2XSE

The structural basis for recognition of J-base containing DNA by a novel DNA-binding domain in JBP1

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)
A	PF18526	e2xseA1	A: alpha arrays	X: Thymine dioxygenase JBP1 DNA-binding domain-like	H: Thymine dioxygenase JBP1 DNA-binding domain (From Topology)	T: Thymine dioxygenase JBP1 DNA-binding domain	F: PF18526	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.1440	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	JBP1, DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18526	Thymine dioxygenase JBP1 DNA-binding domain (DB_JBP1)	Thymine dioxygenase JBP1 DNA-binding domain	The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (beta-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. ...	The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (beta-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. JBP1 recognizes J-containing DNA (J-DNA) through the DNA-Binding JBP1 domain (DB-JBP1), which binds to J-DNA with approximately the same affinity and specificity as full-length JBP1. Structure analysis of DB-JBP1 revealed a helix-turn-helix variant fold, a 'helical bouquet' with a 'ribbon' helix encompassing the amino acids responsible for DNA binding. Mutation of a single residue (Asp525) in the ribbon helix abrogates specificity toward J-DNA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	THYMINE DIOXYGENASE JBP1	DNA binding binding organic cyclic compound binding nucleic acid binding oxidoreductase activity thymine dioxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity cation binding ion binding metal ion binding small molecule binding	primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA modification organic substance metabolic process macromolecule modification metabolic process base J metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR043111	JBP1, DNA-binding domain superfamily	Homologous Superfamily
A	IPR041241	Thymine dioxygenase JBP1, DNA-binding domain	Domain
A	IPR024779	2OGFeDO JBP1/TET, oxygenase domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.