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PTM Viewer

PTM Info

Plant PTM Viewer contains data of the 24 PTM types below

Lysine Acetylation (ac)

Lysine Acetylation Lysine acetylation is one of the most common PTM in eukaryotes, targeting the ε- amino groups of Lys residues. Lysine is acetylated by a battery of lysine acetylases and deacetylases.

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Sites: K
Δ Mass: +42.011 Da

Lysine 2-Hydroxyisobuturylation (bu)

Lysine 2-Hydroxyisobuturylation 2-Hydroxyisobuturylation is a recently discovered PTM. The short-chain acylation of Lys side-chains neutralizes the positive charge of Lys. A recent proteomic study identified 2-Hydroxyisobuturylation sites in rice seeds on histone and non-histone proteins.

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Sites: K
Δ Mass: +86.03 Da

Carbonylation (ca)

Carbonylation Irreversible oxidation of protein residues, unlike Cys and Met oxidation. The addition of carbonyl groups to the proteins may result in protein misfolding, loss of function and degradation by proteasome. Carbonylation products for four amino acids are characterized: of arginine to glutamic semialdehyde, lysine modified to aminoadipic semialdehyde, proline to 5-oxo-proline, and threonine to 2-amino-3-ketobutyric acid.

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Sites: R, K, P, T
Δ Mass: +258.12 Da (R), +240.10 Da (K), +241.11 Da (P), +199.06 Da (T)

S-cyanylation (cn)

S-cyanylation Hydrogen cyanide (HCN) is a gaseous acid that produced as a metabolic byproduct and enzymatically detoxified by the mitochondrial β-CYANOALANINE SYNTHASE (CAS-C1) in plant cells. Reaction of cystine peptides or mixed disulfides with cyanide can form S-cyanylated cysteine. Internal S-cyanylated residues lead to an unstable cyclization form that spontaneously hydrolizes releasing an upstream 2-imino-thiazolidine-4-carboxylyl COOH-terminal peptide.

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Sites: C
Δ Mass: +25 Da

Lysine Carbamylation (lc)

Lysine Carbamylation Carbon dioxide (CO2) can react with ε[epsilon]-amino groups of Lys residues, leading to Lys carbamylation. Carbamate formation is reversible and requires covalent trapping for identification by MS. Arabidopsis proteomes were first profiled by Linthwaite et al. using triethyloxonium tetrafluoroborate, identifying high confident Lys carbamylation sites next to the well-characterized RuBisCO carbamylation in plants.

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Sites: K
Δ Mass: +72.0211 Da (O-ethylated, TEO)

Lysine Malonylation (ma)

Lysine Malonylation Malonylation is, like acetylation and succinylation, a PTM derived from metabolic intermediates. Recent large-scale malonylation studies have been performed in plant crops and indicated high overlap with acetylation and succinylation sites. In addition, the positively charged residues Lys and Arg frequently flanked the malonylated Lys.

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Sites: K
Δ Mass: +86.00 Da

Monomethylation (me1)

Monomethylation Methylation is catalyzed by lysine and arginine methyltransferases that add a methyl moiety Lys and Arg respectively. S-adenosyl methionine (SAM) is the primary methyl group donor. Methylation increases the hydrophobicity of the protein. Methylation is known to be involved in epigenetic regulation by targeting histones.

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Sites: R, K, rare: N-terminus and C-terminus
Δ Mass: +14.02 Da

Dimethylation (me2)

Dimethylation Lysine dimethyl (Kme2) is catalyzed by protein lysine methyltransferases (PKMTs), while three types of protein arginine methyltransferases (PRMTs) can yield asymmetric dimethyl arginine (aDMA) or symmetric dimethyl arginine (sDMA) residues. Dimethylated residues can be targeted via immunopurification strategies.

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Sites: R, K
Δ Mass: +28.0313 Da Da

Trimethylation (me3)

Trimethylation Lysine trimethyl (Kme3) is catalyzed by protein lysine methyltransferases (PKMTs). Trimethylated residues can be targeted via immunopurification strategies.

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Sites: K
Δ Mass: +42.04695 Da

Methionine Oxidation (mo)

Methionine Oxidation Methionine Oxidation refers in Plant PTM Viewer to reversible oxidation of Met and Cys thiols. Methionine sulfoxidation can be reverted via Methionine sulfoxide reductases (MSRs), whereas sulfenic acid (oxidized Cys) can be intercoverted and finally reduced via thio- and glutaredoxin enzymes. Cysteine oxidation is well-studied and known to regulate the function of many proteins, whereas the functional knowledge of Met oxidation is less understood in plants.

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Sites: M, C
Δ Mass: +15.99 Da

Myristoylation (my)

Myristoylation Myristoylation is a lipid N-terminal modification, attaching a myristoyl group to the amino group of N-terminal glycine residues. The reaction is catalyzed by N-myristoyltransferases. It has an important role in membrane targeting and catalyzing protein-protein interactions.

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Sites: N-term G
Δ Mass: +210.20 Da

N-terminal Acetylation (na)

N-terminal Acetylation N-terminal acetylation is a very frequent modification that can take place co-translationally and target the α- amino group of the protein N-terminus. N-terminal acetylation is catalyzed by N-acetyltransferases (Nat) with different specifities. NatA can target Ser, Ala, Thr, Gly and Cys N-terminal residues exposed after N-terminal methionine excision. NatB and NatC can acetylate the initiator Met followed by acidic or hydrophobic residues respectively. Deacetylases of protein N-termini have not yet been identified and is in contrast to lysine acetylation considered as irreversible.

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Sites: N-terminus
Δ Mass: +42.011 Da

N-glycosylation (ng)

N-glycosylation N-linked (N-)glycosylation is the attachments of glycans (oligosaccharides) to the amide nitrogen of Asn. Chemical structure of N-glycans vary between species, late N-glycan maturation steps in the Golgi differ significantly in plants giving rise to complex N-glycans. N-glycosylation is important during protein folding, stability and protein-protein interactions.

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Sites: N-!P-[ST]
Δ Mass: Variable, dependent on N-glycan.

S-Nitrosylation (no)

S-Nitrosylation S-nitrosylation is a reversible attachment of NO to the thiol groups of Cys induced under NO-inducing conditions. Denitrosylation is mediated by enzymes such as S-nitrosoglutathione reductase (GSNOR) and thioredoxins. Nitrosylation is known to affect protein functions by various manners.

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Sites: C
Δ Mass: +28.99 Da

N-terminus Proteolysis (nt)

N-terminus Proteolysis Novel N-termini can be exposed within proteins by proteases that cleave peptide bonds. Plants encode hundreds of proteases divided in distinct classes according their catalytic mechanism. During orgenellar import, to for instance mitochondria or chloroplasts, targeting peptides are removed by proteases. In addition, protein cleavage occurs frequently co-translationally, as initiator Met is cleaved by Met aminopeptidase. Novel exposed N-termini can be modified by other PTMs or be a hallmark for degradation in the N-end rule. Note that N-terminal peptides matching the native protein N-terminus, i.e. the initiation Met, are not included as PTMs.

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Sites: Any
Δ Mass: -

N-terminal Ubiquitination (nu)

N-terminal Ubiquitination Although Lysine is predominantly identified at Lys sidechains, rare cases of N-terminal ubiquitination have been reported. In the study of Walton et al. 2016, 7 N-terminal ubiquitination sites are reported, although this number might increase in the future with improved ubiquitination detection techniques. For instance, the recent UbiSite technology identified a significant portion of N-terminal ubiquitination in human cell lines (Akimov et al., 2018, PMID: 29967540).

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Sites: N-terminus
Δ Mass: +114.04 Da (GlyGly remnant)

O-GlcNAcylation (og)

O-GlcNAcylation O-GlcNAcylation (O-linked N-acetylglucosamine) can occur on Thr and Ser, sharing similarities and having interplay with phosphorylation. It is mediates by O-GlcNAc transferases (OGTs) and O-GlcNAcases (OGAs).

