Page last updated: 2024-10-24

histone methyltransferase activity

Definition

Target type: molecularfunction

Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or a lysine residue. [GOC:curators]

Histone methyltransferases (HMTs) are a family of enzymes that catalyze the transfer of a methyl group from a donor molecule, typically S-adenosyl methionine (SAM), to a specific lysine or arginine residue within histone proteins. This methylation process plays a crucial role in regulating gene expression by altering the accessibility of DNA to transcription factors and other regulatory proteins.

HMTs are highly specific for both the histone target and the methylation site, and their activity is regulated by a variety of factors, including cellular signaling pathways, developmental stage, and environmental cues. The addition of a methyl group to a histone tail can have different effects on gene expression depending on the specific residue modified, the number of methyl groups added, and the context of the surrounding chromatin environment.

**Specific examples of the molecular function of histone methyltransferase activity include:**

* **Activation of gene expression:** Methylation of lysine 4 on histone H3 (H3K4me) is generally associated with active transcription, as it attracts proteins that promote transcription initiation and elongation.
* **Repression of gene expression:** Methylation of lysine 9 on histone H3 (H3K9me) is often linked to gene silencing, as it recruits proteins that condense chromatin and hinder transcription factor access.
* **Regulation of DNA replication and repair:** Methylation of histone H3 lysine 79 (H3K79me) plays a role in DNA replication and repair processes.
* **Chromatin remodeling:** Methylation of histone H3 lysine 27 (H3K27me) is involved in the formation of silent chromatin domains, which can be targeted for specific developmental or differentiation programs.

**Mechanism of HMT Activity:**

HMTs typically consist of a SET domain, which is a highly conserved catalytic domain responsible for transferring the methyl group. They often interact with other proteins, such as histone chaperones or chromatin-remodeling complexes, to facilitate their access to histone substrates.

The catalytic cycle of an HMT involves the following steps:

1. Binding of the HMT to its histone substrate and SAM.
2. Transfer of a methyl group from SAM to the target lysine or arginine residue on the histone tail.
3. Release of the methylated histone and S-adenosyl homocysteine (SAH), the byproduct of the reaction.

**Dysregulation of HMT activity is associated with a variety of diseases, including cancer, developmental disorders, and neurological diseases.**'
"

Proteins (17)

ProteinDefinitionTaxonomy
Protein arginine N-methyltransferase 5A protein arginine N-methyltransferase 5 that is encoded in the genome of human. [PRO:DNx, UniProtKB:O14744]Homo sapiens (human)
Protein arginine N-methyltransferase 7A protein arginine N-methyltransferase 7 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9NVM4]Homo sapiens (human)
Protein arginine N-methyltransferase 3A protein arginine N-methyltransferase 3 that is encoded in the genome of human. [PRO:DNx, UniProtKB:O60678]Homo sapiens (human)
N-lysine methyltransferase KMT5AAn N-lysine methyltransferase KMT5A that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9NQR1]Homo sapiens (human)
N-terminal Xaa-Pro-Lys N-methyltransferase 1A methyltransferase-like protein 11A that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9BV86]Homo sapiens (human)
Protein arginine N-methyltransferase 1A protein arginine N-methyltransferase 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q99873]Homo sapiens (human)
Protein arginine N-methyltransferase 6A protein arginine N-methyltransferase 6 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q96LA8]Homo sapiens (human)
Histone-lysine N-methyltransferase SETD7A histone-lysine N-methyltransferase SETD7 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q8WTS6]Homo sapiens (human)
Histone-lysine N-methyltransferase, H3 lysine-79 specificA histone-lysine N-methyltransferase, H3 lysine-79 specific that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q8TEK3]Homo sapiens (human)
Histone-lysine N-methyltransferase 2CA histone-lysine N-methyltransferase 2C that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q8NEZ4]Homo sapiens (human)
Histone-arginine methyltransferase CARM1A histone-arginine methyltransferase CARM1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q86X55]Homo sapiens (human)
Histone-lysine N-methyltransferase KMT5BA histone-lysine N-methyltransferase KMT5B that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q4FZB7]Homo sapiens (human)
Histone-lysine N-methyltransferase EZH2A histone-lysine N-methyltransferase EZH2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q15910]Homo sapiens (human)
Polycomb protein SUZ12A polycomb protein SUZ12 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q15022]Homo sapiens (human)
Polycomb protein EEDA polycomb protein EED that is encoded in the genome of human. [PRO:DNx, UniProtKB:O75530]Homo sapiens (human)
Histone-lysine N-methyltransferase SUV39H1A histone-lysine N-methyltransferase SUV39H1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:O43463]Homo sapiens (human)
Protein arginine N-methyltransferase 5A protein arginine N-methyltransferase 5 that is encoded in the genome of human. [PRO:DNx, UniProtKB:O14744]Homo sapiens (human)

