Annotations: 4NM6

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Tet_JBP	e4nm6A1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Tet_JBP	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF12851	Oxygenase domain of the 2OGFeDO superfamily (Tet_JBP)	Oxygenase domain of the 2OGFeDO superfamily	A double-stranded beta helix (DSBH) fold domain of the 2-oxoglutarate (2OG)-Fe(II)-dependent dioxygenase (2OGFeDO) superfamily found in various eukaryotes, bacteria and bacteriophages [1]. Members of this family catalyze nucleic acid modifications, ...	A double-stranded beta helix (DSBH) fold domain of the 2-oxoglutarate (2OG)-Fe(II)-dependent dioxygenase (2OGFeDO) superfamily found in various eukaryotes, bacteria and bacteriophages [1]. Members of this family catalyze nucleic acid modifications, such as thymidine hydroxylation during base J synthesis in kinetoplastids [2], and the conversion of 5 methyl-cytosine (5-mC) to 5-hydroxymethyl-cytosine (hmC) [3], or further oxidation to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) [4]. Metazoan TET proteins contain a cysteine-rich region inserted into the core of the DSBH fold. Vertebrate TET proteins are oncogenes that are mutated in various myeloid cancers [5]. Fungal and algal versions of this family are linked to a predicted transposase and show lineage-specific expansions [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Methylcytosine dioxygenase TET2	DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding iron ion binding ion binding ferrous iron binding metal ion binding small molecule binding 5-methylcytosine dioxygenase activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding iron ion binding ion binding ferrous iron binding metal ion binding small molecule binding 5-methylcytosine dioxygenase activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity zinc ion binding	developmental process cellular developmental process hemopoiesis cell differentiation anatomical structure development cell development cellular process leukocyte differentiation nucleobase-containing compound metabolic process chromosomal 5-methylcytosine DNA demethylation pathway metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process developmental process cellular developmental process hemopoiesis cell differentiation anatomical structure development cell development cellular process leukocyte differentiation nucleobase-containing compound metabolic process chromosomal 5-methylcytosine DNA demethylation pathway metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process response to stimulus response to chemical response to organic cyclic compound carbohydrate derivative biosynthetic process cellular biosynthetic process cellular metabolic process glycoprotein biosynthetic process carbohydrate derivative metabolic process glycoprotein metabolic process protein glycosylation macromolecule biosynthetic process biosynthetic process glycosylation macromolecule modification macromolecule glycosylation protein O-linked glycosylation protein metabolic process protein modification process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process positive regulation of gene expression via chromosomal CpG island demethylation positive regulation of gene expression, epigenetic cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis transcription initiation at RNA polymerase II promoter epigenetic regulation of gene expression DNA-templated transcription initiation positive regulation of gene expression transcription initiation-coupled chromatin remodeling myeloid cell differentiation	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B, C	5'-D(APCPCPAPCP(5CM)PGPGPTPGPGPT)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR046942	Methylcytosine dioxygenase TET1-3, oxygenase domain	Domain
A	IPR024779	2OGFeDO JBP1/TET, oxygenase domain	Domain
A	IPR040175	Methylcytosine dioxygenase TET1/2/3	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q6N021	acquired polycythemia vera myelodysplastic syndrome primary myelofibrosis mature T-cell and NK-cell non-Hodgkin lymphoma acute promyelocytic leukemia renal cell carcinoma essential thrombocythemia angioimmunoblastic T-cell lymphoma Sezary syndrome myelodysplastic syndrome with excess blasts Neoplasm Recurrence, Local collecting duct carcinoma sarcomatoid renal cell carcinoma myelofibrosis acute myeloid leukemia acquired polycythemia vera myelodysplastic syndrome primary myelofibrosis mature T-cell and NK-cell non-Hodgkin lymphoma acute promyelocytic leukemia renal cell carcinoma essential thrombocythemia angioimmunoblastic T-cell lymphoma Sezary syndrome myelodysplastic syndrome with excess blasts Neoplasm Recurrence, Local collecting duct carcinoma sarcomatoid renal cell carcinoma myelofibrosis acute myeloid leukemia papillary renal cell carcinoma cancer prostate cancer chromophobe renal cell carcinoma colorectal cancer cutaneous melanoma familial polycythemia ulcerative colitis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia attention deficit hyperactivity disorder, inattentive type polycythemia breast carcinoma primitive neuroectodermal tumor chronic myelomonocytic leukemia renal carcinoma congenital anemia spina bifida melanoma ovarian cancer aleukemic leukemia bone marrow disease primary biliary cholangitis chronic obstructive pulmonary disease refractory anemia colorectal adenoma systemic mastocytosis invasive ductal breast carcinoma myeloproliferative neoplasm acute myeloid leukemia with multilineage dysplasia ovarian carcinoma bone marrow neoplasm prostate carcinoma clear cell renal carcinoma rheumatoid arthritis

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.