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Information on EC 2.1.1.354 - [histone H3]-lysine4 N-trimethyltransferase and Organism(s) Homo sapiens and UniProt Accession Q9H7B4

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IUBMB Comments
This entry describes several enzymes that successively methylate the L-lysine4 residue of histone H3 (H3K4), ultimately generating a trimethylated form. These modifications influence the binding of chromatin-associated proteins. In most cases the trimethylation of this position is associated with gene activation. EC 2.1.1.364, [histone H3]-lysine4 N-methyltransferase, describes enzymes that can catalyse only monomethylation of this substrate (the first sub-reaction of this entry); EC 2.1.1.370, [histone H3]-lysine4 N-dimethyltransferase, describes enzymes that catalyse only dimethylation of this substrate (the first two sub-reactions of this entry)
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This record set is specific for:
Homo sapiens
UNIPROT: Q9H7B4
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Word Map
The taxonomic range for the selected organisms is: Homo sapiens
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Synonyms
compass, dot1l, smyd3, kmt2d, prdm9, kmt2a, smyd2, kmt2c, ash2l, setd1a, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
histone H3K4 methyltransferase
-
Ash1L
-
-
-
-
DOT1L
-
-
H3K4 methyltransferase
-
-
histone 3 lysine 4 trimethyltransferase
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histone H3 methyltransferase
-
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histone H3K4 methyltransferase
-
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histone H3K4 methyltransferase complex
-
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KMT2A
-
-
-
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KMT2B
-
-
-
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KMT2C
-
-
-
-
KMT2D
-
-
-
-
KMT2E
-
-
-
-
KMT2F
-
-
-
-
KMT2G
-
-
-
-
KMT2H
-
-
-
-
KMT3C
-
-
-
-
KMT3E
-
-
-
-
MLL1
-
-
-
-
MLL2
-
-
-
-
MLL3/MLL4
-
a histone H3K4 methyltransferase complex
MLL5
-
-
-
-
PA1
-
subunit of the MLL3/MLL4 complex
PR domain-containing protein 7
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PRDM7
Prdm9
-
-
-
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set1 histone H3-Lys4 methyltransferase complex
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Setd1A
Setd1B
-
-
SMYD1
-
-
-
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Smyd2
-
-
-
-
Smyd3
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
show the reaction diagram
PATHWAY SOURCE
PATHWAYS
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:[histone H3]-L-lysine4 N6-methyltransferase
This entry describes several enzymes that successively methylate the L-lysine4 residue of histone H3 (H3K4), ultimately generating a trimethylated form. These modifications influence the binding of chromatin-associated proteins. In most cases the trimethylation of this position is associated with gene activation. EC 2.1.1.364, [histone H3]-lysine4 N-methyltransferase, describes enzymes that can catalyse only monomethylation of this substrate (the first sub-reaction of this entry); EC 2.1.1.370, [histone H3]-lysine4 N-dimethyltransferase, describes enzymes that catalyse only dimethylation of this substrate (the first two sub-reactions of this entry)
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3 S-adenosyl-L-methionine + a [histone H3]-L-lysine4
3 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine4
show the reaction diagram
overall reaction
-
-
?
S-adenosyl-L-methionine + a [histone H3]-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine4
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine4
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine4
show the reaction diagram
-
-
-
?
3 S-adenosyl-L-methionine + a [histone H3]-L-lysine4
3 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine4
show the reaction diagram
overall reaction
-
-
?
S-adenosyl-L-methionine + a [histone H3]-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine4
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine4
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine4
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + ART(Kme1)QTARKSTGGKAPRKQLATKAA-GK-biotin
S-adenosyl-L-homocysteine + ART(Kme2)QTARKSTGGKAPRKQLATKAA-GK-biotin
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + ART(Kme2)QTARKSTGGKAPRKQLATKAA-GK-biotin
S-adenosyl-L-homocysteine + ART(Kme3)QTARKSTGGKAPRKQLATKAA-GK-biotin
show the reaction diagram
highest activity
-
-
?
S-adenosyl-L-methionine + ARTKQTARKSTGGKAPRKQLATKAA-GK-biotin
S-adenosyl-L-homocysteine + ART(Kme1)QTARKSTGGKAPRKQLATKAA-GK-biotin
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + histone H3(K4)
?
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + histone H3(K79)
?
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + histone L-lysine
S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
show the reaction diagram
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
3 S-adenosyl-L-methionine + a [histone H3]-L-lysine4
3 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine4
show the reaction diagram
overall reaction
-
-
?
S-adenosyl-L-methionine + a [histone H3]-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine4
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine4
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine4
show the reaction diagram
-
-
-
?
3 S-adenosyl-L-methionine + a [histone H3]-L-lysine4
3 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine4
show the reaction diagram
overall reaction
-
-
?
S-adenosyl-L-methionine + a [histone H3]-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine4
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine4
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine4
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine4
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + histone L-lysine
S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine
show the reaction diagram
-
-
-
?
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
heat shock protein 90
-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0002 - 0.002
ART(Kme1)QTARKSTGGKAPRKQLATKAA-GK-biotin
0.00026 - 0.004
ART(Kme2)QTARKSTGGKAPRKQLATKAA-GK-biotin
0.00017 - 0.0017
ARTKQTARKSTGGKAPRKQLATKAA-GK-biotin
0.014 - 0.9
S-adenosyl-L-methionine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0022 - 7.5
ART(Kme1)QTARKSTGGKAPRKQLATKAA-GK-biotin
0.0167 - 6.444
ART(Kme2)QTARKSTGGKAPRKQLATKAA-GK-biotin
0.0025 - 5.833
ARTKQTARKSTGGKAPRKQLATKAA-GK-biotin
0.0186 - 5.583
S-adenosyl-L-methionine
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
Manually annotated by BRENDA team
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
the enzyme is involved in calcium dependent signaling pathways through forming complexes with the phospholipase PLCB3, calcium/calmodulin dependent kinase CAMK2B, or calcineurin inhibitor RCAN3. The enzyme is involved in epigenetic transcriptional regulation
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
SMYD3_HUMAN
428
0
49097
Swiss-Prot
other Location (Reliability: 4)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
450000
Western analysis of Set1/CXXC finger protein 1 complex
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
S289N
the PRDM7 mutant loses the dimethylated substrate specificity and instead gains the ability to methylate H3K36 similar to, but less efficiently than its evolutionary predecessor PRDM9
S289N/S312W/S357Y
the PRDM7 mutant regains the substrate specificities and catalytic activities similar to its evolutionary predecessor PRDM9, including the ability to efficiently methylate histone H3 lysine 36
S312W
the PRDM7 mutant loses the dimethylated substrate specificity and instead gains the ability to methylate H3K36 similar to, but less efficiently than its evolutionary predecessor PRDM9
S357Y
the PRDM7 mutant regains the substrate specificities and catalytic activities similar to its evolutionary predecessor PRDM9, including the ability to efficiently methylate histone H3 lysine 36
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
anti-FLAG antibody immunoprecipitation
-
Ni-NTA column chromatography and Superdex S200 gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
into the pEGFP-C2 vector
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Yeates, T.O.
Structures of SET domain proteins: protein lysine methyltransferases make their mark
Cell
111
5-7
2002
Homo sapiens
Manually annotated by BRENDA team
Lee, J.H.; Skalnik, D.G.
CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex
J. Biol. Chem.
280
41725-41731
2005
Mus musculus, Homo sapiens (O15047), Homo sapiens
Manually annotated by BRENDA team
Wu, X.; Hua, X.
Menin, histone H3 methyltransferases, and regulation of cell proliferation: current knowledge and perspective
Curr. Mol. Med.
8
805-815
2008
Drosophila melanogaster, Homo sapiens
Manually annotated by BRENDA team
Butler, J.S.; Lee, J.H.; Skalnik, D.G.
CFP1 interacts with DNMT1 independently of association with the Setd1 histone H3K4 methyltransferase complexes
DNA Cell Biol.
27
533-543
2008
Homo sapiens
Manually annotated by BRENDA team
Cho, Y.W.; Hong, S.; Ge, K.
Affinity purification of MLL3/MLL4 histone H3K4 methyltransferase complex
Methods Mol. Biol.
809
465-472
2012
Homo sapiens
Manually annotated by BRENDA team
Blazer, L.L.; Lima-Fernandes, E.; Gibson, E.; Eram, M.S.; Loppnau, P.; Arrowsmith, C.H.; Schapira, M.; Vedadi, M.
PR domain-containing protein 7 (PRDM7) is a histone 3 lysine 4 trimethyltransferase
J. Biol. Chem.
291
13509-13519
2016
Homo sapiens (Q9NQW5)
Manually annotated by BRENDA team
Zhang, Y.; Li, C.; Yang, Z.
Is MYND domain-mediated assembly of SMYD3 complexes involved in calcium dependent signaling?
Front. Mol. Biosci.
6
121
2019
Homo sapiens (Q9H7B4)
Manually annotated by BRENDA team