Compounds (63)

CompoundDefinitionClassesRoles
astemizoleastemizole : A piperidine compound having a 2-(4-methoxyphenyl)ethyl group at the 1-position and an N-[(4-fluorobenzyl)benzimidazol-2-yl]amino group at the 4-position.

Astemizole: Antihistamine drug now withdrawn from the market in many countries because of rare but potentially fatal side effects.
benzimidazoles;
piperidines
anti-allergic agent;
anticoronaviral agent;
H1-receptor antagonist
cyproheptadinecyproheptadine : The product resulting from the formal oxidative coupling of position 5 of 5H-dibenzo[a,d]cycloheptene with position 4 of 1-methylpiperidine resulting in the formation of a double bond between the two fragments. It is a sedating antihistamine with antimuscarinic and calcium-channel blocking actions. It is used (particularly as the hydrochloride sesquihydrate) for the relief of allergic conditions including rhinitis, conjunctivitis due to inhalant allergens and foods, urticaria and angioedema, and in pruritic skin disorders. Unlike other antihistamines, it is also a seratonin receptor antagonist, making it useful in conditions such as vascular headache and anorexia.

Cyproheptadine: A serotonin antagonist and a histamine H1 blocker used as antipruritic, appetite stimulant, antiallergic, and for the post-gastrectomy dumping syndrome, etc.
piperidines;
tertiary amine
anti-allergic agent;
antipruritic drug;
gastrointestinal drug;
H1-receptor antagonist;
serotonergic antagonist
fluorescitefluorescein (acid form) : A xanthene dye that is highly fluorescent and commonly used as a fluorescent tracer.benzoic acids;
cyclic ketone;
hydroxy monocarboxylic acid;
organic heterotricyclic compound;
phenols;
xanthene dye
fluorescent dye;
radioopaque medium
pentamidinepentamidine : A diether consisting of pentane-1,5-diol in which both hydroxyl hydrogens have been replaced by 4-amidinophenyl groups. A trypanocidal drug that is used for treatment of cutaneous leishmaniasis and Chagas disease.

Pentamidine: Antiprotozoal agent effective in trypanosomiasis, leishmaniasis, and some fungal infections; used in treatment of PNEUMOCYSTIS pneumonia in HIV-infected patients. It may cause diabetes mellitus, central nervous system damage, and other toxic effects.
aromatic ether;
carboxamidine;
diether
anti-inflammatory agent;
antifungal agent;
calmodulin antagonist;
chemokine receptor 5 antagonist;
EC 2.3.1.48 (histone acetyltransferase) inhibitor;
NMDA receptor antagonist;
S100 calcium-binding protein B inhibitor;
trypanocidal drug;
xenobiotic
pimethixenepimethixene: structurethioxanthenes
saccharinsaccharin : A 1,2-benzisothiazole having a keto-group at the 3-position and two oxo substituents at the 1-position. It is used as an artificial sweetening agent.

