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Information on EC 2.1.1.B130 - [histone H3]-N-methyllysine9 N-methyltransferase

for references in articles please use BRENDA:EC2.1.1.B130

preliminary BRENDA-supplied EC number

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EC Tree

2 Transferases

2.1 Transferring one-carbon groups

2.1.1 Methyltransferases

2.1.1.B130 [histone H3]-N-methyllysine9 N-methyltransferase

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The expected taxonomic range for this enzyme is: Arabidopsis thaliana

Reaction Schemes

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N6-methyl-L-lysyl9-[histone H3]

S-adenosyl-L-methionine

N6,N6-dimethyl-L-lysyl9-[histone H3]

S-adenosyl-L-homocysteine

N6-methyl-L-lysyl9-[histone H3]

S-adenosyl-L-methionine

N6,N6,N6-trimethyl-L-lysyl9-[histone H3]

S-adenosyl-L-homocysteine

Synonyms

su(var)3-9 related4, show all synonyms

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SYNONYM

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

SU(VAR)3-9 RELATED4

SUVR4

758783, 759859, 760011

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REACTION

REACTION DIAGRAM

COMMENTARY

ORGANISM

UNIPROT

LITERATURE

N6-methyl-L-lysyl9-[histone H3] + 2 S-adenosyl-L-methionine = N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 2 S-adenosyl-L-homocysteine

2 entries

N6-methyl-L-lysyl9-[histone H3] + S-adenosyl-L-methionine = N6,N6-dimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-homocysteine

2 entries

N6-methyl-L-lysyl9-[histone H3] + 2 S-adenosyl-L-methionine = N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 2 S-adenosyl-L-homocysteine

(2), reaction in the presence of ubiquitin

Arabidopsis thaliana

Q8W595

759859

N6-methyl-L-lysyl9-[histone H3] + 2 S-adenosyl-L-methionine = N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 2 S-adenosyl-L-homocysteine

N6-methyl-L-lysyl9-[histone H3] + S-adenosyl-L-methionine = N6,N6-dimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-homocysteine

(1), reaction in the absence of ubiquitin

Arabidopsis thaliana

Q8W595

759859

N6-methyl-L-lysyl9-[histone H3] + S-adenosyl-L-methionine = N6,N6-dimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-homocysteine

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SYSTEMATIC NAME

IUBMB Comments

S-adenosyl-L-methionine:[histone H3]-N6-methyl-L-lysine9 N6-methyltransferase

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SUBSTRATE

PRODUCT

REACTION DIAGRAM

ORGANISM

UNIPROT

COMMENTARY
(Substrate)

LITERATURE
(Substrate)

COMMENTARY
(Product)

LITERATURE
(Product)

Reversibility
r=reversible
ir=irreversible
?=not specified

N6,N6-dimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-methionine

N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-homocysteine

Arabidopsis thaliana

Q8W595

760011

N6-methyl-L-lysyl9-[histone H3 peptide 1-20] + S-adenosyl-L-methionine

N6,N6-dimethyl-L-lysyl9-[histone H3 peptide 1-20] + S-adenosyl-L-homocysteine

Arabidopsis thaliana

Q8W595

759859

N6-methyl-L-lysyl9-[histone H3 peptide 5-11] + S-adenosyl-L-methionine

N6,N6-dimethyl-L-lysyl9-[histone H3 peptide 5-11] + S-adenosyl-L-homocysteine

Arabidopsis thaliana

Q8W595

759859

N6-methyl-L-lysyl9-[histone H3] + 2 S-adenosyl-L-methionine

N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 2 S-adenosyl-L-homocysteine

Arabidopsis thaliana

Q8W595

760011

N6-methyl-L-lysyl9-[histone H3] + S-adenosyl-L-methionine

N6,N6-dimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-homocysteine

Arabidopsis thaliana

Q8W595

759859, 760011

additional information

2 entries

additional information

Arabidopsis thaliana

Q8W595

in the absence of ubiquitin, SUVR4 converts 40.9% of the H3K9me1 peptide to H3K9me2, while 0% is converted to H3K9me3. In the presence of ubiquitin, 90.2% of the H3K9me1 peptide is converted to H3K9me2 while 3.5% is converted to H3K9me3. When H3K9me2 peptides are used as substrate, there is no conversion to H3K9me3 above background level in the absence of ubiquitin. When ubiquitin is present together with SUVR4, a 16.4% conversion from H3K9me2 to H3K9me3 is found

760011

additional information

Arabidopsis thaliana

Q8W595

SUVR4 protein shows very low histone methyltransferase activity against the unmethylated histone H3 1-20 peptide. SUVR4 is also unable to methylate H3 1-20 peptides monomethylated at K4 or dimethylated at K9. SUVR4 is able to methylate histone H3 peptides of variable size when monomethylated at K9, but not when monomethylated at K4 or K27 or dimethylated on K9

