6VFO | pdb_00006vfo

Solution structure of the PHD of mouse UHRF1 (NP95)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
A	d6vfoa_	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RNase_P_p30	e6vfoA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: RNase_P_p30	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.1150	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	E3 ubiquitin-protein ligase UHRF1	histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity binding nucleic acid binding protein binding histone binding aminoacyltransferase activity catalytic activity, acting on a protein acyltransferase activity 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 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 H3K14 ubiquitin ligase 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 hemi-methylated DNA-binding identical protein binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding histone H3K23 ubiquitin ligase activity histone H3K18 ubiquitin ligase activity	protein autoubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process protein catabolic process protein autoubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process cellular component organization chromatin organization cellular component organization or biogenesis chromosomal DNA methylation maintenance following DNA replication cellular response to stimulus response to stimulus DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress DNA repair regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of protein metabolic process regulation of protein metabolic process negative regulation of gene expression via chromosomal CpG island methylation chromatin remodeling epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization microtubule cytoskeleton organization membraneless organelle assembly mitotic cell cycle 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin membrane-bounded organelle nucleus membrane-enclosed lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear lumen nuclear matrix nucleoplasm replication fork euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.