Saccharin: Flavoring agent and non-nutritive sweetener.
1,2-benzisothiazole;
N-sulfonylcarboxamide
environmental contaminant;
sweetening agent;
xenobiotic
sulfathiazolesulfathiazole : A 1,3-thiazole compound having a 4-aminobenzenesulfonamido group at the 2-position.

Sulfathiazole: A sulfathiazole compound that is used as a short-acting anti-infective agent. It is no longer commonly used systemically due to its toxicity, but may still be applied topically in combination with other drugs for the treatment of vaginal and skin infections, and is still used in veterinary medicine.
1,3-thiazoles;
substituted aniline;
sulfonamide;
sulfonamide antibiotic
antiinfective agent;
drug allergen;
EC 2.5.1.15 (dihydropteroate synthase) inhibitor;
environmental contaminant;
xenobiotic
suraminsuramin : A member of the class of phenylureas that is urea in which each of the amino groups has been substituted by a 3-({2-methyl-5-[(4,6,8-trisulfo-1-naphthyl)carbamoyl]phenyl}carbamoyl)phenyl group. An activator of both the rabbit skeletal muscle RyR1 and sheep cardiac RyR2 isoform ryanodine receptor channels, it has been used for the treatment of human African trypanosomiasis for over 100 years.

Suramin: A polyanionic compound with an unknown mechanism of action. It is used parenterally in the treatment of African trypanosomiasis and it has been used clinically with diethylcarbamazine to kill the adult Onchocerca. (From AMA Drug Evaluations Annual, 1992, p1643) It has also been shown to have potent antineoplastic properties.
naphthalenesulfonic acid;
phenylureas;
secondary carboxamide
angiogenesis inhibitor;
antinematodal drug;
antineoplastic agent;
apoptosis inhibitor;
EC 2.7.11.13 (protein kinase C) inhibitor;
GABA antagonist;
GABA-gated chloride channel antagonist;
purinergic receptor P2 antagonist;
ryanodine receptor agonist;
trypanocidal drug
gliotoxingliotoxin : A pyrazinoindole with a disulfide bridge spanning a dioxo-substituted pyrazine ring; mycotoxin produced by several species of fungi.

Gliotoxin: A fungal toxin produced by various species of Trichoderma, Gladiocladium fimbriatum, Aspergillus fumigatus, and Penicillium. It is used as an immunosuppressive agent.
dipeptide;
organic disulfide;
organic heterotetracyclic compound;
pyrazinoindole
antifungal agent;
EC 2.5.1.58 (protein farnesyltransferase) inhibitor;
immunosuppressive agent;
mycotoxin;
proteasome inhibitor
alizarindihydroxyanthraquinonechromophore;
dye;
plant metabolite
lawsonelawsone : 1,4-Naphthoquinone carrying a hydroxy function at C-2. It is obtained from the leaves of Lawsonia inermis.

lawsone: a molluscacide from leaves of Lawsonia inermis L. topical sunscreening agent; structure; powdered leaves of Lawsonia inermis(Lythraceae) used as brown hair dye
7-amino-4-hydroxy-2-naphthalenesulfonic acid7-amino-4-hydroxy-2-naphthalenesulfonic acid : An aminonaphthalenesulfonic acid that is 2-naphthalenesulfonic acid substituted by an amino group at position 7 and a hydroxy group at position 4 respectively.

7-amino-4-hydroxy-2-naphthalenesulfonic acid: structure given in first source
aminonaphthalenesulfonic acid;
naphthols
metabolite
1-naphthol-8-amino-3,6-disulfonic acid1-naphthol-8-amino-3,6-disulfonic acid: dye and found in industrial waste
methyl redmethyl red : An azo dye consisting of benzoic acid substituted at position 2 by a 4-[(dimethylamino)phenyl]diazenyl group.

methyl red: RN given refers to parent cpd; structure
toyocamycintoyocamycin : An N-glycosylpyrrolopyrimidine that is tubercidin in which the hydrogen at position 5 of the pyrrolopyrimidine moiety has been replaced by a cyano group.

