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The gene SPAC20G4.05c in Schizosaccharomyces pombe (strain 972 / ATCC 24843) encodes a mitochondrial protein adenylyltransferase of the SELO family (UniProt: O13890). This protein is the fission yeast ortholog of selenoprotein O (SelO/SELENOO), a highly conserved pseudokinase found across all domains of life. While direct literature on the S. pombe SelO is limited, extensive functional characterization has been performed on orthologs in Escherichia coli, Saccharomyces cerevisiae (where the ortholog is known as Fmp40), Pseudomonas syringae, and Homo sapiens, providing robust functional inference for the S. pombe protein. The S. pombe protein contains the hallmark SelO domain (IPR003846/PF02696) and belongs to the SELO protein family, consistent with its annotation.
SelO is a pseudokinase that catalyzes protein AMPylation — the covalent transfer of adenosine monophosphate (AMP) from ATP to serine, threonine, and tyrosine residues on protein substrates via a phosphodiester bond (sreelatha2018proteinampylationby pages 1-3, sreelatha2018proteinampylationby pages 4-7). This post-translational modification is distinct from conventional kinase-mediated phosphorylation. Rather than transferring the γ-phosphate of ATP (as canonical kinases do), SelO transfers the α-phosphate group together with the adenosine moiety, resulting in AMP attachment to the target protein with a characteristic mass shift of 329 Da (sreelatha2018proteinampylationby pages 4-7). The enzyme requires Mg²⁺ and Ca²⁺ as essential metal cofactors and utilizes ATP as its preferred co-substrate with a Km of approximately 2.0 mM (sreelatha2018proteinampylationby pages 4-7).
The structural basis for SelO's adenylyltransferase activity was elucidated through X-ray crystallography of the P. syringae ortholog, solved at 2.27 Å resolution (sreelatha2018proteinampylationby pages 21-22). SelO adopts a canonical protein kinase-like fold with 12 β-strands and 22 α-helices, but with a critical difference: ATP binds in a "flipped" or inverted orientation in the active site compared to canonical kinases (pon2023redefiningpseudokinasesa pages 3-4, sreelatha2018proteinampylationby pages 3-4). In this unusual configuration, the γ-phosphate is buried between the N- and C-lobes with the adenosine moiety facing outward, while the α-, β-, and γ-phosphates occupy positions corresponding to the typical γ-, β-, and α-phosphates of standard protein kinases (sreelatha2018proteinampylationby pages 3-4). This inversion positions the α-phosphate for transfer to protein substrates rather than the γ-phosphate (sreelatha2018proteinampylationby pages 3-4). Key active site residues include K113, E136, R176, and R183, which coordinate nucleotide binding (sreelatha2018proteinampylationby pages 4-7). SelO lacks the canonical catalytic aspartate of protein kinases but contains a migrated aspartate (D252) that approaches the substrate from the opposite side compared to typical kinases like PKA (sreelatha2018proteinampylationby pages 10-11). The C-terminal domains (CTD1 and CTD2) play regulatory roles analogous to cyclin activation of CDK2, positioning the αC helix and bridging the activation loop to achieve the active conformation (sreelatha2018proteinampylationby pages 32-33).
SelO AMPylates multiple mitochondrial proteins, with particular specificity for those involved in redox homeostasis and cellular metabolism. The following table summarizes experimentally characterized substrates across organisms:
| Substrate | Organism | AMPylation Site | Biological Function | Reference |
|---|---|---|---|---|
| Glutaredoxin A (GrxA/Grx) | Escherichia coli; conserved mechanism also supported in yeast | Tyr13 | Thioredoxin-like redoxin that catalyzes deglutathionylation; SelO-mediated AMPylation inhibits Grx activity and helps maintain protein S-glutathionylation during oxidative stress | (sreelatha2018proteinampylationby pages 7-8, sreelatha2018proteinampylationby pages 10-11) |
| sucA (α-ketoglutarate dehydrogenase E1 component homolog) | Bacteria | Thr405 | Oxidative metabolism/TCA-linked enzyme component; identified as a SelO substrate connected to redox homeostasis and oxidative phosphorylation | (sreelatha2018proteinampylationby pages 7-8, chatterjee2021ficandnonfic pages 6-6) |
| Trx3 (thioredoxin 3) | Saccharomyces cerevisiae | Thr66 | Mitochondrial thioredoxin/redoxin; AMPylation at T66 is important for proper protein level and maturation during mitochondrial import | (panja2024profilingofyeast pages 1-3, panja2024profilingofyeast pages 3-5) |
| Prx1 (peroxiredoxin) | Saccharomyces cerevisiae | Not specified in available evidence | Mitochondrial peroxiredoxin involved in peroxide detoxification/redox homeostasis; identified as an in vivo Fmp40/SelO-interacting substrate | (panja2024profilingofyeast pages 1-3) |
| Grx2 (glutaredoxin 2) | Saccharomyces cerevisiae | Not specified in available evidence | Mitochondrial glutaredoxin involved in redox regulation/glutathione chemistry; reported as one of the few known yeast Fmp40/SelO substrates prior to global AMPylome profiling | (panja2024profilingofyeast pages 13-15) |
| Glutamate dehydrogenase | Mammals (SelO/SELENOO study) | Not specified in available evidence | Mitochondrial metabolic enzyme; SelO substrate implicated in regulation of metabolic flux and linked to TCA/2-oxocarboxylic acid metabolism | (gonzalez2025arepurposedamp pages 6-7, gonzalez2025arepurposedamp pages 1-2) |
| Pyruvate dehydrogenase | Mammals (SelO/SELENOO study) | Not specified in available evidence | Central mitochondrial enzyme linking glycolysis to the TCA cycle; identified as a SelO substrate involved in metabolic regulation by AMPylation | (gonzalez2025arepurposedamp pages 1-2) |
Table: This table summarizes experimentally reported SelO/Fmp40 substrates across organisms, the known AMPylation sites where available, and the biological roles of those target proteins. It is useful for comparing conserved redox-related targets with more recently identified metabolic substrates.
The best-characterized substrate is glutaredoxin (GrxA), which is AMPylated at a conserved active-site tyrosine residue (Tyr13) (sreelatha2018proteinampylationby pages 7-8, sreelatha2018proteinampylationby pages 10-11). AMPylation of this residue inhibits glutaredoxin's deglutathionylation activity, likely by creating steric hindrance for glutathione binding (sreelatha2018proteinampylationby pages 10-11). In S. cerevisiae, the SelO ortholog Fmp40 additionally AMPylates thioredoxin 3 (Trx3) at Thr66, peroxiredoxin Prx1, and glutaredoxin Grx2 (panja2024profilingofyeast pages 1-3, panja2024profilingofyeast pages 13-15). Recent work identified approximately 124 mitochondrial proteins enriched as SelO substrates in mammalian cells, with gene ontology analysis revealing enrichment in TCA cycle and 2-oxocarboxylic acid metabolism pathways (gonzalez2025arepurposedamp pages 6-7). Notably, glutamate dehydrogenase and pyruvate dehydrogenase were identified as key mammalian SelO substrates, establishing a role in metabolic regulation beyond redox homeostasis (gonzalez2025arepurposedamp pages 1-2).
A comprehensive profiling of the yeast mitochondrial "AMPylome" identified 169 AMPylated proteins across 318 distinct modification sites, with the majority occurring on threonine, serine, or tyrosine residues (55%), and significant lysine modifications also detected (31%) (panja2024profilingofyeast pages 13-15). Importantly, AMPylated proteins were also found in Fmp40-deleted cells, suggesting the existence of additional, as-yet-unidentified AMPylases in yeast mitochondria (panja2024profilingofyeast pages 13-15).
SelO localizes to the mitochondria, consistent with the presence of an N-terminal mitochondrial targeting peptide that is cleaved upon import (sreelatha2018proteinampylationby pages 4-7). This mitochondrial localization has been confirmed across multiple organisms. In S. cerevisiae, SelO (Fmp40) was expressed with a GFP-myc tag and confirmed to localize to enriched mitochondrial fractions (sreelatha2018proteinampylationby pages 18-20). Human SelO similarly localizes to mitochondria, where it functions in both redox protection and metabolic regulation (chatterjee2021ficandnonfic pages 6-6). The S. pombe protein is annotated as a mitochondrial precursor (UniProt O13890), consistent with this conserved localization pattern.
The primary characterized role of SelO is in regulating protein S-glutathionylation — a protective post-translational modification in which glutathione is conjugated to protein cysteine residues during oxidative stress. SelO AMPylates glutaredoxin, the enzyme responsible for removing glutathione from modified proteins (deglutathionylation) (sreelatha2018proteinampylationby pages 10-11, pon2023redefiningpseudokinasesa pages 3-4). By inhibiting glutaredoxin through AMPylation, SelO maintains elevated protein S-glutathionylation levels during oxidative stress, thereby protecting protein cysteine residues from irreversible overoxidation (sreelatha2018proteinampylationby pages 10-11, pon2023redefiningpseudokinasesa pages 3-4). This mechanism has been experimentally validated through immunoblot assays showing reduced S-glutathionylation levels in SelO-deficient E. coli and S. cerevisiae cells (sreelatha2018proteinampylationby pages 10-11).
SelO activity is itself regulated by the cellular redox state through an intramolecular disulfide bond formed between a cysteine residue in the activation loop and a C-terminal cysteine (or selenocysteine in vertebrates) (pon2023redefiningpseudokinasesa pages 3-4). The oxidized, disulfide-bonded form of SelO has reduced catalytic activity, while the reduced monomeric form exhibits significantly higher AMPylation activity (pon2023redefiningpseudokinasesa pages 3-4). The thioredoxin system, using NADPH as a reducing equivalent, can reduce SelO and activate it, creating a redox-sensitive regulatory switch (sreelatha2018proteinampylationby pages 7-8). In the reduced state, a salt bridge forms between a glutamate residue and a conserved lysine in the VAIK motif, indicating the catalytically active conformation (pon2023redefiningpseudokinasesa pages 3-4).
