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PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.

Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E - Nucleic Acids Res. (2014)

Bottom Line: Two new downloads are available from PSP.The 'Regulatory sites' dataset includes curated information about modification sites that regulate downstream cellular processes, molecular functions and protein-protein interactions.PTMVars include 18 548 phosphorlyation sites, 3412 ubiquitylation sites, 2316 acetylation sites, 685 methylation sites and 245 succinylation sites.

View Article: PubMed Central - PubMed

Affiliation: Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923, USA phornbeck@cellsignal.com.

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Classification of modification sites in the PTMVar dataset. Class I PTMVars are those in which a site is lost by an amino acid substitution of the modified residue. The variant in this case, PAH S16P (VAR_000869), causes phenylketonuria (2). Class Ia PTMVars are those in which the variant AA can still be enzymatically modified with the same side group as the wt substrate. The variant in this case, TIE2 Y897S (VAR_008716), is associated with venous malformations (VMCM; OMIM 600195) (29). Class II PTMVars are those in which the mutation occurs on a flanking residues ±5 amino acids from the modification site. The variant in this case, PKAR1α R74C (VAR_046895), is associated with Carney complex (CNC), a familial multiple neoplasia syndrome (30).
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Figure 4: Classification of modification sites in the PTMVar dataset. Class I PTMVars are those in which a site is lost by an amino acid substitution of the modified residue. The variant in this case, PAH S16P (VAR_000869), causes phenylketonuria (2). Class Ia PTMVars are those in which the variant AA can still be enzymatically modified with the same side group as the wt substrate. The variant in this case, TIE2 Y897S (VAR_008716), is associated with venous malformations (VMCM; OMIM 600195) (29). Class II PTMVars are those in which the mutation occurs on a flanking residues ±5 amino acids from the modification site. The variant in this case, PKAR1α R74C (VAR_046895), is associated with Carney complex (CNC), a familial multiple neoplasia syndrome (30).

Mentions: Non-synonymous mutations are missense mutations that change one amino acid for another in a protein's coding region. If the mutation is at or near the site of a PTM that participates in cell signaling, it can significantly impact signaling networks in which the affected site participates. Class I PTMVars are those in which a PTM site is lost by altering the relevant amino acid (Figure 4). In the Class I example in Figure 4, Ser-16 of phenylalanine hydroxylase (PAH) is changed to Pro. PAH, requiring phosphorylation of Ser-16 for activation, is defective with the S16P mutation, leading to the buildup of phenylalanine and subsequently to phenylketonuria (2). Class Ia PTMVars are those in which the variant AA can still be enzymatically modified with the same side group as the wt. The variant in this case, TIE2 Y897S (VAR_008716), is associated with venous malformations (VMCM; OMIM 600195).


PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.

Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E - Nucleic Acids Res. (2014)

Classification of modification sites in the PTMVar dataset. Class I PTMVars are those in which a site is lost by an amino acid substitution of the modified residue. The variant in this case, PAH S16P (VAR_000869), causes phenylketonuria (2). Class Ia PTMVars are those in which the variant AA can still be enzymatically modified with the same side group as the wt substrate. The variant in this case, TIE2 Y897S (VAR_008716), is associated with venous malformations (VMCM; OMIM 600195) (29). Class II PTMVars are those in which the mutation occurs on a flanking residues ±5 amino acids from the modification site. The variant in this case, PKAR1α R74C (VAR_046895), is associated with Carney complex (CNC), a familial multiple neoplasia syndrome (30).
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Related In: Results  -  Collection

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Show All Figures
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Figure 4: Classification of modification sites in the PTMVar dataset. Class I PTMVars are those in which a site is lost by an amino acid substitution of the modified residue. The variant in this case, PAH S16P (VAR_000869), causes phenylketonuria (2). Class Ia PTMVars are those in which the variant AA can still be enzymatically modified with the same side group as the wt substrate. The variant in this case, TIE2 Y897S (VAR_008716), is associated with venous malformations (VMCM; OMIM 600195) (29). Class II PTMVars are those in which the mutation occurs on a flanking residues ±5 amino acids from the modification site. The variant in this case, PKAR1α R74C (VAR_046895), is associated with Carney complex (CNC), a familial multiple neoplasia syndrome (30).
Mentions: Non-synonymous mutations are missense mutations that change one amino acid for another in a protein's coding region. If the mutation is at or near the site of a PTM that participates in cell signaling, it can significantly impact signaling networks in which the affected site participates. Class I PTMVars are those in which a PTM site is lost by altering the relevant amino acid (Figure 4). In the Class I example in Figure 4, Ser-16 of phenylalanine hydroxylase (PAH) is changed to Pro. PAH, requiring phosphorylation of Ser-16 for activation, is defective with the S16P mutation, leading to the buildup of phenylalanine and subsequently to phenylketonuria (2). Class Ia PTMVars are those in which the variant AA can still be enzymatically modified with the same side group as the wt. The variant in this case, TIE2 Y897S (VAR_008716), is associated with venous malformations (VMCM; OMIM 600195).

Bottom Line: Two new downloads are available from PSP.The 'Regulatory sites' dataset includes curated information about modification sites that regulate downstream cellular processes, molecular functions and protein-protein interactions.PTMVars include 18 548 phosphorlyation sites, 3412 ubiquitylation sites, 2316 acetylation sites, 685 methylation sites and 245 succinylation sites.

View Article: PubMed Central - PubMed

Affiliation: Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923, USA phornbeck@cellsignal.com.

Show MeSH
Related in: MedlinePlus