3SHB | pdb_00003shb

Crystal Structure of PHD Domain of UHRF1

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FYVE/PHD zinc finger	8084742	3001459	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	Avidin	e3shbA1	A: alpha bundles	X: Cystatin-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Avidin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

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 DNA damage sensor activity molecular sensor activity molecular function regulator activity 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	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress 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 response to stimulus cellular response to stress response to stimulus DNA damage response response to stress 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 metabolic process cellular component organization or biogenesis 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 nucleobase-containing compound metabolic process homologous recombination DNA recombination DNA metabolic process nucleic acid metabolic process catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process chromosomal DNA methylation maintenance following DNA replication 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 transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription 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 negative regulation of gene expression negative regulation of gene expression, epigenetic localization protein localization to chromatin protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation double-strand break repair recombinational repair double-strand break repair via homologous recombination DNA repair 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	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin cytoskeleton spindle microtubule cytoskeleton membrane-bounded organelle nucleus intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin cytoskeleton spindle microtubule cytoskeleton membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear lumen nuclear matrix nucleoplasm replication fork euchromatin
B	Histone H3 peptide	-	-	-

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q96T88	adenoid cystic carcinoma salivary gland adenoid cystic carcinoma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm psoriasis skin basal cell carcinoma atopic eczema breast cancer endometriosis hypothyroidism large cell medulloblastoma malignant glioma nasopharyngeal carcinoma ovarian cancer adenoid cystic carcinoma salivary gland adenoid cystic carcinoma medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm psoriasis skin basal cell carcinoma atopic eczema breast cancer endometriosis hypothyroidism large cell medulloblastoma malignant glioma nasopharyngeal carcinoma ovarian cancer pilocytic astrocytoma adrenal cortex carcinoma tuberculosis attention deficit hyperactivity disorder, inattentive type breast carcinoma glioblastoma interstitial cystitis lung adenocarcinoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor Sjogren syndrome astrocytic tumor vitiligo atypical teratoid rhabdoid tumor ductal breast carcinoma in situ hepatocellular carcinoma invasive ductal breast carcinoma malignant ependymoma

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.