5FWE image
Deposition Date 2016-02-15
Release Date 2016-04-06
Last Version Date 2024-10-23
Entry Detail
PDB ID:
5FWE
Keywords:
Title:
JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE
Biological Source:
Source Organism:
HOMO SAPIENS (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.05 Å
R-Value Free:
0.25
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 21 21 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:LYSINE-SPECIFIC DEMETHYLASE 4A
Gene (Uniprot):KDM4A
Chain IDs:A, B
Chain Length:381
Number of Molecules:2
Biological Source:HOMO SAPIENS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SYNTHETIC PEPTIDE
Gene (Uniprot):H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16
Chain IDs:C, D
Chain Length:15
Number of Molecules:2
Biological Source:HOMO SAPIENS
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MR C ARG N3, N4-DIMETHYLARGININE
Primary Citation
Arginine Demethylation is Catalysed by a Subset of Jmjc Histone Lysine Demethylases.
Nat.Commun. 7 11974 ? (2016)
PMID: 27337104 DOI: 10.1038/NCOMMS11974

Abstact

While the oxygen-dependent reversal of lysine N(ɛ)-methylation is well established, the existence of bona fide N(ω)-methylarginine demethylases (RDMs) is controversial. Lysine demethylation, as catalysed by two families of lysine demethylases (the flavin-dependent KDM1 enzymes and the 2-oxoglutarate- and oxygen-dependent JmjC KDMs, respectively), proceeds via oxidation of the N-methyl group, resulting in the release of formaldehyde. Here we report detailed biochemical studies clearly demonstrating that, in purified form, a subset of JmjC KDMs can also act as RDMs, both on histone and non-histone fragments, resulting in formaldehyde release. RDM catalysis is studied using peptides of wild-type sequences known to be arginine-methylated and sequences in which the KDM's methylated target lysine is substituted for a methylated arginine. Notably, the preferred sequence requirements for KDM and RDM activity vary even with the same JmjC enzymes. The demonstration of RDM activity by isolated JmjC enzymes will stimulate efforts to detect biologically relevant RDM activity.

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Primary Citation of related structures