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Literature summary for 1.14.11.67 extracted from

  • Lee, J.; Thompson, J.; Botuyan, M.; Mer, G.
    Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor (2008), Nat. Struct. Mol. Biol., 15, 109-111.
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

Crystallization (Comment) Organism
JMJD2A-tudor in complex with H4K20me3, X-ray diffraction structure determination and analysis at 2.8 A resolution Homo sapiens

Protein Variants

Protein Variants Comment Organism
D939R the mutation increases the Kd of JMJD2A for H4K20me3 by about 200fold but does not markedly change the affinity for H3K4me3 Homo sapiens
D945R the mutation increases the Kd of JMJD2A for H3K4me3 by about 200fold, but does not affect the interaction with H4K20me3 Homo sapiens
H18G the mutation increases the Kd for H3K4me3 by fivefold compared to the wild-type enzyme Homo sapiens
N940R the mutation does not perturb JMJD2A binding to H4K20me3 but decreases its affinity for H3K4me3 by about 46fold Homo sapiens
T968A the mutation does not appreciably alter the interaction of JMJD2A with either H3K4me3 or H4K20me3 Homo sapiens
T968R the mutation does not appreciably alter the interaction of JMJD2A with either H3K4me3 or H4K20me3 Homo sapiens
Y942A the mutation has no marked effect on the Kd of JMJD2A for H3K4me3 or H4K20me3 Homo sapiens
Y942R the mutation has no marked effect on the Kd of JMJD2A for H3K4me3 or H4K20me3 Homo sapiens

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
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additional information Kd values for H3K4me3 peptide with wild-type and mutant enzymes, overview Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
[histone H3]-N6,N6,N6-trimethyl-L-lysine4 + 3 2-oxoglutarate + 3 O2 Homo sapiens
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[histone H3]-L-lysine4 + 3 succinate + 3 formaldehyde + 3 CO2
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?

Organism

Organism UniProt Comment Textmining
Homo sapiens O75164
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Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information JMJD2A also demethylates histone H3 dimethylated or trimethylated at lysine 9 and lysine 36, by means of an N-terminal catalytic domain, as well as peptides from H4K20me3, recognized through its tudor domains. The hybrid tudor domains at the C terminus of JMJD2A are necessary for the demethylation activity of JMJD2A in vivo. H3K4me3 and H4K20me3 are recognized with similar affinities by JMJD2A, binding structures, overview. Two other amino acids of JMJD2A, Tyr942 and Thr968, involved in weaker intermolecular hydrogen bonds, selectively contact one peptide and not the other. The hydroxyl group of Thr968 in the wild-type structure forms a hydrogen bond with the guanido group of H4K20me3 Arg23 but does not contact H3K4me3. Tyr942 and Thr968 are not essential for the tight binding of JMJD2A to H3K4me3 and H4K20me3 Homo sapiens ?
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?
[histone H3]-N6,N6,N6-trimethyl-L-lysine4 + 3 2-oxoglutarate + 3 O2
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Homo sapiens [histone H3]-L-lysine4 + 3 succinate + 3 formaldehyde + 3 CO2
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?
[histone H3]-N6,N6,N6-trimethyl-L-lysine4 + 3 2-oxoglutarate + 3 O2 JMJD2A has the unique property of binding trimethylated peptides from histone sequences, H3K4me3 through itstandem hybrid tudor domains. JMJD2A Asp945 and Asp940 interact with Arg2 of the H3K4me3 peptide, but not with H4K20me3. Asn940 forms hydrogen bonds with the backbone amide and hydroxyl groups of H3K4me3 Thr3 Homo sapiens [histone H3]-L-lysine4 + 3 succinate + 3 formaldehyde + 3 CO2
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?

Subunits

Subunits Comment Organism
More the hybrid tudor domains at the C terminus of JMJD2A are necessary for the demethylation activity of JMJD2A in vivo Homo sapiens

Synonyms

Synonyms Comment Organism
JMJD2A
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Homo sapiens
JMJD2A-tudor
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Homo sapiens
lysine demethylase
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Homo sapiens