Annotations: 5XGU

Escherichia coli. RNase R

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)
B [auth A]	Hydrolase	e5xguA1	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Hydrolase	ECOD (v295.2)
A [auth B]	Hydrolase	e5xguB1	A: alpha arrays	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Hydrolase	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A]	PF17876	Cold shock domain (CSD2)	Cold shock domain	Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2 ...	Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding [1] [2].	Domain
A [auth B], B [auth A]	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 [auth B], B [auth A]	PF00773	RNB domain (RNB)	RNB domain	This domain is the catalytic domain of ribonuclease II [1].	Domain
A [auth B], B [auth A]	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 [auth B], B [auth A]	Ribonuclease R	3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exoribonuclease II activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity nucleic acid conformation isomerase activity 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exoribonuclease II activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity nucleic acid conformation isomerase activity isomerase activity helicase activity 3'-5' RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA ATP-dependent activity macromolecular conformation isomerase activity RNA binding binding nucleic acid binding	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic 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 negative regulation of metabolic process biological regulation regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic 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 negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression 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 response to stimulus response to stress response to abiotic stimulus response to cold response to temperature stimulus nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A]	IPR011129	Cold-shock domain	Domain
A [auth B], B [auth A]	IPR003029	S1 domain	Domain
A [auth B], B [auth A]	IPR013223	Ribonuclease B, N-terminal OB domain	Domain
A [auth B], B [auth A]	IPR050180	RNR Ribonuclease	Family
A [auth B], B [auth A]	IPR013668	Ribonuclease R winged-helix domain	Domain
A [auth B], B [auth A]	IPR040476	RNase II/RNase R, cold shock domain	Domain
A [auth B], B [auth A]	IPR022966	Ribonuclease II/R, conserved site	Conserved Site
A [auth B], B [auth A]	IPR004476	Ribonuclease II/ribonuclease R	Family
A [auth B], B [auth A]	IPR001900	Ribonuclease II/R	Domain
A [auth B], B [auth A]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A [auth B], B [auth A]	IPR011805	Ribonuclease R	Family

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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.

5XGU | pdb_00005xgu

Escherichia coli. RNase R

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage