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Literature summary for 2.1.1.369 extracted from

  • Bergamin, E.; Sarvan, S.; Malette, J.; Eram, M.S.; Yeung, S.; Mongeon, V.; Joshi, M.; Brunzelle, J.S.; Michaels, S.D.; Blais, A.; Vedadi, M.; Couture, J.F.
    Molecular basis for the methylation specificity of ATXR5 for histone H3 (2017), Nucleic Acids Res., 45, 6375-6387 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 2.1.1.369

Crystallization (Commentary)

Crystallization (Comment) Organism
structure of the PHD domain (residues 23-77) bound to the unmodified histone H3 tail. The domain adopts a canonical crossbraced PHD domain architecture with two loops containing the Cys4-His-Cys3 motif that coordinates two zinc atoms, a double-stranded twisted antiparallel beta-sheet and two short 310 alpha-helices Ricinus communis

Protein Variants

Protein Variants Comment Organism
L49W about 5fold decrease in catalytic efficiency Ricinus communis
additional information deletion or mutation of the PHD domain reduces the catalytic efficiency of ATXR5 up to 58fold Ricinus communis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0011
-
 [histone H3.1]-L-lysine27 mutant L49W, pH 8.0, 30°C Ricinus communis
0.0015
-
 [histone H3.1]-L-lysine27 wild-type, pH 8.0, 30°C Ricinus communis
0.0019
-
 [histone H3.1]-L-lysine27 PHD domain deletion mutant, pH 8.0, 30°C Ricinus communis
0.016
-
 S-adenosyl-L-methionine wild-type, pH 8.0, 30°C Ricinus communis
0.045
-
 S-adenosyl-L-methionine mutant L49W, pH 8.0, 30°C Ricinus communis
0.192
-
 S-adenosyl-L-methionine PHD domain deletion mutant, pH 8.0, 30°C Ricinus communis

Organism

Organism UniProt Comment Textmining
Ricinus communis B9RU15 isoform ATXR5
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
S-adenosyl-L-methionine + [histone H3.1 peptide KAARKSAPATVGGK]-L-lysine27 peptide corresponds to residues K23-K36 Ricinus communis S-adenosyl-L-homocysteine + [histone H3.1 peptide KAARK*SAPATVGGK]-N6-methyl-L-lysine27
-
 ?
S-adenosyl-L-methionine + [histone H3.1]-L-lysine27
-
 Ricinus communis S-adenosyl-L-homocysteine + [histone H3.1]-N6-methyl-L-lysine27
-
 ?

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0178
-
 [histone H3.1]-L-lysine27 PHD domain deletion mutant, pH 8.0, 30°C Ricinus communis
0.0406
-
 [histone H3.1]-L-lysine27 mutant L49W, pH 8.0, 30°C Ricinus communis
0.0778
-
 [histone H3.1]-L-lysine27 wild-type, pH 8.0, 30°C Ricinus communis

General Information

General Information Comment Organism
physiological function isoform ATXR5 discriminates between histone H3 variants and preferentially methylates K27 on histone H3.1. ATXR5 preferentially methylates the R/F-K*-S/C-G/A-P/C motif with striking preference for hydrophobic and aromatic residues in positions flanking this core of five amino acids. Posttranscriptional modifications of residues neighboring K27 that are typically associated with actively transcribed chromatin are detrimental to ATXR5 activity. The ATXR5 PHD domain employs a narrow binding pocket to selectively recognize unmethylated K4 of histone H3. Deletion or mutation of the PHD domain reduces the catalytic efficiency of ATXR5 up to 58fold Ricinus communis

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.08
-
 S-adenosyl-L-methionine PHD domain deletion mutant, pH 8.0, 30°C Ricinus communis
0.89
-
 S-adenosyl-L-methionine mutant L49W, pH 8.0, 30°C Ricinus communis
4.86
-
 S-adenosyl-L-methionine wild-type, pH 8.0, 30°C Ricinus communis