3Q0C | pdb_00003q0c

Crystal structure of SUVH5 SRA-fully methylated CG DNA complex in space group P6122

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth X]	SCOP2B Superfamily	PUA domain-like	8087511	3001015	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	PUA domain-like	8087511	3001015	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 [auth X]	SAD_SRA	e3q0cX1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: SAD_SRA	ECOD (1.6)
B [auth A]	SAD_SRA	e3q0cA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: SAD_SRA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth X]	2.30.280.10	Mainly Beta	Roll	PUA domain-like	SRA-YDG	CATH (4.3.0)
B [auth A]	2.30.280.10	Mainly Beta	Roll	PUA domain-like	SRA-YDG	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth X], B [auth A]	PF02182	SAD/SRA domain (SAD_SRA)	SAD/SRA domain	The domain goes by several names including SAD [1], SRA [2] and YDG [3]. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria [4]. Versions of this domain are known to bind hemi-me ...	The domain goes by several names including SAD [1], SRA [2] and YDG [3]. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria [4]. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix [5].The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base [4][5]. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks [2]. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination [4]. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions [4]. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains [6]. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth X], B [auth A]	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity histone modifying activity transferase activity methyltransferase activity catalytic activity histone methyltransferase activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity histone H3K9me2 methyltransferase activity histone H3K9 methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity histone modifying activity transferase activity methyltransferase activity catalytic activity histone methyltransferase activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity histone H3K9me2 methyltransferase activity histone H3K9 methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity lysine N-methyltransferase activity N-methyltransferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	methylation metabolic process cellular process regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process methylation metabolic process cellular process regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process cellular component organization or biogenesis macromolecule metabolic process regulation of metabolic process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process heterochromatin formation negative regulation of metabolic process regulatory ncRNA-mediated gene silencing negative regulation of gene expression regulatory ncRNA-mediated heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle chromosome, centromeric region intracellular membraneless organelle chromosome chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C, D [auth B]	DNA (5'-D(APCPTPAP(5CM)PGPTPAPGPTP*T)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth X], B [auth A]	IPR015947	PUA-like superfamily	Homologous Superfamily
A [auth X], B [auth A]	IPR007728	Pre-SET domain	Domain
A [auth X], B [auth A]	IPR046341	SET domain superfamily	Homologous Superfamily
A [auth X], B [auth A]	IPR051357	Histone-lysine N-methyltransferase SUVAR3-9	Family
A [auth X], B [auth A]	IPR001214	SET domain	Domain
A [auth X], B [auth A]	IPR025794	Histone H3-K9 methyltransferase, plant	Family
A [auth X], B [auth A]	IPR003105	SRA-YDG	Domain
A [auth X], B [auth A]	IPR036987	SRA-YDG superfamily	Homologous Superfamily
A [auth X], B [auth A]	IPR003616	Post-SET domain	Domain

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.