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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1h3ia1	All beta proteins	open-sided beta-meander	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1h3ia2	All beta proteins	beta-clip	SET domain	Histone lysine methyltransferases	Histone H3 K4-specific methyltransferase SET7/9 catalytic domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1h3ib1	All beta proteins	open-sided beta-meander	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1h3ib2	All beta proteins	beta-clip	SET domain	Histone lysine methyltransferases	Histone H3 K4-specific methyltransferase SET7/9 catalytic domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
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)
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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00856	SET domain (SET)	SET domain	-	Family
A, B	PF02493	MORN repeat (MORN)	MORN repeat	-	Repeat
A, B	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

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	HISTONE H3 LYSINE 4 SPECIFIC METHYLTRANSFERASE	p53 binding protein binding binding protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity histone modifying activity p53 binding protein binding binding protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity histone modifying activity histone methyltransferase activity histone H3 methyltransferase activity histone H3K4 monomethyltransferase activity histone H3K4 methyltransferase activity chromatin binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process peptidyl-lysine methylation protein methylation peptidyl-lysine modification peptidyl-lysine monomethylation primary metabolic process macromolecule methylation protein alkylation methylation cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process peptidyl-lysine methylation protein methylation peptidyl-lysine modification peptidyl-lysine monomethylation primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification metabolic process protein metabolic process macromolecule metabolic process protein modification process cellular component organization chromatin organization heterochromatin organization cellular component organization or biogenesis peptidyl-lysine dimethylation regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process response to alcohol response to chemical response to oxygen-containing compound response to ethanol	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen chromosome nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR046341	SET domain superfamily	Homologous Superfamily
A, B	IPR017155	Histone-lysine N-methyltransferase SETD7	Family
A, B	IPR001214	SET domain	Domain
A, B	IPR054533	Histone-lysine methyltransferase SETD7, N-terminal	Domain
A, B	IPR003409	MORN repeat	Repeat
A, B	IPR044436	SETD7, SET domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8WTS6	atypical teratoid rhabdoid tumor malignant ependymoma pituitary cancer Crohn disease ovarian cancer ulcerative colitis invasive ductal breast carcinoma pancreatic ductal adenocarcinoma

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	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] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.1.1.43 (PDB Primary Data) Search M-CSA Motif + EC 2.1.1.43 EC: 2.1.1.364 (UniProt) Search M-CSA Motif + EC 2.1.1.364

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.