Toyocamycin: 4-Amino-5-cyano-7-(D-ribofuranosyl)-7H- pyrrolo(2,3-d)pyrimidine. Antibiotic antimetabolite isolated from Streptomyces toyocaensis cultures. It is an analog of adenosine, blocks RNA synthesis and ribosome function, and is used mainly as a tool in biochemistry.
antibiotic antifungal agent;
N-glycosylpyrrolopyrimidine;
nitrile;
ribonucleoside
antimetabolite;
antineoplastic agent;
apoptosis inducer;
bacterial metabolite
nsc 65346sangivamycin : A nucleoside analogue that is adenosine in which the nitrogen at position 7 is replaced by a carbamoyl-substituted carbon. It is a potent inhibitor of protein kinase C.

sangivamycin: RN given refers to parent cpd
nucleoside analogueprotein kinase inhibitor
2-methoxy-1,4-naphthoquinone2-methoxy-1,4-naphthoquinone : A naphthoquinone that is naphthalene-1,4-dione substituted by a methoxy group at position 2. It has been isolated from the roots of Rubia yunnanensis.

2-methoxy-1,4-naphthoquinone: isolated from Swertia calycina; structure in first source
1,4-naphthoquinones;
enol ether
antimicrobial agent;
metabolite;
plant metabolite
s-adenosylmethionineacylcarnitine: structure in first source

S-adenosyl-L-methioninate : A sulfonium betaine that is a conjugate base of S-adenosyl-L-methionine obtained by the deprotonation of the carboxy group.
sulfonium betainehuman metabolite
adenosinequinquefolan B: isolated from roots of Panax quinquefolium L.; RN not in Chemline 10/87; RN from Toxlitadenosines;
purines D-ribonucleoside
analgesic;
anti-arrhythmia drug;
fundamental metabolite;
human metabolite;
vasodilator agent
epigallocatechin gallate(-)-epigallocatechin 3-gallate : A gallate ester obtained by the formal condensation of gallic acid with the (3R)-hydroxy group of (-)-epigallocatechin.

epigallocatechin gallate: a steroid 5alpha-reductase inhibitor and antimutagen in green tea (Camellia sinensis)
flavans;
gallate ester;
polyphenol
antineoplastic agent;
antioxidant;
apoptosis inducer;
geroprotector;
Hsp90 inhibitor;
neuroprotective agent;
plant metabolite
hexamidinehexamidine : A polyether that is the bis(4-guanidinophenyl) ether of hexane-1,6-diol.aromatic ether;
guanidines;
polyether
antimicrobial agent;
antiseptic drug
sinefunginadenosines;
non-proteinogenic alpha-amino acid
antifungal agent;
antimicrobial agent
fluorone blackfluorone Black: structure
3-deazaneplanocin3-deazaneplanocin: S-adenosylhomocysteine hydrolase antagonist
c.i. direct red 23C.I. Direct Red 23: azo dye; structure in first source
5-iodotubercidin7-iodotubercidin: inhibits Toxoplasma gondii adenosine kinaseorganoiodine compound
tanshinonetanshinone: from root of Salvia miltiorrhiza Bunge; RN given refers to tanshinone I; cardioprotective agent and neuroprotective agentabietane diterpenoidanticoronaviral agent
przewaquinone dprzewaquinone D: isolated from root of Salvia przewalskii; structure given in first source; RN given refers to the trans- isomer, przewaquinone D
furamidinefuramidine: RN given refers to parent cpd; WR 199385 refers to di-HCl; pafuramidine is a prodrug of this
tanshinone ii atashinone IIA: a cardiovascular agent with antineoplastic activity; isolated from Salvia miltiorrhiza; structure in first sourceabietane diterpenoid
s-adenosyl-3-thiopropylamineS-adenosyl-3-thiopropylamine : A thioadenosine that is adenosine in which the hydroxy group at C-5' is replaced by a 3-aminopropyl group.

