Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AJmjCe2ybpA1 A: beta sandwichesX: jelly-rollH: Double-stranded beta-helix (From Topology)T: Double-stranded beta-helixF: JmjCECOD (1.6)
BJmjCe2ybpB1 A: beta sandwichesX: jelly-rollH: Double-stranded beta-helix (From Topology)T: Double-stranded beta-helixF: JmjCECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A2.60.120.650 Mainly Beta Sandwich Jelly Rolls CupinCATH (4.3.0)
B2.60.120.650 Mainly Beta Sandwich Jelly Rolls CupinCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF02373JmjC domain, hydroxylase (JmjC)JmjC domain, hydroxylaseThe JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the ...The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].
Domain
A, B
PF02375jmjN domain (JmjN)jmjN domain- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B
LYSINE-SPECIFIC DEMETHYLASE 4A
C, D
HISTONE H3.1T

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
C, D
M3L Parent Component: LYS

RESIDAA0074

PSI-MOD :  N6,N6,N6-trimethyl-L-lysine MOD:00083

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
lysine-specific [histone H3] demethylase  M-CSA #370

Jumonji Domain protein 2A (JMJD2A or lysine-specific demethylase 4A, KDM4A) is a 2-oxoglutarate dependent oxygenase which catalyses the hydroxylation of methyl groups present on lysine residues within histone protein 3, utilising a Fe(II) dependent redox reaction, with spontaneous deformylation to produce the demethylated lysine and formaldehyde. The enzyme catalyses the removal of methyl groups specifically from lysine residues K9 and K36. JMJD2A has been shown to be over-expressed relative to normal physiological levels in several cancers, and is of interest for its influence over epigenetic factors associated with cancer progression.

The enzyme substrate specificity is determined by amino acids within the JMJD2A active site, and also the flexibility of residues positioned around the reactive lysine in the peptide backbone. The enzyme is most active with the tri-methyl substrate. Each of the three methyl groups binds in a discrete pocket, restricting rotation around the functional group and demethylation proceeds rapidly. In the presence of two methyl groups, the functional groups can flip between a more reactive and less reactive pocket, one which binds methyl groups weakly, but closer to the reactive Fe(II), and vice versa. JMJD2A is not active towards the mono-methyl lysine substrate. The single methyl group stays bound to the less reactive pocket, and cannot be demethylated.

Defined by 6 residues: GLY:A-192 [auth A-170]TYR:A-199 [auth A-177]HIS:A-210 [auth A-188]GLU:A-212 [auth A-190]HIS:A-298 [auth A-276]SER:A-310 [auth A-288]
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