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Sites: S, T
Δ Mass: +203.08 Da (HexNAc)

Phosphorylation (ph)

Phosphorylation Phosphorylation is by far the best characterized PTM given its multiple proteomic studies and diversity in enrichment methodologies. Phosphorylation is mediated by kinases and removed via phosphatases. Phosphorylation has a plethora of functional consequences and can for instance work in a cascade where phosphorylation activates a downstream kinase.

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Sites: S, T, Y, N-term (rare)
Δ Mass: +79.97 Da

Reversible Cysteine Oxidation (ro)

Reversible Cysteine Oxidation Reversible Cysteine Oxidation is used here as a grouping term to indicate oxidized Cys sites (i.e. disulfides, S-glutathionylation, sulfenic acid) that could be reversible reduced and captured by reductome studies. In brief, these studies irreversible block all free, non-oxidized thiols, after which oxidized thiols are reduced and identified by mass spectrometry. The drawback of this indirect detection method is that the precise oxidized form remains elusive.

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Sites: C
Δ Mass: -

S-Glutathionylation (sg)

S-Glutathionylation S-glutathionylation is the reversible disulfide linkage of the low-molecular-mass thiol glutathione to Cys thiols. It is transferred by glutathione S-transferases and reduced by glutaredoxins. Glutathionylation can have a protective role by preventing overoxidation or proteolysis.

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Sites: C
Δ Mass: +305.07 Da

Lysine SUMOylation (sm)

Lysine SUMOylation SUMOylation is the attachment of the Small Ubiquitin-like MOdifier (SUMO) to lysine sidechains of target proteins. SUMOylation can affect the protein function in diverse ways. Like ubiquitin, SUMOylation is also controlled by E1 activating, E2 conjugating and E3 ligating enzymes, and reversible due to deSUMOylation proteases. For the detection of SUMO sites, a mutagenized SUMO was engineered and expressed in Arabidopsis. This incorporates an Arg instead of His at the C-terminus and leaves after trypsin cleavage a four amino acid remnant Glu-Thr-Gly-Gly.

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Sites: K
Δ Mass: +349.149 Da (GluThrGlyGly remnant)

S-sulfenylation (so)

S-sulfenylation Hydrogen peroxide (H2O2) can oxidize specific protein cysteine thiols to sulfenic acid (SOH), a process known as S-sulfenylation. S-sulfenylation functions as an intermediate on the path toward other redox modifications, such as disulfide formation, S-glutathionylation, and overoxidation to sulfinic (SO2H) and sulfonic (SO3H) acids. With cysteines as reactive residues often participating in active sites of proteins, these modifications can have a direct impact on protein function. Genetic- or chemical-based approach have been developed to trap and identify S-sulfenylated cysteines by mass spectrometry.

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Sites: C
Δ Mass: +15.995 Da

Lysine Succinylation (su)

Lysine Succinylation Succinylation is similar to acetylation, though structurally larger and changing charge of Lys from +1 to -1 at physiological pH. These physicochemical properties are believed to have drastic consequences to protein structure and function, though further experimental studies are required for this emerging PTM.

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Sites: K
Δ Mass: +100.016 Da

Lysine Ubiquitination (ub)

Lysine Ubiquitination Lysine ubiquitination is the addition of the 8.5 kDa protein ubiquitine to Lys side-chains at the epsilon (ε) amino group. Ubiquitination involves three main steps: activation, conjugation, and ligation, steps all catalyzed by specialized enzymatic families. Either a single ubiquitin protein (monoubiquitination) can be attached or a chain of ubiquitin (polyubiquitination). Ubiquitin chains will target proteins for proteasomal degradation. Although most renowned for its degradation function, ubiquitination can also alter the protein cellular location, and steer protein interactions.

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Sites: K
Δ Mass: +114.04 Da (GlyGly remnant)
"The Plant PTM Viewer, a central resource for exploring plant protein modifications"
Willems P, Horne A, Van Parys T, Goormachtig S, De Smet I, Botzki A, Van Breusegem F, Gevaert K. ; Plant J. 2019 Aug;99(4):752-762.
© VIB Bioinformatics Core 2018