S-adenosyl-3-thiopropylamine: decarboxylated S-adenosylhomocysteine; RN given refers to parent cpd
organic sulfide;
primary amino compound;
thioadenosine
nsc 663284NSC 663284: structure in first sourcequinolone
s-adenosylhomocysteineS-adenosyl-L-homocysteine : An organic sulfide that is the S-adenosyl derivative of L-homocysteine.

S-Adenosylhomocysteine: 5'-S-(3-Amino-3-carboxypropyl)-5'-thioadenosine. Formed from S-adenosylmethionine after transmethylation reactions.
adenosines;
amino acid zwitterion;
homocysteine derivative;
homocysteines;
organic sulfide
cofactor;
EC 2.1.1.72 [site-specific DNA-methyltransferase (adenine-specific)] inhibitor;
EC 2.1.1.79 (cyclopropane-fatty-acyl-phospholipid synthase) inhibitor;
epitope;
fundamental metabolite
5'-methylthioadenosine5'-methylthioadenosine: structure

5'-S-methyl-5'-thioadenosine : Adenosine with the hydroxy group at C-5' substituted with a methylthio (methylsulfanyl) group.
thioadenosinealgal metabolite;
Escherichia coli metabolite;
human metabolite;
mouse metabolite;
Saccharomyces cerevisiae metabolite
eriodictyoleriodictyol : A tetrahydroxyflavanone that is flavanone substituted by hydroxy groups at positions 5, 7, 3' and 4' respectively.

eriodictyol: structure
3'-hydroxyflavanones;
tetrahydroxyflavanone
shikoninshikonin: a naphthazarin; has antineoplastic and angiogenesis inhibiting activitieshydroxy-1,4-naphthoquinone
2-methyl-5-(4-methylanilino)-1,3-benzothiazole-4,7-dioneaminotoluene
sch-202676SCH-202676: An allosteric modulator of both agonist and antagonist binding to G protein-coupled receptors; structure in first source
verticillinsverticillins: 3 antibiotics isolated from imperfect fungus Verticillium: verticillin A, verticillin B (mono-3-hydroxymethyl analog of verticillin A), & verticillin C (differs from verticillin B in that 1 of dioxopiperazine rings has a trisulfide rather than a disulfide bridge; active against gram-positive bacteria & mycobacteria but not against gram-negative bacteria & fungi; RN given refers to cpd with unknown MF; structure (verticillins A & B))
N-(3-nitrophenyl)-1,3-benzodioxole-5-carboxamidearomatic amide
luteolin3'-hydroxyflavonoid;
tetrahydroxyflavone
angiogenesis inhibitor;
anti-inflammatory agent;
antineoplastic agent;
apoptosis inducer;
c-Jun N-terminal kinase inhibitor;
EC 2.3.1.85 (fatty acid synthase) inhibitor;
immunomodulator;
nephroprotective agent;
plant metabolite;
radical scavenger;
vascular endothelial growth factor receptor antagonist
kaempferol7-hydroxyflavonol;
flavonols;
tetrahydroxyflavone
antibacterial agent;
geroprotector;
human blood serum metabolite;
human urinary metabolite;
human xenobiotic metabolite;
plant metabolite
galangin5,7-dihydroxyflavonol: antimicrobial from the twigs of Populus nigra x Populus deltoides; structure in first source

galangin : A 7-hydroxyflavonol with additional hydroxy groups at positions 3 and 5 respectively; a growth inhibitor of breast tumor cells.
7-hydroxyflavonol;
trihydroxyflavone
antimicrobial agent;
EC 3.1.1.3 (triacylglycerol lipase) inhibitor;
plant metabolite
kaempferidekaempferide : A monomethoxyflavone that is the 4'-O-methyl derivative of kaempferol.

kaempferide: structure in first source
7-hydroxyflavonol;
monomethoxyflavone;
trihydroxyflavone
antihypertensive agent;
metabolite
morinmorin : A pentahydroxyflavone that is 7-hydroxyflavonol bearing three additional hydroxy substituents at positions 2' 4' and 5.

