4PEI

Dbr1 in complex with synthetic branched RNA analog

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	e4peiA2	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	e4peiA1	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 [auth B]	EUF08022	e4peiB2	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 [auth B]	Metallophos_2_1	e4peiB1	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)
G [auth C]	EUF08022	e4peiC2	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)
G [auth C]	Metallophos_2_1	e4peiC1	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)
J [auth D]	EUF08022	e4peiD2	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)
J [auth D]	Metallophos_2_1	e4peiD1	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)
M [auth E]	EUF08022	e4peiE2	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)
M [auth E]	Metallophos_2_1	e4peiE1	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, D [auth B], G [auth C], J [auth D], M [auth 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, D [auth B], G [auth C], J [auth D], M [auth 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
A, D [auth B], G [auth C], J [auth D], M [auth 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 organic cyclic compound binding nucleic acid binding RNA lariat debranching enzyme activity endonuclease activity 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 organic cyclic compound binding nucleic acid binding RNA lariat debranching enzyme activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity	RNA splicing cellular biosynthetic process cellular metabolic process 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 cellular biosynthetic process cellular metabolic process 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	intracellular anatomical structure perinuclear region of cytoplasm cytoplasm cellular anatomical entity membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B [auth V], E [auth W], H [auth X], K [auth Y], N [auth Z]	RNA (5'-R(UPAPAPCP*A)-3')	-	-	-
C [auth Q], F [auth R], I [auth S], L [auth T], O [auth U]	RNA (5'-R((G46)PU)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B], G [auth C], J [auth D], M [auth E]	IPR004843	Calcineurin-like phosphoesterase domain, ApaH type	Domain
A, D [auth B], G [auth C], J [auth D], M [auth E]	IPR049499	Dbr1, C-terminal domain	Domain
A, D [auth B], G [auth C], J [auth D], M [auth E]	IPR041816	Lariat debranching enzyme, N-terminal metallophosphatase domain	Domain
A, D [auth B], G [auth C], J [auth D], M [auth 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.