4JRP

Structure of E. coli Exonuclease I in complex with a 5cy-dT13 oligonucleotide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	Ribonuclease H-like	8044547	3000143	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Ribonuclease H-like	8044547	3000143	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth A]	PF00929,PF08411	e4jrpA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00929,PF08411	ECOD (1.6)
D [auth B]	PF00929,PF08411	e4jrpB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00929,PF08411	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C [auth A]	3.30.1520.20	Alpha Beta	2-Layer Sandwich	PX Domain	Exonuclease ExoI, domain 2	CATH (4.3.0)
C [auth A]	1.20.1280.70	Mainly Alpha	Up-down Bundle	Monooxygenase	Exonuclease ExoI, domain 3	CATH (4.3.0)
C [auth A]	1.10.287.1240	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D [auth B]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D [auth B]	3.30.1520.20	Alpha Beta	2-Layer Sandwich	PX Domain	Exonuclease ExoI, domain 2	CATH (4.3.0)
D [auth B]	1.20.1280.70	Mainly Alpha	Up-down Bundle	Monooxygenase	Exonuclease ExoI, domain 3	CATH (4.3.0)
D [auth B]	1.10.287.1240	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF08411	Exonuclease C-terminal (Exonuc_X-T_C)	Exonuclease C-terminal	-	Family
C [auth A], D [auth B]	PF00929	Exonuclease (RNase_T)	Exonuclease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth D]	5cy-dT13	-	-	-
C [auth A], D [auth B]	Exodeoxyribonuclease I	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity DNA exonuclease activity 3'-5' exonuclease activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity DNA binding organic cyclic compound binding single-stranded DNA binding nucleic acid binding	catabolic process primary metabolic process DNA metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process catabolic process primary metabolic process DNA metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process organic substance catabolic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress cellular process DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR038649	Exonuclease I, SH3-like domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR023607	Exodeoxyribonuclease I	Family
C [auth A], D [auth B]	IPR034747	Exonuclease I, SH3-like domain	Domain
C [auth A], D [auth B]	IPR034748	Exonuclease I, C-terminal alpha-helical domain	Domain
C [auth A], D [auth B]	IPR013620	Exodeoxyribonuclease I, C-terminal	Domain
C [auth A], D [auth B]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR013520	Exonuclease, RNase T/DNA polymerase III	Domain
C [auth A], D [auth B]	IPR022894	Oligoribonuclease	Family

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 R01GM133198.