EC 2.1.1.366 - [histone H3]-N(6),N(6)-dimethyl-lysine(9) N-methyltransferase.

_EC 2.1.1.366 [histone H3]-N(6),N(6)-dimethyl-lysine(9) N-methyltransferase.

33 PDB entries

EC 2.-.-.- Transferases. [47,784 PDB entries]

EC 2.1.-.- Transferring one-carbon groups. [5,181 PDB entries]

EC 2.1.1.- Methyltransferases. [4,592 PDB entries]

EC 2.1.1.366 [histone H3]-N(6),N(6)-dimethyl-lysine(9) N-methyltransferase. [33 PDB entries]

1g6z

Reaction: N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine = N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L- homocysteine + H(+).

N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3]
+
S-adenosyl-L-methionine
= N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3]
+
S-adenosyl-L- homocysteine
+ H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

Comments: The enzyme methylates only dimethylated lysine(9) of histone H3 (H3K9), forming the trimethylated form. This modification influences the binding of chromatin-associated proteins. In general, the methylation of H3K9 leads to transcriptional repression of the affected target genes. The enzyme is highly up-regulated in Huntington disease patients. cf. Ec 2.1.1.355, Ec 2.1.1.367, and Ec 2.1.1.368.

Links: [IntEnz] [ExPASy] [KEGG]

There are 33 PDB entries in enzyme class E.C.2.1.1.366

PDB code Protein

1g6z

Solution structure of the clr4 chromo domain

Source: Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Gene: clr4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Chain: A (70 residues) CATH domain: 2.40.50.40

1mvh

Structure of the set domain histone lysine methyltransferase clr4

Source: Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (269 residues) CATH domain: 2.170.270.10

1mvx

Structure of the set domain histone lysine methyltransferase clr4

Source: Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (269 residues) CATH domain: 2.170.270.10

2lxe

S4wyild

Source: Arabidopsis thaliana. Mouse-ear cress,thale-cress. Organism_taxid: 3702. Gene: suvr4, sdg31, set31, at3g04380, t27c4.2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Chain: A (109 residues) CATH domain: 1.10.8.850

3dlm

Crystal structure of tudor domain of human histone-lysine n- methyltransferase setdb1

Source: Homo sapiens. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli.

Chain: A (208 residues) CATH domains: 2.30.30.140 Unassigned 2.30.30.140

5kch

Setdb1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy into weak electron density

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (212 residues) CATH domains: 2.30.30.140 Unassigned 2.30.30.140

Bound ligand: Het Group 6RN is 41.38% similar to enzyme product S-adenosyl-L-homocysteine

5kco

Setdb1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (212 residues) CATH domains: 2.30.30.140 Unassigned 2.30.30.140

5ke2

Crystal structure of setdb1 tudor domain in complex with inhibitor xst06472a

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (207 residues) CATH domains: 2.30.30.140 Unassigned 2.30.30.140

5ke3

Crystal structure of setdb1 tudor domain in complex with fragment mrt0181a

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (207 residues) CATH domains: 2.30.30.140 Unassigned 2.30.30.140

5kh6

Setdb1 in complex with a fragment candidate

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (211 residues) CATH domains: 2.30.30.140 Unassigned 2.30.30.140

5qt1

Pandda analysis group deposition -- partial occupancy interpretation of pandda event map: setdb1 in complex with fmomb000017a

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, eset, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (211 residues)

5qt2

Pandda analysis group deposition -- partial occupancy interpretation of pandda event map: setdb1 in complex with fmopl000074a

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, eset, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (211 residues)

5tfp

Crystal structure of the setdb2 amino terminal domain

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb2, c13orf4, clld8, kmt1f. Expressed in: escherichia coli. Expression_system_taxid: 562

Chains: A, B (59 residues)

6au2

Crystal structure of setdb1 tudor domain with aryl triazole fragments

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 562.

Chain: A (210 residues)

6au3

Crystal structure of setdb1 tudor domain with aryl triazole fragments

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 562.

