2ID0 | pdb_00002id0

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D		e2id0D1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: KOW, Ribosomal_L26	F:	ECOD (20:10:01)
C		e2id0C1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: KOW, Ribosomal_L26	F:	ECOD (20:10:01)
B		e2id0B1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: KOW, Ribosomal_L26	F:	ECOD (20:10:01)
A		e2id0A1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: KOW, Ribosomal_L26	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	PF00773	RNB domain (RNB)	RNB domain	This domain is the catalytic domain of ribonuclease II [1].	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	hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 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 RNA exonuclease activity RNA nuclease activity exoribonuclease II activity RNA binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 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 RNA exonuclease activity RNA nuclease activity exoribonuclease II activity RNA binding binding nucleic acid binding	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process tRNA metabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process tRNA decay RNA catabolic process catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process tRNA metabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process tRNA decay RNA catabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011129	Cold-shock domain	Domain
A, B, C, D	IPR003029	S1 domain	Domain
A, B, C, D	IPR013223	Ribonuclease B, N-terminal OB domain	Domain
A, B, C, D	IPR050180	RNR Ribonuclease	Family
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	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 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.