4NPM | pdb_00004npm

Crystal structure of Zebrafish ALKBH5 in complex with succinic acid

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	DUF4170	e4npmB1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: DUF4170	ECOD (v294.1)
A	Rep-A_N	e4npmA1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Rep-A_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.590	Mainly Beta	Sandwich	Jelly Rolls	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	CATH (4.3.0)
A	2.60.120.590	Mainly Beta	Sandwich	Jelly Rolls	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	RNA demethylase ALKBH5	mRNA N6-methyladenosine dioxygenase activity 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 oxidative RNA demethylase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity demethylase activity dioxygenase activity molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity cation binding mRNA N6-methyladenosine dioxygenase activity 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 oxidative RNA demethylase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity demethylase activity dioxygenase activity molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity cation binding ion binding binding metal ion binding small molecule binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of localization cellular localization nitrogen compound transport regulation of cellular process nucleocytoplasmic transport transport developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of localization cellular localization nitrogen compound transport regulation of cellular process nucleocytoplasmic transport transport regulation of mRNA export from nucleus nuclear transport mRNA transport localization intercellular transport mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport ribonucleoprotein complex localization regulation of intracellular transport regulation of ribonucleoprotein complex localization regulation of biological process RNA transport regulation of transport regulation of RNA export from nucleus regulation of nucleobase-containing compound transport nucleic acid transport biological regulation intracellular transport regulation of nucleocytoplasmic transport gene expression establishment of localization macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process regulation of cellular localization macromolecule localization cellular process metabolic process macromolecule metabolic process response to decreased oxygen levels response to stimulus response to hypoxia response to stress response to oxygen levels response to abiotic stimulus RNA metabolic process mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process RNA processing regulation of mRNA processing primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process mRNA metabolic process nucleic acid metabolic process regulation of mRNA metabolic process regulation of metabolic process regulation of biosynthetic process regulation of protein metabolic process translation protein biosynthetic process post-transcriptional regulation of gene expression regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process protein metabolic process negative regulation of biological process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process catabolic process positive regulation of biological process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability cellular component biogenesis cellular component organization organelle organization cellular component assembly organelle assembly membraneless organelle assembly cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen paraspeckles

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR032860	RNA demethylase ALKBH5	Family
A, B	IPR037151	Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily	Homologous Superfamily
A, B	IPR027450	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	Domain

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.