VIB PTM Viewer VIB
PTM Viewer

PTM Info

Plant PTM Viewer contains data of the 17 PTM types below

Acetylation (ac)

Acetylation Acetylation is one of the most common PTM in eukaryotes, targeting α - and ε - amino groups of N-termini and Lys residues respectively. N-acetyltransferases target N-termini co- and post-translationally. Lysine is acetylated by a battery of lysine acetylases and deacetylases.

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Sites: N-terminus, K
Δ Mass: +42.011 Da

2-Hydroxyisobuturylation (bu)

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)

Malonylation (ma)

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

Methylation (me)

Methylation 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

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-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: -

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

SUMOylation (sm)

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 a 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)

Succinylation (su)

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

Ubiquitination (ub)

Ubiquitination Ubiquitination is the addition of the 8.5 kDa protein ubiquitine to Lys side-chains. 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, N-term (rare)
Δ Mass: +114.04 Da (GlyGly remnant)
"Plant PTM Viewer - from site-seeing to protein function" manuscript in preparation
© VIB Bioinformatics Core 2018