6IE2 | pdb_00006ie2

Crystal structure of methyladenine demethylase

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	PHD	e6ie2H1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (v294.1)
G	PHD	e6ie2G1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (v294.1)
F	PHD	e6ie2F1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (v294.1)
E	PHD	e6ie2E1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (v294.1)
D	PHD	e6ie2D1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (v294.1)
C	PHD	e6ie2C1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (v294.1)
B	Methyltransf_12	e6ie2B1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: Methyltransf_12	ECOD (v294.1)
A	PHD	e6ie2A1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF13532	2OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy_2)	2OG-Fe(II) oxygenase superfamily		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Nucleic acid dioxygenase ALKBH1	oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA 2-oxoglutarate-dependent tRNA 5-methylcytidine formyltransferase activity 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity cation binding transition metal ion binding iron ion binding ion binding binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA 2-oxoglutarate-dependent tRNA 5-methylcytidine formyltransferase activity 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding tRNA demethylase activity demethylase activity oxidative RNA demethylase activity RNA binding tRNA binding nucleic acid binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity chemoattractant activity signaling receptor activator activity DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity carbon-oxygen lyase activity DNA demethylase activity broad specificity oxidative DNA demethylase activity DNA N6-methyladenine demethylase activity	tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA wobble cytosine modification tRNA wobble base modification metabolic process cellular process macromolecule metabolic process RNA processing developmental process placenta development animal organ development anatomical structure development regulation of cellular process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translational elongation protein metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process translation regulation of gene expression regulation of translation translational elongation regulation of macromolecule biosynthetic process regulation of metabolic process developmental growth growth oxidative RNA demethylation oxidative demethylation demethylation neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development mitochondrial translation regulation of mitochondrial gene expression mitochondrial gene expression regulation of mitochondrial translation RNA repair translational initiation regulation of translational initiation cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair neuron migration cellular developmental process nervous system development generation of neurons neurogenesis cell differentiation cell migration cell motility system development positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization positive regulation of metabolic process positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process epigenetic regulation of gene expression positive regulation of gene expression regulation of translational initiation by tRNA modification plasma membrane bounded cell projection organization cell projection organization cell development neuron projection development neuron differentiation neuron development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen euchromatin membraneless organelle intracellular membraneless organelle chromatin chromosome mitochondrial matrix endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR004574	Alkylated DNA repair protein AlkB	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR027450	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR037151	Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily	Homologous Superfamily

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.