2ID0

Escherichia coli RNase II

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2id0a1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, C-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2id0a2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, middle domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2id0a3	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2id0a4	All beta proteins	OB-fold	Nucleic acid-binding proteins	RNB domain-like	Exoribonuclease 2, RNB	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2id0b1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, C-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2id0b2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, middle domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2id0b3	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2id0b4	All beta proteins	OB-fold	Nucleic acid-binding proteins	RNB domain-like	Exoribonuclease 2, RNB	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d2id0c1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, C-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d2id0c2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, middle domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d2id0c3	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d2id0c4	All beta proteins	OB-fold	Nucleic acid-binding proteins	RNB domain-like	Exoribonuclease 2, RNB	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d2id0d1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, C-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d2id0d2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, middle domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d2id0d3	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exoribonuclease 2, RNB, N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d2id0d4	All beta proteins	OB-fold	Nucleic acid-binding proteins	RNB domain-like	Exoribonuclease 2, RNB	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8034600	3000135	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8034598	3000135	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8034601	3000135	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8034599	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8034598	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8034599	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8034600	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8034601	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8034598	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8034601	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8034599	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8034600	3000135	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleic acid-binding proteins	8034599	3000135	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleic acid-binding proteins	8034598	3000135	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleic acid-binding proteins	8034601	3000135	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleic acid-binding proteins	8034600	3000135	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)
A	OB_RNB	e2id0A2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: OB_RNB	ECOD (1.6)
A	S1_1	e2id0A3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
A	PRK05054	e2id0A1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PRK05054	ECOD (1.6)
A	RNB	e2id0A4	A: beta barrels	X: OB-fold	H: RNB domain-like (From Topology)	T: RNB domain-like	F: RNB	ECOD (1.6)
B	OB_RNB	e2id0B2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: OB_RNB	ECOD (1.6)
B	S1_1	e2id0B3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
B	PRK05054	e2id0B1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PRK05054	ECOD (1.6)
B	RNB	e2id0B4	A: beta barrels	X: OB-fold	H: RNB domain-like (From Topology)	T: RNB domain-like	F: RNB	ECOD (1.6)
C	OB_RNB	e2id0C2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: OB_RNB	ECOD (1.6)
C	S1_1	e2id0C3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
C	PRK05054	e2id0C1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PRK05054	ECOD (1.6)
C	RNB	e2id0C4	A: beta barrels	X: OB-fold	H: RNB domain-like (From Topology)	T: RNB domain-like	F: RNB	ECOD (1.6)
D	OB_RNB	e2id0D2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: OB_RNB	ECOD (1.6)
D	S1_1	e2id0D3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
D	PRK05054	e2id0D1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PRK05054	ECOD (1.6)
D	RNB	e2id0D4	A: beta barrels	X: OB-fold	H: RNB domain-like (From Topology)	T: RNB domain-like	F: RNB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	2.40.50.640	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	2.40.50.640	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C	2.40.50.640	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
D	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
D	2.40.50.640	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00773	RNB domain (RNB)	RNB domain	This domain is the catalytic domain of ribonuclease II [1].	Domain
A, B, C, D	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain
A, B, C, D	PF08206	Ribonuclease B OB domain (OB_RNB)	Ribonuclease B OB domain	This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Exoribonuclease 2	nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity exoribonuclease II activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity exoribonuclease II activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters RNA binding binding organic cyclic compound binding nucleic acid binding	regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process organic substance catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003029	S1 domain	Domain
A, B, C, D	IPR013223	Ribonuclease B, N-terminal OB domain	Domain
A, B, C, D	IPR022966	Ribonuclease II/R, conserved site	Conserved Site
A, B, C, D	IPR004476	Ribonuclease II/ribonuclease R	Family
A, B, C, D	IPR001900	Ribonuclease II/R	Domain
A, B, C, D	IPR011129	Cold shock domain	Domain
A, B, C, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B, C, D	IPR011804	Ribonuclease II	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	RNAse II M-CSA #338	RNAse II catalyses the sequential 3'-5' hydrolysis of single stranded RNA. Catalytic activity of RNAse II is dependent upon the presence of a divalent cation.	Defined by 6 residues: ASP:A-201ASP:A-207ASP:A-209ASP:A-210TYR:A-313ARG:A-500 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1.13.1 (PDB Primary Data) Search M-CSA Motif + EC 3.1.13.1

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.