morin: a light yellowish pigment found in the wood of old fustic (Chlorophora tinctoria)
7-hydroxyflavonol;
pentahydroxyflavone
angiogenesis modulating agent;
anti-inflammatory agent;
antibacterial agent;
antihypertensive agent;
antineoplastic agent;
antioxidant;
EC 5.99.1.2 (DNA topoisomerase) inhibitor;
hepatoprotective agent;
metabolite;
neuroprotective agent
scutellareinscutellarein : Flavone substituted with hydroxy groups at C-4', -5, -6 and -7.

scutellarein: aglycone of scutellarin from Scutellaria baicalensis; carthamidin is 2S isomer of scutellarein; do not confuse with isoscutellarein and/or isocarthamidin which are respective regioisomers, or with the scutelarin protein
tetrahydroxyflavonemetabolite
wedelolactonewedelolactone : A member of the class of coumestans that is coumestan with hydroxy substituents as positions 1, 8 and 9 and a methoxy substituent at position 3.

wedelolactone: antihepatotoxic coumestan from Eclipta prostrata and Wedelia calendulacea (both Asteraceae); structure given in first source
aromatic ether;
coumestans;
delta-lactone;
polyphenol
antineoplastic agent;
apoptosis inducer;
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor;
hepatoprotective agent;
metabolite
stilbamidinestilbamidine: RN given refers to parent cpd
mbx 1090
bvt.948
chetomin
unc 03217-(2-(2-(dimethylamino)ethoxy)ethoxy)-6-methoxy-2-(4-methyl-1,4-diazepan-1-yl)-N-(1-methylpiperidin-4-yl)quinazolin-4-amine: a G9a antagonist; structure in first sourcequinazolines
epz004777N-glycosyl compound
epz-56765'-deoxyribonucleoside
epz005687EPZ005687: inhibits EZH2 protein; structure in first sourceindazoles
epz-6438tazemetostat: a histone methyltransferase EZH2 inhibitor with antineoplastic activity
gsk-2816126GSK-2816126: inhibits EZH2 methyltransferase; structure in first sourcepiperazines;
pyridines
gsk343GSK343 : A member of the class of indazoles that is 1-isopropyl-1H-indazole-4-carboxamide in which the nitrogen of the carboxamide group is substituted by a (6-methyl-2-oxo-4-propyl-1,2-dihydropyridin-3-yl)methyl group and in which the indazole ring is substituted at position 6 by a 2-(4-methylpiperazin-1-yl)pyridin-4-yl group. A highly potent and selective EZH2 inhibitor (IC50 = 4 nM).

GSK343: an EZH2 methyltransferase inhibitor
aminopyridine;
indazoles;
N-alkylpiperazine;
N-arylpiperazine;
pyridone;
secondary carboxamide
antineoplastic agent;
apoptosis inducer;
EC 2.1.1.43 (enhancer of zeste homolog 2) inhibitor
(r)-pfi-2(R)-PFI-2: a potent and selective inhibitor of SETD7 methyltransferase; structure in first source
1-[(1R)-1-(1-ethylsulfonyl-4-piperidinyl)ethyl]-N-[(4-methoxy-6-methyl-2-oxo-1H-pyridin-3-yl)methyl]-2-methyl-3-indolecarboxamide(R)-1-(1-(1-(ethylsulfonyl)piperidin-4-yl)ethyl)-N-((4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1H-indole-3-carboxamide: EZH2 inhibitorindolecarboxamide
6,7-dimethoxy-2-(pyrrolidin-1-yl)-n-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amine6,7-dimethoxy-2-(pyrrolidin-1-yl)-N-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amine: a SETD8 inhibitor; structure in first source
gsk3235025GSK3235025: an inhibitor of protein arginine methyltransferase-5 (PRMT5); structure in first source
sgc707