Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary for 1.14.11.69 extracted from

  • Chang, Y.; Wu, J.; Tong, X.J.; Zhou, J.Q.; Ding, J.
    Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism (2010), Biochem. J., 433, 295-302.
    View publication on PubMed

Crystallization (Commentary)

Crystallization (Comment) Organism
catalytic core of Rph1, hanging drop vapour diffusion method, X-ray diffraction structure determination and analysis at 2.5 A resolution Saccharomyces cerevisiae

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information binding affinities of c-Rph1 with H3K36 and H3K9 peptides, overview Saccharomyces cerevisiae

Metals/Ions

Metals/Ions Comment Organism Structure
Ni2+ the Ni2+ ion at the active site is chelated by conserved residues and the cofactor 2-oxoglutarate Saccharomyces cerevisiae

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
histone H3 N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 Saccharomyces cerevisiae
-
histone H3 N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3 N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 Saccharomyces cerevisiae
-
histone H3 N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3 N6-methyl-L-lysine36 + 2-oxoglutarate + O2 Saccharomyces cerevisiae
-
histone H3 L-lysine36 + succinate + formaldehyde + CO2
-
?
additional information Saccharomyces cerevisiae Rph1 is a histone demethylase that can specifically demethylate tri- and dimethylated Lys36 of histone H3. 2-Oxoglutarate forms hydrogen-bonding interactions with the side chains of conserved residues. The substrate-binding cleft of Rph1 is formed with several structural elements of the JmjC domain, the long beta-hairpin and the mixed structural motif, and the methylated Lys36 of H3 is recognized by several conserved residues of the JmjC domain. Molecular basis for the substrate specificity of Rph1, overview ?
-
?

Organism

Organism UniProt Comment Textmining
Saccharomyces cerevisiae P39956
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
histone H3 N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
-
Saccharomyces cerevisiae histone H3 N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3 N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 calf thymus type II-A histones Saccharomyces cerevisiae histone H3 N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3 N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
-
Saccharomyces cerevisiae histone H3 N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3 N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 calf thymus type II-A histones Saccharomyces cerevisiae histone H3 N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3 N6-methyl-L-lysine36 + 2-oxoglutarate + O2
-
Saccharomyces cerevisiae histone H3 L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3 N6-methyl-L-lysine36 + 2-oxoglutarate + O2 calf thymus type II-A histones Saccharomyces cerevisiae histone H3 L-lysine36 + succinate + formaldehyde + CO2
-
?
additional information Rph1 is a histone demethylase that can specifically demethylate tri- and dimethylated Lys36 of histone H3. 2-Oxoglutarate forms hydrogen-bonding interactions with the side chains of conserved residues. The substrate-binding cleft of Rph1 is formed with several structural elements of the JmjC domain, the long beta-hairpin and the mixed structural motif, and the methylated Lys36 of H3 is recognized by several conserved residues of the JmjC domain. Molecular basis for the substrate specificity of Rph1, overview Saccharomyces cerevisiae ?
-
?

Subunits

Subunits Comment Organism
More the structure of c-Rph1 is composed of a JmjN, Jumonji N, domain, a long beta-hairpin, a mixed structural motif and a JmjC domain Saccharomyces cerevisiae

Synonyms

Synonyms Comment Organism
Rph1
-
Saccharomyces cerevisiae

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
-
assay at Saccharomyces cerevisiae

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
assay at Saccharomyces cerevisiae

General Information

General Information Comment Organism
physiological function c-Rph1, the catalytic core of Rph1, is responsible for the demethylase activity, which is essential for the transcription elongation of some actively transcribed genes Saccharomyces cerevisiae