2ZKD

Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E [auth A]	d2zkda1	All beta proteins	PUA domain-like	PUA domain-like	SRA domain-like	E3 ubiquitin-protein ligase UHRF1	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth B]	d2zkdb_	All beta proteins	PUA domain-like	PUA domain-like	SRA domain-like	E3 ubiquitin-protein ligase UHRF1	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2 Family	SRA domain-like	8026221	4001997	SCOP2 (2022-06-29)
E [auth A]	SCOP2 Superfamily	PUA domain-like	8038600	3001015	SCOP2 (2022-06-29)
F [auth B]	SCOP2B Superfamily	PUA domain-like	8038600	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)
E [auth A]	SAD_SRA	e2zkdA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: SAD_SRA	ECOD (1.6)
F [auth B]	SAD_SRA	e2zkdB1	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)
E [auth A]	2.30.280.10	Mainly Beta	Roll	PUA domain-like	SRA-YDG	CATH (4.3.0)
F [auth B]	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
E [auth A], F [auth B]	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-m ...	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 C], C [auth E]	DNA (5'-D(DCPDTPDAPDCPDCPDGPDGPDAPDTPDTPDGPDC)-3')	-	-	-
B [auth D], D [auth F]	DNA (5'-D(DGPDCPDAPDAPDTPDCP(5CM)PDGPDGPDTPDAPDG)-3')	-	-	-
E [auth A], F [auth B]	E3 ubiquitin-protein ligase UHRF1	binding organic cyclic compound binding nucleic acid binding protein binding histone binding aminoacyltransferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity histone ubiquitin ligase activity ubiquitin-protein transferase activity ubiquitin-like protein transferase activity histone H3 ubiquitin ligase activity ubiquitin-like protein ligase activity binding organic cyclic compound binding nucleic acid binding protein binding histone binding aminoacyltransferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity histone ubiquitin ligase activity ubiquitin-protein transferase activity ubiquitin-like protein transferase activity histone H3 ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity histone modifying activity catalytic activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding hemi-methylated DNA-binding methylated histone binding modification-dependent protein binding methylation-dependent protein binding identical protein binding	regulation of biological process organonitrogen compound metabolic process positive regulation of protein metabolic process regulation of protein metabolic process biological regulation positive regulation of biological process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process organic substance metabolic process metabolic process positive regulation of macromolecule metabolic process protein metabolic process regulation of biological process organonitrogen compound metabolic process positive regulation of protein metabolic process regulation of protein metabolic process biological regulation positive regulation of biological process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process organic substance metabolic process metabolic process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular 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 cellular process protein autoubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process organic substance catabolic process cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation cellular response to stimulus response to stimulus DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process cellular response to stress DNA damage response response to stress DNA repair heterochromatin formation non-membrane-bounded organelle assembly microtubule cytoskeleton organization mitotic cell cycle cellular component biogenesis cellular component assembly mitotic sister chromatid segregation cell cycle chromosome segregation microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process mitotic nuclear division organelle assembly organelle fission chromosome organization sister chromatid segregation spindle assembly mitotic spindle organization mitotic spindle assembly organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation microtubule-based process cytoskeleton organization negative regulation of RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix cytoplasm membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix cytoplasm cytosol nucleoplasm protein-containing complex protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle replication fork heterochromatin euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR015947	PUA-like superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR001965	Zinc finger, PHD-type	Domain
E [auth A], F [auth B]	IPR003105	SRA-YDG	Domain
E [auth A], F [auth B]	IPR019787	Zinc finger, PHD-finger	Domain
E [auth A], F [auth B]	IPR047406	E3 ubiquitin-protein ligase UHRF1, ubiquitin-like domain	Domain
E [auth A], F [auth B]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
E [auth A], F [auth B]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
E [auth A], F [auth B]	IPR000626	Ubiquitin-like domain	Domain
E [auth A], F [auth B]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
E [auth A], F [auth B]	IPR021991	UHRF1, tandem tudor domain	Domain
E [auth A], F [auth B]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR045134	UHRF1/2-like	Family
E [auth A], F [auth B]	IPR001841	Zinc finger, RING-type	Domain
E [auth A], F [auth B]	IPR036987	SRA-YDG superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.