Beyond redox homeostasis, recent work has expanded SelO's functional scope to include regulation of mitochondrial metabolism. Mammalian SelO AMPylates glutamate dehydrogenase and pyruvate dehydrogenase, key enzymes in the TCA cycle and pyruvate metabolism, thereby modulating metabolic flux (gonzalez2025arepurposedamp pages 6-7, gonzalez2025arepurposedamp pages 1-2). In S. cerevisiae, global AMPylome profiling revealed SelO/Fmp40 substrates spanning oxidative phosphorylation, TCA cycle metabolism, redox regulation, and mitochondrial DNA maintenance (panja2024profilingofyeast pages 13-15). AMPylation of thioredoxin 3 (Trx3) at Thr66 was found to be critical for proper Trx3 protein levels and maturation during mitochondrial import (panja2024profilingofyeast pages 1-3).
Functional studies in yeast demonstrate that SelO is important for protection against oxidative stress. In S. cerevisiae, SelO/Fmp40 expression increases when cells are grown on non-fermentable carbon sources (glycerol, lactate, acetate) that require mitochondrial respiration and generate more reactive oxygen species (sreelatha2018proteinampylationby pages 8-10). SelO-deficient yeast exhibit decreased survival when challenged with hydrogen peroxide and show menadione-dependent growth defects (sreelatha2018proteinampylationby pages 8-10). These phenotypes are rescued by expression of wild-type SelO but not by catalytically inactive mutants, confirming that the AMPylation activity is essential for the protective function (sreelatha2018proteinampylationby pages 8-10). Yeast glutaredoxin mutants similarly show increased sensitivity to menadione and hydrogen peroxide, further linking SelO-mediated regulation of glutaredoxin to oxidative stress defense (sreelatha2018proteinampylationby pages 10-11).
SelO is among the most highly conserved members of both the protein kinase superfamily and the selenoprotein family (sreelatha2018proteinampylationby pages 3-4). Jackhmmer searches against reference proteomes identified 3,427 SelO homolog sequences across diverse organisms (sreelatha2018proteinampylationby pages 21-22). The protein is found in bacteria (particularly Proteobacteria and Cyanobacteria), archaea, and eukaryotes (sreelatha2018proteinampylationby pages 3-4). Most eukaryotic phyla contain approximately one SelO gene per genome (sreelatha2018proteinampylationby pages 3-4).
A key distinguishing feature across evolution is the identity of a critical C-terminal residue: in vertebrates and chordates, SelO contains a selenocysteine (Sec, the 21st amino acid) at this position, while in lower eukaryotes (including S. pombe and S. cerevisiae) and prokaryotes, an invariant cysteine occupies the equivalent position (sreelatha2018proteinampylationby pages 3-4, mukherjee2025theriseof pages 4-5). Selenocysteine has a lower pKa than cysteine and confers superior nucleophilicity and oxidoreductase efficiency at physiological pH (sreelatha2018proteinampylationby pages 3-4). The human genome encodes 25 selenoproteins containing selenocysteine, of which SelO is one (mukherjee2025theriseof pages 4-5). The S. pombe SPAC20G4.05c protein contains cysteine rather than selenocysteine, consistent with the absence of selenocysteine incorporation machinery in most fungi.
Direct experimental studies on the S. pombe SelO (SPAC20G4.05c) are not available in the published literature. The functional annotation presented here is based on robust evidence from orthologs in E. coli, S. cerevisiae (Fmp40), P. syringae, and H. sapiens, which share the conserved SelO domain (IPR003846) and demonstrate highly conserved enzymatic activity and biological function. Given the exceptional evolutionary conservation of SelO across all domains of life, including both yeast species, and the shared domain architecture, the S. pombe protein is very likely to function as a mitochondrial protein adenylyltransferase that AMPylates redox-related and metabolic substrates to protect against oxidative stress, analogous to its characterized orthologs.
The S. pombe SPAC20G4.05c gene encodes a mitochondrial protein adenylyltransferase of the SELO family. The protein catalyzes AMPylation — the transfer of AMP from ATP to serine, threonine, and tyrosine residues on mitochondrial protein substrates — through a unique pseudokinase fold with an inverted ATP binding orientation. Its primary biological role is maintaining redox homeostasis by AMPylating and thereby inhibiting glutaredoxins, which preserves protective protein S-glutathionylation during oxidative stress. SelO is also emerging as a regulator of mitochondrial metabolic flux through AMPylation of key metabolic enzymes. The enzyme's own activity is regulated by a redox-sensitive intramolecular disulfide bond, creating a feedforward loop responsive to the cellular redox environment.
References
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