5K78 | pdb_00005k78

Dbr1 in complex with 16-mer branched RNA

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)
A	EUF08022	e5k78A1	A: alpha arrays	X: C-terminal domain of Dbr1 (From Topology)	H: C-terminal domain of Dbr1 (From Topology)	T: C-terminal domain of Dbr1	F: EUF08022	ECOD (1.6)
A	Metallophos_2_1	e5k78A2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
C	EUF08022	e5k78C1	A: alpha arrays	X: C-terminal domain of Dbr1 (From Topology)	H: C-terminal domain of Dbr1 (From Topology)	T: C-terminal domain of Dbr1	F: EUF08022	ECOD (1.6)
C	Metallophos_2_1	e5k78C2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
D	EUF08022	e5k78D2	A: alpha arrays	X: C-terminal domain of Dbr1 (From Topology)	H: C-terminal domain of Dbr1 (From Topology)	T: C-terminal domain of Dbr1	F: EUF08022	ECOD (1.6)
D	Metallophos_2_1	e5k78D1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
E	EUF08022	e5k78E1	A: alpha arrays	X: C-terminal domain of Dbr1 (From Topology)	H: C-terminal domain of Dbr1 (From Topology)	T: C-terminal domain of Dbr1	F: EUF08022	ECOD (1.6)
E	Metallophos_2_1	e5k78E2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
B	EUF08022	e5k78B2	A: alpha arrays	X: C-terminal domain of Dbr1 (From Topology)	H: C-terminal domain of Dbr1 (From Topology)	T: C-terminal domain of Dbr1	F: EUF08022	ECOD (1.6)
B	Metallophos_2_1	e5k78B1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF00149	Calcineurin-like phosphoesterase (Metallophos)	Calcineurin-like phosphoesterase	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or ...	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or yeast MRE11 Swiss:P32829. The most conserved regions in this superfamily centre around the metal chelating residues.	Domain
A, B, C, D, E	PF20890	Dbr1, C-terminal domain (Dbr1_C)	Dbr1, C-terminal domain	Dbr1 is an eukaryotic intron debranching enzyme that hydrolyses the linkages produced by the spliceosome in RNA for them to be processed into essential cellular factors, such as snoRNA and miRNA. This protein is organized into an N-terminal metalloph ...	Dbr1 is an eukaryotic intron debranching enzyme that hydrolyses the linkages produced by the spliceosome in RNA for them to be processed into essential cellular factors, such as snoRNA and miRNA. This protein is organized into an N-terminal metallophosphoesterase (MPE) domain (Pfam:PF00149) and a C-terminal domain (CTD, this entry). This domain consists of four alpha-helices and three connecting loops. It is located on the posterior of the protein, opposite the active site and is joined to the MPE domain by an extended linker region [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth x], I [auth y]	branch 2 of branched RNA 5'-UACUAA(2'-GUAUGU)CAAGU-3'	-	-	-
F [auth X], H [auth Y]	branch 1 of branched RNA 5'-UACUAA(2'-GUAUGU)CAAGU-3'	-	-	-
A, B, C, D, E	RNA lariat debranching enzyme, putative	cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding manganese ion binding zinc ion binding RNA binding nucleic acid binding RNA lariat debranching enzyme activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding manganese ion binding zinc ion binding RNA binding nucleic acid binding RNA lariat debranching enzyme activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process RNA processing	cellular anatomical structure intracellular anatomical structure perinuclear region of cytoplasm cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR049499	Dbr1, C-terminal domain	Domain
A, B, C, D, E	IPR041816	Lariat debranching enzyme, N-terminal metallophosphatase domain	Domain
A, B, C, D, E	IPR004843	Calcineurin-like, phosphoesterase domain	Domain
A, B, C, D, E	IPR029052	Metallo-dependent phosphatase-like	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.