1H3I
Crystal structure of the Histone Methyltransferase SET7/9
External Resource: Annotation
- Domain Annotation: SCOP/SCOPe Classification
- Domain Annotation: SCOP2 Classification
- Domain Annotation: ECOD Classification
- Domain Annotation: CATH
- Protein Family Annotation
- Gene Ontology: Gene Product Annotation
- InterPro: Protein Family Classification
- Pharos: Disease Associations
- Structure Motif: Primary M-CSA Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
B | SCOP2B Superfamily | Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain | 8042398 | 3001729 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | SET domain | 8042399 | 3000162 | SCOP2B (2022-06-29) |
A | SCOP2 Family | Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain | 8030019 | 4002773 | SCOP2 (2022-06-29) |
A | SCOP2 Family | Histone lysine methyltransferases | 8030020 | 4000376 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain | 8042398 | 3001729 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | SET domain | 8042399 | 3000162 | SCOP2 (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
B | SET | e1h3iB1 | A: beta barrels | X: beta-clip | H: SET domain-like (From Topology) | T: SET domain-like | F: SET | ECOD (1.6) |
B | KOG1079_3rd_1 | e1h3iB2 | A: beta meanders | X: open-sided beta-meander | H: Histone H3 K4-specific methyltransferase SET7/9-N (From Topology) | T: Histone H3 K4-specific methyltransferase SET7/9-N | F: KOG1079_3rd_1 | ECOD (1.6) |
A | SET | e1h3iA1 | A: beta barrels | X: beta-clip | H: SET domain-like (From Topology) | T: SET domain-like | F: SET | ECOD (1.6) |
A | KOG1079_3rd_1 | e1h3iA2 | A: beta meanders | X: open-sided beta-meander | H: Histone H3 K4-specific methyltransferase SET7/9-N (From Topology) | T: Histone H3 K4-specific methyltransferase SET7/9-N | F: KOG1079_3rd_1 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
B | 2.20.110.10 | Mainly Beta | Single Sheet | Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain | Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain | CATH (4.3.0) |
B | 2.170.270.10 | Mainly Beta | Beta Complex | Beta-clip-like | SET domain | CATH (4.3.0) |
A | 2.20.110.10 | Mainly Beta | Single Sheet | Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain | Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain | CATH (4.3.0) |
A | 2.170.270.10 | Mainly Beta | Beta Complex | Beta-clip-like | SET domain | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00856 | SET domain (SET) | SET domain | - | Family | |
PF02493 | MORN repeat (MORN) | MORN repeat | - | Repeat | |
PF22648 | Histone H3 K4-specific methyltransferase SET7 N-terminal (SET7_N) | Histone H3 K4-specific methyltransferase SET7 N-terminal | - | Repeat |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR046341 | SET domain superfamily | Homologous Superfamily | |
IPR017155 | Histone-lysine N-methyltransferase SETD7 | Family | |
IPR001214 | SET domain | Domain | |
IPR003409 | MORN repeat | Repeat | |
IPR044436 | SETD7, SET domain | Domain |
Pharos: Disease Associations Pharos Homepage Annotation
Chains | Drug Target   | Associated Disease |
---|---|---|
Q8WTS6 | : 
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
histone-lysine N-methyltransferase (SET7/9 subfamily) M-CSA #350 | Human methyltransferase SET7/9 catalyses the transfer of a methyl group from the cosubstrate ADOmet to a Lysine residue in Histone H3. Such methylation is used in the regulation of transcription of DNA: it inactivates the DNA towards transcription by creating a silenced chromatin domain. The enzyme displays homology to other SET containing proteins both in humans and in other eukaryotes such as fission yeast (S. cereviseae), with high levels of sequence and structural similarity between the proteins. As a result the SET catalytic domain conserved between the proteins is considered to have the same mechanism in all the methyltransferases. Several studies have been done on this enzyme, however the method of deprotonation of the histone-lysine is still unclear [PMID:21266482]. Although the mechanism seems to be the same among different proteins, there is a variability in the active site and in presence of zinc finger containing domains. The latter seems to be involved in substrate recognition and binding [PMID:12372304]. Tyr335, Tyr245, and His297 residues are highly conserved [PMID:12372305]. The histidine residues are believed to assist the tyrosine residues with their catalytic function [PMID:12514135]. Tyr305, present only in SET7/9 proteins, appears to assume the role of Tyr335 when this residue is mutated [PMID:20675860]. SET7/9 proteins only perform monomethylation of histone-lysine, whereas other proteins can perform further di- and trimethylations [PMID:12887903]. The rearrangement of water molecules in the active site is proposed to promote this further methylation [8]. The geometry optimisation of SET7/9 complex with SAM substrate showed the formation of CH...O hydrogen bonds AdoMet methyl and His293 main chain carbonyl and Tyr335 hydroxyl [PMID:21454678]. The unusually high pH optimum [PMID:12887903, PMID:12372305] suggests partial deprotonation of the target lysine and hydroxyl group of the tyrosine. Nonetheless, pKa calculations [PMID:18391193] contradict the presence of tyrosine hydroxyl anion. | Defined by 5 residues: TYR:A-194 [auth A-245]HIS:A-242 [auth A-293]HIS:A-246 [auth A-297]TYR:A-254 [auth A-305]TYR:A-284 [auth A-335] | EC: 2.1.1.43 (PDB Primary Data) |