759859

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INHIBITOR

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

IMAGE

additional information

Arabidopsis thaliana

Q8W595

presence of trimethyl-H3K4 reduces SUVR4 activity significantly

760011

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ACTIVATING COMPOUND

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

IMAGE

ubiquitin

Arabidopsis thaliana

Q8W595

addition of free ubiquitin stimulates enzymatic activity of the SUVR4 protein on histone H3 but does not affect its specificity. In presence of ubiquitin, methylation of H3K9me1 modified peptides increases 2.5-3fold. Trimethylation of the H3K9me2 peptide is observed in the presence of ubiquitin

760011

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ORGANISM

COMMENTARY

LITERATURE

UNIPROT

SEQUENCE DB

SOURCE

UniProt

brenda

Arabidopsis thaliana

at least two different transcripts are expressed. SUVR4a contains 9 exons with an ORF of 1395 bp (465 amino acids). Alternative splice variant, SUVR4b, retains the 81 bp second intron, resulting in an ORF of 1476 bp

759859

Q8W595

UniProt

brenda

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LOCALIZATION

ORGANISM

UNIPROT

COMMENTARY

GeneOntology No.

LITERATURE

SOURCE

brenda

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GENERAL INFORMATION

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

physiological function

2 entries

physiological function

Arabidopsis thaliana

Q8W595

SUVR4 binds histone H3 irrespective of the methylation status of lysine 9

759859

physiological function

Arabidopsis thaliana

Q8W595

the N-terminal WIYLD domain of the SUVR4 HKMTase binds ubiquitin and the SUVR4 product specificity shifts from di- to trimethylation in the presence of free ubiquitin, enabling conversion of H3K9me1 to H3K9me3 in vitro. SUVR4 in vivo specifically converts H3K9me1 to H3K9me3 at transposons and pseudogenes and has a locus-specific repressive effect on the expression of such elements. This repression involves both DNA methylation-dependent and -independent mechanisms

760011

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UNIPROT

ENTRY NAME

ORGANISM

NO. OF AA

NO. OF TRANSM. HELICES

MOLECULAR WEIGHT[Da]

SOURCE

SEQUENCE

LOCALIZATION PREDICTION

The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).

Q8W595 pBLAST

SUVR4_ARATH

Arabidopsis thaliana

492

55855

Swiss-Prot

Show Sequence

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CRYSTALLIZATION (Commentary)

ORGANISM

UNIPROT

LITERATURE

SUVR4 WIYLD-domain is a domain with a four-helix bundle structure binding ubiquitin. Residues of helix alpha1 (Q38, L39, and D40) and helix alpha4 (N68, T70, A71, V73, D74, I76, S78, and E82) of WIYLD and residues between the first and second beta-strands (T9 and G10) and on beta-strands 3 (R42, G47, K48, and Q49) and 4 (H68, R72, and L73) undergo significant chemical shift changes when the two proteins interact

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PROTEIN VARIANTS

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

A32E

Arabidopsis thaliana

Q8W595

mutation in WIYLD domain, reduces the binding affinity to ubiquitin by 37%. The mutation disrupts the entire domain structure

758783

W405F

Arabidopsis thaliana

Q8W595

loss of catalytic activity

759859

W405Y

Arabidopsis thaliana

Q8W595

loss of catalytic activity

759859

W61R

Arabidopsis thaliana

Q8W595

mutation in WIYLD domain, reduces the binding affinity to ubiquitin by 75%

758783

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REF.

AUTHORS

TITLE

JOURNAL

VOL.

PAGES

YEAR

ORGANISM (UNIPROT)

PUBMED ID

SOURCE

758783

Rahman, M.A.; Kristiansen, P.E.; Veiseth, S.V.; Andersen, J.T.; Yap, K.L.; Zhou, M.M.; Sandlie, I.; Thorstensen, T.; Aalen, R.B.

The Arabidopsis histone methyltransferase SUVR4 binds ubiquitin via a domain with a four-helix bundle structure

Biochemistry

2091-2100

2014

Arabidopsis thaliana (Q8W595), Arabidopsis thaliana

24625295

brenda

759859

Thorstensen, T.; Fischer, A.; Sandvik, S.V.; Johnsen, S.S.; Grini, P.E.; Reuter, G.; Aalen, R.B.

The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9

Nucleic Acids Res.

5461-5470

2006

Arabidopsis thaliana (Q8W595)

17020925

brenda

760011

Veiseth, S.V.; Rahman, M.A.; Yap, K.L.; Fischer, A.; Egge-Jacobsen, W.; Reuter, G.; Zhou, M.M.; Aalen, R.B.; Thorstensen, T.

The SUVR4 histone lysine methyltransferase binds ubiquitin and converts H3K9me1 to H3K9me3 on transposon chromatin in Arabidopsis

PLoS Genet.

e1001325

2011

Arabidopsis thaliana (Q8W595)

21423664

brenda

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EXTERNAL LINKS (specific for EC-Number 2.1.1.B130)

ExplorEnz (official portal for IUBMB Enzyme Nomenclature)

Expasy Enzyme Nomenclature Database

KEGG

MetaCyc

SABIO-RK

NCBI: PubMed, Protein, Nucleotide, Structure, Gene, OMIM

Enzyme Nomenclature (alternative site)

UniProt

PDB

PROSITE Database of protein families and domains

InterPro (database of protein families, domains and functional sites)

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