4PW7 | pdb_00004pw7

structure of UHRF2-SRA in complex with a 5mC-containing DNA

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d4pw7f_	All beta proteins	PUA domain-like	PUA domain-like	SRA domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4pw7e_	All beta proteins	PUA domain-like	PUA domain-like	SRA domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4pw7b_	All beta proteins	PUA domain-like	PUA domain-like	SRA domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4pw7a_	All beta proteins	PUA domain-like	PUA domain-like	SRA domain-like	automated matches	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)
F	SCOP2B Superfamily	PUA domain-like	8087509	3001015	SCOP2B (2022-06-29)
E	SCOP2 Family	SRA domain-like	8087508	4001997	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	PUA domain-like	8087509	3001015	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PUA domain-like	8087509	3001015	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PUA domain-like	8087509	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)
F	SAD_SRA	e4pw7F1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: SAD_SRA	ECOD (1.6)
E	SAD_SRA	e4pw7E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: SAD_SRA	ECOD (1.6)
B	SAD_SRA	e4pw7B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: SAD_SRA	ECOD (1.6)
A	SAD_SRA	e4pw7A1	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)
F	2.30.280.10	Mainly Beta	Roll	PUA domain-like	SRA-YDG	CATH (4.3.0)
E	2.30.280.10	Mainly Beta	Roll	PUA domain-like	SRA-YDG	CATH (4.3.0)
B	2.30.280.10	Mainly Beta	Roll	PUA domain-like	SRA-YDG	CATH (4.3.0)
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, B, E, F	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
D, H	5mC-containing DNA2	-	-	-
C, G	5mC-containing DNA1	-	-	-
A, B, E, F	E3 ubiquitin-protein ligase UHRF2	histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding histone binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding aminoacyltransferase activity ubiquitin-like protein transferase activity histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding histone binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity SUMO transferase activity DNA binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process cellular developmental process cell differentiation cellular process regulation of cellular process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process developmental process cellular developmental process cell differentiation cellular process regulation of cellular process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process protein autoubiquitination primary metabolic process protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal peptidyl-lysine modification protein sumoylation peptidyl-amino acid modification RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription cell cycle regulation of cell cycle	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen pericentric heterochromatin intracellular membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen pericentric heterochromatin intracellular membraneless organelle chromatin chromosome heterochromatin chromosomal region membraneless organelle chromosome, centromeric region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E, F	IPR015947	PUA-like superfamily	Homologous Superfamily
A, B, E, F	IPR001965	Zinc finger, PHD-type	Domain
A, B, E, F	IPR047407	E3 ubiquitin-protein ligase UHRF2, first Tudor domain	Domain
A, B, E, F	IPR047468	E3 ubiquitin-protein ligase UHRF2, ubiquitin-like domain	Domain
A, B, E, F	IPR003105	SRA-YDG	Domain
A, B, E, F	IPR019787	Zinc finger, PHD-finger	Domain
A, B, E, F	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B, E, F	IPR047466	E3 ubiquitin-protein ligase UHRF2, RING finger, HC subclass	Domain
A, B, E, F	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, B, E, F	IPR047467	E3 ubiquitin-protein ligase UHRF2, PHD finger	Domain
A, B, E, F	IPR000626	Ubiquitin-like domain	Domain
A, B, E, F	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, E, F	IPR021991	UHRF1, tandem tudor domain	Domain
A, B, E, F	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B, E, F	IPR045134	UHRF1/2-like	Family
A, B, E, F	IPR001841	Zinc finger, RING-type	Domain
A, B, E, F	IPR036987	SRA-YDG superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, E, F	Pharos: Q96PU4	colorectal cancer ovarian cancer juvenile dermatomyositis pancreatic ductal adenocarcinoma osteosarcoma

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.