 2 cycle. |
| GO:0009853 photorespiration | IMP PMID:15980259 D-GLYCERATE 3-KINASE, the last unknown enzyme in the photore... | ACCEPT | Summary: Two independent glyk knockouts arrest at the cotyledon stage in air, grow in elevated CO2, lack leaf glycerate kinase activity and accumulate glycerate. Reason: GLYK performs the final C2-cycle reaction, converting glycerate to 3-phosphoglycerate, so it does part of the work of photorespiration. Core process. Supporting Evidence: PMID:15980259 Arabidopsis T-DNA insertional knockout mutants show no GLYK activity and are not viable in normal air; however, they grow under elevated CO 2 , providing direct evidence of the obligatory nature of the ultimate step of the C 2 cycle. PMID:22303256 Knock-out of this gene results in a conditionally lethal photorespiratory phenotype. |
| GO:0009854 oxidative photosynthetic carbon pathway | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway mapping (photorespiration; 3-phospho-D-glycerate from glycine, step 4/4) to the C2 pathway term. Reason: GO:0009854 is the C2 carbon pathway (two 2-phosphoglycolate to one 3-phosphoglycerate plus CO2) and is part of photorespiration. GLYK catalyses its final step, so the more specific term is correct. The core function nonetheless uses the broader GO:0009853 photorespiration, so that every C2-cycle step and ammonia refixation share one process term (see modules/photorespiration_c2_cycle.yaml). Supporting Evidence: PMID:15980259 They also show that the replenishment of the C 3 cycle with salvaged C 2 cycle carbon occurs exclusively via glycerate and 3PGA, thus providing direct and conclusive evidence on the nature of the final enzymatic step of the C 2 cycle. |
| GO:0009941 chloroplast envelope | HDA PMID:12938931 Proteomic study of the Arabidopsis thaliana chloroplastic en... | MARK AS OVER ANNOTATED | Summary: Detected in a MudPIT/GeLC-MS proteome of chloroplast "mixed" envelope membranes. Reason: GLYK is a soluble stromal enzyme: it purifies from leaf homogenates by ammonium sulfate precipitation and chromatography without detergent, and the subplastidial proteome assigns it to the stroma. Envelope preparations commonly contain soluble stromal proteins, and envelope proteomics studies note this. The detection is not wrong as data, but "located in chloroplast envelope" overstates it. The cached record is abstract-only, so a peripheral envelope association cannot be excluded. Supporting Evidence: PMID:12766230 Some soluble proteins, like proteases, proteins involved in carbon metabolism, or proteins involved in responses to oxidative stress, were associated with envelope membranes. PMID:15980259 The protein fraction obtained by (NH 4 ) 2 SO 4 precipitation (25 to 75%) was dissolved 0.1 M sodium phosphate buffer |
| GO:0016301 kinase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the PRK/uridine kinase domain to generic kinase activity. Reason: Correct but general. The specific activity, already carried by GLYK (IDA, IBA, IEA), is glycerate kinase activity; the purified enzyme lacks the phosphoribulokinase and uridine kinase activities suggested by the domain match. Proposed replacements: glycerate kinase activity Supporting Evidence: PMID:15980259 We therefore tested whether purified Arabidopsis GLYK exhibits PRK or uridine kinase (UK) activity and found that neither of the two reactions is catalyzed ( Table 2 ). |
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Download this section (compressed HTML)Q: Where does glycerate phosphorylated by the cytoplasmic GLYK isoform come from and go, and how does a cytosolic 3-phosphoglycerate pool from the bypass re-enter the chloroplast (for example through the triose phosphate/phosphate translocator)?
Q: What is the metabolic role of GLYK homologs in fungi and cyanobacteria, which do not run a plant-type C2 cycle?
Experiment: Determine the structure of Arabidopsis GLYK with glycerate and ATP analogs to define how the PRK/uridine-kinase-like P-loop fold was adapted to glycerate, and test the conserved GLYK-1 and GLYK-2 motifs by mutagenesis.
Type: structural biology
Experiment: Complement glyk mutants separately with the plastid (isoform 1) and cytoplasmic (isoform 3) forms and compare growth and photoinhibition under constant and fluctuating light to quantify the contribution of each pool.
Type: genetic complementation
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