Chain: A (206 residues)

6bhd

Crystal structure of setdb1 with a modified h3 peptide

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 9606

Chain: A (217 residues)

6bhe

Crystal structure of setdb1 with a modified h3 peptide

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 9606

Chain: A (216 residues)

6bhg

Crystal structure of setdb1 with a modified h3 peptide

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 9606

Chain: A (215 residues)

6bhh

Crystal structure of setdb1 with a modified h3 peptide

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 9606

Chain: A (211 residues)

6bhi

Crystal structure of setdb1 with a modified h3 peptide

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 9606

Chain: A (216 residues)

6box

Structure of the s. Pombe clr4 catalytic domain bound to sah

Source: Schizosaccharomyces pombe (strain 972 / atcc 24843). Fission yeast. Organism_taxid: 284812. Strain: 972 / atcc 24843. Gene: clr4, kmt1, spbc428.08c. Expressed in: escherichia coli. Expression_system_taxid: 562

Chains: A, B (270 residues)

Bound ligand: Het Group SAH corresponds to enzyme product S-adenosyl-L-homocysteine

6bp4

Structure of the s. Pombe clr4 catalytic domain bound to sam

Source: Schizosaccharomyces pombe (strain 972 / atcc 24843). Fission yeast. Organism_taxid: 284812. Strain: 972 / atcc 24843. Gene: clr4, kmt1, spbc428.08c. Expressed in: escherichia coli. Expression_system_taxid: 562

Chains: B, A (282 residues)

Bound ligand: Het Group SAM corresponds to enzyme reactant S-adenosyl-L-methionine

6bpi

Crystal structure of setdb1 tudor domain with aryl triazole fragment peptide conjugates

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606

Chain: A (207 residues)

6z2a

Structure of clr4 mutant - f256a/f310a/f427a bound to sah

Source: Schizosaccharomyces pombe (strain 972 / atcc 24843). Organism_taxid: 284812. Gene: clr4, kmt1, spbc428.08c. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: rosettaii. Expression_system_cell_line: rosettaii

Chains: A, B (283 residues)

Bound ligand: Het Group SAH corresponds to enzyme product S-adenosyl-L-homocysteine

7c9n

Crystal structure of setdb1 tudor domain in complexed with compound 1.

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, eset, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 562

Chains: B, A (215 residues)

7caj

Crystal structure of setdb1 tudor domain in complexed with compound 2.

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, eset, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 562

Chains: D, A (211 residues)

7cd9

Crystal structure of setdb1 tudor domain in complexed with compound 6

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, eset, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 562

Chains: A, B (215 residues)

7cjt

Crystal structure of setdb1 tudor domain in complexed with (r,r)-59

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, eset, kiaa0067, kmt1e. Expressed in: escherichia coli. Expression_system_taxid: 562

Chains: D, A, B, C (212 residues)

8g5e

Crystal structure of setdb1 tudor domain in complex with unc6535

Source: Homo sapiens

Chain: A (211 residues)

8hfp

Crystal structure of the methyl-cpg-binding domain of setdb2 in complex with the cysteine-rich domain of c11orf46 protein

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: arl14ep, arf7ep, c11orf46. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: setdb2, c13orf4, clld8, kmt1f. Expression_system_taxid: 469008

Chains: C, D (87 residues)

8uwp

Crystal structure of setdb1 tudor domain in complex with mr46747

Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: setdb1, kiaa0067, kmt1e. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: -prare2.

Chains: A, B (212 residues)

9isz

Structure of clr4 catalyzing k14-ubiquitinated histone h3 k9 methylation

Source: Schizosaccharomyces pombe 972h-. Organism_taxid: 284812. Strain: 972 / atcc 24843. Atcc: 24843. Gene: clr4, kmt1, spbc428.08c. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human.

Chains: A, B (279 residues)

9it4

Structure of clr4 catalyzing histone h3 k9 methylation

Source: Schizosaccharomyces pombe 972h-. Organism_taxid: 284812. Strain: 972. Variant: 972 / atcc 24843. Atcc: 24843. Gene: clr4, kmt1, spbc428.08c. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes.

Chain: B (272 residues)